NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln)
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
Pathogenic (56); Likely pathogenic (6)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln)
Variation ID: 17890 Accession: VCV000017890.156
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 2p24.1 2: 21006288 (GRCh38) [ NCBI UCSC ] 2: 21229160 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 23, 2013 Jul 14, 2026 Apr 21, 2026 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000384.3(APOB):c.10580G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NM_000384.3:c.10580G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000375.3:p.Arg3527Gln missense NC_000002.12:g.21006288C>T NC_000002.11:g.21229160C>T NG_011793.1:g.42786G>A NP_000375.2:p.Arg3527Gln - Protein change
- R3527Q
- Other names
-
R3500Q
9775G>A
- Canonical SPDI
- NC_000002.12:21006287:C:T
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
Exome Aggregation Consortium (ExAC) 0.00023
The Genome Aggregation Database (gnomAD) 0.00028
Trans-Omics for Precision Medicine (TOPMed) 0.00087
The Genome Aggregation Database (gnomAD), exomes 0.00040
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| APOB | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh38 GRCh37 |
4874 | 5126 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic/Likely pathogenic (9) |
criteria provided, multiple submitters, no conflicts
|
Jun 9, 2022 | RCV000019479.56 | |
| Pathogenic (16) |
criteria provided, multiple submitters, no conflicts
|
Apr 14, 2026 | RCV000254882.75 | |
| Pathogenic/Likely pathogenic (28) |
criteria provided, multiple submitters, no conflicts
|
Apr 21, 2026 | RCV000412515.66 | |
| Likely pathogenic (1) |
criteria provided, single submitter
|
Nov 30, 2015 | RCV000499833.13 | |
| Pathogenic/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
Feb 3, 2025 | RCV000771116.19 | |
| Pathogenic (1) |
criteria provided, single submitter
|
Nov 2, 2020 | RCV000844612.14 | |
| Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Jan 22, 2023 | RCV000851289.12 | |
| Pathogenic/Likely pathogenic (5) |
criteria provided, multiple submitters, no conflicts
|
Jan 27, 2026 | RCV001837437.23 | |
| Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
May 3, 2025 | RCV002399330.11 | |
|
See cases
|
Likely pathogenic (1) |
criteria provided, single submitter
|
Mar 22, 2022 | RCV004584331.3 |
|
APOB-related disorder
|
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Aug 25, 2025 | RCV004528126.3 |
| not provided (1) |
no classification provided
|
- | RCV005862731.1 | |
| click to load more conditions click to collapse | ||||
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Collapse all rows
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
|---|---|---|---|---|---|
|
Pathogenic
(Mar 01, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia
(Autosomal dominant inheritance)
|
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge
Accession: SCV000322853.1
First in ClinVar: Oct 15, 2016 Last updated: Oct 15, 2016 |
Observation:
2
Observation 1
Collection method: research
Allele origin: germline
Affected status: yes
Comment on evidence:
%MAF (ExAC):0.02311
Observation 2
Collection method: research
Allele origin: germline
Affected status: yes
Comment on evidence:
Heterozygous patient LDL, U937 cells proliferation / Heterologous cells (HepG2), FACS assays
Result:
40-50 % cells proliferation / 40-50% LDL binding and uptake
|
|
|
Pathogenic
(Mar 01, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia
(Autosomal dominant inheritance)
|
Fundacion Hipercolesterolemia Familiar
Study: SAFEHEART
Accession: SCV000607384.1 First in ClinVar: Sep 30, 2017 Last updated: Sep 30, 2017 |
Observation:
2
Observation 1
Collection method: research
Allele origin: germline
Affected status: unknown
Comment on evidence:
%MAF(ExAC):0.02311
Observation 2
Collection method: research
Allele origin: germline
Affected status: unknown
Comment on evidence:
Htz patient LDL, U937 cells proliferation / Heterologous cells (HepG2), FACS assays
Result:
40-50 % cells proliferation / 40-50% LDL binding and uptake
|
|
|
Pathogenic
(Apr 18, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Athena Diagnostics
Accession: SCV000612386.1
First in ClinVar: Dec 19, 2017 Last updated: Dec 19, 2017 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Nov 02, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Homozygous familial hypercholesterolemia
(Autosomal dominant inheritance)
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000271309.3
First in ClinVar: May 29, 2016 Last updated: May 29, 2021 |
Comment:
show
The p.Arg3527Gln variant in APOB is a well-established pathogenic variant that is mainly found in individuals of European descent. It has been previously reported in >500 individuals with familial hypercholesterolemia (FH) and segregated with disease in >50 affected relatives (Soria 1989 PMID: 2563166, März 1993 PMID: 8254047, Leren 1997 PMID: 9104431, Ludwig 1990 PMID: 1977310, Bednarska-Makaruk 2001 PMID: 11781700, Horvath 2001 PMID: 11494965, Kalina 2001 PMID: 11137107). It has also been reported by other clinical laboratories in ClinVar (Variation ID 17890) and has been identified in 0.06% (76/128568) of European chromosomes, including 1 homozygote, by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This frequency is low enough to be consistent with the frequency of FH in the general population. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant familial hypercholesterolemia based upon presence in multiple affected individuals and segregation studies. Please note that pathogenic variants in APOB can have reduced penetrance and a less severe phenotype than disease-causing LDLR or PCSK9 variants (Youngblom and Knowles, GeneReviews, PMID: 24404629). ACMG/AMP Criteria applied: PS4_Strong; PP1_Strong. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Number of individuals with the variant: 52
|
|
|
Pathogenic
(Jan 22, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypobetalipoproteinemia 1 |
Baylor Genetics
Accession: SCV003835921.1
First in ClinVar: Mar 11, 2023 Last updated: Mar 11, 2023 |
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
|
Pathogenic
(Jan 22, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Baylor Genetics
Accession: SCV001520602.2
First in ClinVar: Mar 22, 2021 Last updated: Mar 11, 2023 |
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
|
Pathogenic
(Jun 17, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
(Autosomal dominant inheritance)
|
Institute of Human Genetics Munich, TUM University Hospital
Accession: SCV006302653.5
First in ClinVar: Aug 03, 2025 Last updated: Sep 22, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dystonic disorder (present)
|
|
|
Pathogenic
(Feb 01, 2026)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001746348.31
First in ClinVar: Jul 10, 2021 Last updated: Jun 20, 2026 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 37
|
|
|
Likely pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial Hypercholesterolemia
(Autosomal dominant inheritance)
|
Institute for Integrative and Experimental Genomics, University of Luebeck
Accession: SCV000212143.1
First in ClinVar: Jun 20, 2015 Last updated: Jun 20, 2015 |
Observation: 1
Collection method: research
Allele origin: germline
Affected status: yes
Observation 1
Collection method: research
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Mar 01, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia
(Autosomal dominant inheritance)
|
Laboratory of Genetics and Molecular Cardiology, University of São Paulo
Study: HipercolBrasil
Accession: SCV000588451.1 First in ClinVar: Aug 13, 2017 Last updated: Aug 13, 2017 |
Observation:
2
Observation 1
Collection method: research
Allele origin: germline
Affected status: unknown
Comment on evidence:
%MAF(ExAC):0.02311
Observation 2
Collection method: research
Allele origin: germline
Affected status: unknown
Comment on evidence:
Assay description:Htz patient LDL, U937 cells proliferation / Heterologous cells (HepG2), FACS assays
Result:
40-50 % cells proliferation / 40-50% LDL binding and uptake
|
|
|
Pathogenic
(Mar 01, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia
(Autosomal dominant inheritance)
|
Iberoamerican FH Network
Accession: SCV000748075.1
First in ClinVar: May 19, 2018 Last updated: May 19, 2018
Comment:
Variant present in the databases from Argentina, Chile, and Uruguay
|
Observation:
2
Observation 1
Collection method: research
Allele origin: germline
Affected status: unknown
Comment on evidence:
%MAF(ExAC):0.02311
Observation 2
Collection method: research
Allele origin: germline
Affected status: unknown
Comment on evidence:
Assay Description:Htz patient LDL, U937 cells proliferation / Heterologous cells (HepG2), FACS assays
Result:
40-50 % cells proliferation / 40-50% LDL binding and uptake
|
|
|
Pathogenic
(Nov 10, 2017)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia |
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918478.1
First in ClinVar: May 31, 2019 Last updated: May 31, 2019 |
Comment:
show
Variant summary: The APOB c.10580G>A (p.Arg3527Gln) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 79/279708 control chromosomes at a frequency of 0.0002824, which is approximately 9 times the estimated maximal expected allele frequency of a pathogenic APOB variant (0.0000313). However, this is a well-characterized pathogenic mutation and is known to be frequent in certain populations. The variant has been identified in many affected individuals and families with hypercholesterolemia and is common in central Europe, particularly in Switzerland (frequency, 1:209) and Belgium (frequency, 1:250) (Sabbagh_APOB_MolBiolRep_2007). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Aug 21, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypobetalipoproteinemia 1 |
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: AGHI GT
Accession: SCV000778605.2 First in ClinVar: May 26, 2018 Last updated: Sep 24, 2019 |
Observation:
6
Observation 1
Collection method: research
Allele origin: unknown
Affected status: unknown
Number of individuals with the variant: 1
Observation 2
Collection method: research
Allele origin: unknown
Affected status: unknown
Number of individuals with the variant: 1
Observation 3
Collection method: research
Allele origin: unknown
Affected status: unknown
Number of individuals with the variant: 1
Observation 4
Collection method: research
Allele origin: unknown
Affected status: unknown
Number of individuals with the variant: 1
Observation 5
Collection method: research
Allele origin: unknown
Affected status: unknown
Number of individuals with the variant: 1
Observation 6
Collection method: research
Allele origin: unknown
Affected status: unknown
Number of individuals with the variant: 1
|
|
|
Pathogenic
(Mar 28, 2018)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: CSER-SouthSeq
Accession: SCV000891787.1 First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
Observation 1
Collection method: research
Allele origin: maternal
Affected status: unknown
Number of individuals with the variant: 1
|
|
|
Pathogenic
(Sep 01, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: HudsonAlpha-AGHI-WGS
Accession: SCV001870329.1 First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021 |
Observation 1
Collection method: research
Allele origin: unknown
Affected status: yes
Number of individuals with the variant: 1
|
|
|
Pathogenic
(Jan 22, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
(Autosomal dominant inheritance)
|
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV001422754.2
First in ClinVar: Jul 19, 2020 Last updated: Feb 05, 2022 |
Comment:
show
The p.Arg3527Gln variant in APOB has been reported in at least 640 individuals with high LDL, segregated with disease in 6 affected relatives from 1 family (PMID: 28428224; doi:10.4172/2157-7412), and has been Identified in 0.05911% (76/128568) of European (non-Finnish) Chromosomes, and at lower frequencies in other populations, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs5742904). This variant has also been reported in ClinVar (VariationID: 17890) as likely pathogenic by 3 submitters, pathogenic by 16 submitters, and as a VUS by 1 submitter. Animal models in mice demonstrating decreased binding affinity of LDL for its receptor have shown that this variant causes high LDL (PMID: 9486979). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Multiple variants in the same region as p.Arg3527Gln variant have been reported in association with disease in ClinVar and the literature and the variant is located in a region of APOB that is essential to normal receptor binding, suggesting that this variant is in a hot spot and functional domain and supports pathogenicity (PMID: 9486979; Variation ID: 40223, 440523). The two additional pathogenic and likely pathogenic variants, resulting in a different amino acid change at the same position, p.Arg3527Trp and p.Arg3527Leu, have been reported in association with the disease in the literature and ClinVar, supporting that a change at this position may not be tolerated (VariationID: 40223, 440523). In summary, this variant meets criteria to be classified as pathogenic for high LDL in an autosomal dominant manner based on the prevalence of the variant in affected individuals and relatives, the reports that the variant is essential for normal receptor binding, and mouse models demonstrating the variant to be causative of disease. ACMG/AMP Criteria applied: PS4, PM5, PM1, PS3_moderate, PP1_moderate, PP3 (Richards 2015). (less)
Observation: 1
Collection method: curation
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: curation
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Apr 07, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Accession: SCV002061702.2
First in ClinVar: Jan 22, 2022 Last updated: Feb 05, 2022 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Secondary finding: yes
|
|
|
Pathogenic
(Jul 10, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
GeneDx
Accession: SCV000322134.9
First in ClinVar: Oct 09, 2016 Last updated: Mar 04, 2023 |
Comment:
show
Also denoted as R3500Q due to the use of alternate nomenclature; Functional studies indicate that the R3527Q variant causes decreased binding of the APOB protein to the LDL receptor (Fisher et al., 1999); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26643808, 26036859, 26415676, 22859806, 31028937, 24106285, 24507774, 20736250, 18325181, 21868016, 9105560, 18222178, 21919778, 15797858, 2563166, 24956927, 8318993, 10388479, 23375686, 26636822, 27497240, 27872105, 27831900, 27824480, 28502510, 27765764, 28104544, 9259199, 21382890, 30030251, 29555771, 28965616, 27784735, 28428224, 9603795, 30122538, 30592178, 30270359, 31106297, 29284604, 30291343, 32591292, 31447099, 31980526, 34040191, 34570182, 11238294, 21059979, 34037665, 33303402, 32719484, 32522009, 33740630, 33111339, 33418990, 33269076, 1892487, 2067318, 32770674, 33069457) (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Apr 18, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV004026259.1
First in ClinVar: Aug 19, 2023 Last updated: Aug 19, 2023 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
|
|
|
Pathogenic
(Aug 16, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Genomic Medicine Lab, University of California San Francisco
Accession: SCV004847141.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024 |
Observation: 1
Collection method: clinical testing
Allele origin: paternal
Affected status: no
Observation 1
Collection method: clinical testing
Allele origin: paternal
Affected status: no
|
|
|
Pathogenic
(Sep 02, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
(Autosomal dominant inheritance)
|
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Accession: SCV005398745.1
First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024 |
Comment:
show
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with familial hypercholesterolaemia, 2 (MIM#144010) and hypobetalipoproteinaemia (MIM#615558). (I) 0108 - This gene is associated with both recessive and dominant disease. Familial hypercholesterolaemia 2 (MIM#144010) is inherited in an autosomal dominant manner, whereas hypobetalipoproteinaemia (MIM#615558) is recessive (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 24404629). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v3) <0.01 (103 heterozygotes, 1 homozygote). This includes 62 heterozygotes from the Amish sub-population, in which this variant is known to be a founder mutation (PMID: 35300601). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (45 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0704 - Another missense variant comparable to the one identified in this case has limited previous evidence for pathogenicity. p.(Arg3527Trp) has been classified as pathogenic by multiple clinical laboratories in ClinVar. (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic and likely pathogenic by multiple clinical laboratories in ClinVar and is well reported to cause familial hypercholesterolaemia (PMID: 35300601). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Sep 27, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
(Autosomal dominant inheritance)
|
All of Us Research Program, National Institutes of Health
Accession: SCV004822888.2
First in ClinVar: Apr 20, 2024 Last updated: Dec 14, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
|
Comment:
show
This missense variant replaces arginine with glutamine at codon 3527 in the beta 2 domain of the APOB protein. This variant is also known as p.Arg3500Gln in the mature protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. Functional studies have shown that the variant affects APOB protein conformation and impairs its binding to the LDLR protein (PMID: 8254047, 9486979, 10388479, 11115503, 15797858). This variant has been reported in numerous individuals with familial hypercholesterolemia in multiple populations (PMID: 1466657, 2563166, 8254047, 9104431, 9105560, 9603795, 10388479, 11137107, 11494965, 11781700, 18222178, 18325181, 1977310, 21059979, 21868016, 23375686, 24956927, 32591292, 35052492, 35741760, 37593691) and has been shown to segregate with hypercholesterolemia in multiple families (PMID: 2563166, 8254047, 21868016). A different missense variant at the same position, p.Arg3527Trp, is known to be pathogenic (ClinVar variation ID 40223), indicating that arginine at this position is important for APOB protein function. This variant has been identified in 83/282162 chromosomes in the general population by the Genome Aggregation Database (gnomAD). APOB mutations show incomplete penetrance, and individuals with APOB mutations may show a less severe phenotype than familial hypercholesterolemia patients with LDLR mutations (PMID: 8141833, 21868016, 21513517; GeneReviews NBK174884). In summary, the mutant APOB protein harboring this variant is functionally defective and has shown significant clinical association with familial hypercholesterolemia. Based on the available evidence, this variant is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Number of individuals with the variant: 117
Zygosity: 117 Single Heterozygotes
|
|
|
Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
(Autosomal dominant inheritance)
|
Institute of Human Genetics Greifswald, Research Division, University Medicine Greifswald
Accession: SCV005880353.1
First in ClinVar: Mar 11, 2025 Last updated: Mar 11, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Likely pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia |
Laboratory of Molecular Genetics, National Medical Research Center for Therapy and Preventive Medicine
Accession: SCV001482456.2
First in ClinVar: Mar 07, 2021 Last updated: Apr 13, 2025 |
Observation:
8
Observation 1
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 30-39 years
Sex: female
Observation 2
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 60-69 years
Sex: male
Observation 3
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 60-69 years
Sex: female
Observation 4
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 40-49 years
Sex: female
Observation 5
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 20-29 years
Sex: male
Observation 6
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 60-69 years
Sex: male
Observation 7
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 50-59 years
Sex: female
Observation 8
Collection method: research
Allele origin: germline
Affected status: yes
Zygosity: 1 Single Heterozygote
Age: 40-49 years
Sex: male
|
|
|
Pathogenic
(Jun 09, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, familial, 1 |
MGZ Medical Genetics Center
Accession: SCV002580122.2
First in ClinVar: Oct 15, 2022 Last updated: Apr 13, 2025
Comment:
ACMG criteria applied: PS3, PS4, PP1_STR, PM5, PP3, PP4
|
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 6
Sex: female
|
|
|
Likely pathogenic
(Aug 02, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
Familial hypobetalipoproteinemia 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. |
Institute of Human Genetics, Heidelberg University
Accession: SCV005440680.2
First in ClinVar: Jan 04, 2025 Last updated: Apr 13, 2025
Comment:
secondary finding
|
Observation: 1
Collection method: clinical testing
Allele origin: paternal
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: paternal
Affected status: unknown
Sex: male
|
|
|
Pathogenic
(May 03, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Cardiovascular phenotype |
Ambry Genetics
Accession: SCV002713792.4
First in ClinVar: Nov 29, 2022 Last updated: Jul 13, 2025 |
Comment:
show
The p.R3527Q pathogenic mutation (also known as c.10580G>A), located in coding exon 26 of the APOB gene, results from a G to A substitution at nucleotide position 10580. The arginine at codon 3527 is replaced by glutamine, an amino acid with highly similar properties. This alteration (also reported as p.R3500Q) was initially reported in seven unrelated probands with familial hypercholesterolemia (FH) and found to segregate with disease in two families (Soria et al. Proc Natl Acad Sci USA. 1989; 86(2):587-91). This pathogenic mutation has been reported to be responsible for 2-6% of Western European FH cases and has been reported as an Amish founder mutation (Heath KE et al. Atherosclerosis. 1999;143(1):41-54; Lombardi et al. Clin Genet. 2000;57(2):116-24; Chmara M et al. J Appl Genet. 2010;51(1):95-106; Shen H et al. Arch Intern Med. 2010;170(20):1850-5). In addition, this alteration has been reported to result in defective low-density lipoprotein receptor binding (Boren J et al. J Clin Invest. 1998;101(5):1084-93). Two alterations at the same codon, p.R3527L and p.R3527W (reported as p.R3500L and p.R3500W), have also been associated with FH (Gaffney D et al. Arterioscler. Thromb. Vasc. Biol. 1995;15:1025-9; Fouchier SW et al. Hum. Mutat. 2005;26:550-6). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
Familial hypobetalipoproteinemia 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. |
Juno Genomics, Hangzhou Juno Genomics, Inc
Accession: SCV005418341.3
First in ClinVar: Nov 30, 2024 Last updated: Oct 05, 2025 |
Comment:
show
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.;Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.;Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.;Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Dec 09, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001713959.4
First in ClinVar: Jun 15, 2021 Last updated: Jan 11, 2026 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Number of individuals with the variant: 21
|
|
|
Pathogenic
(Mar 25, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
(Autosomal dominant inheritance)
|
Variantyx, Inc.
Accession: SCV007294377.1
First in ClinVar: Jan 17, 2026 Last updated: Jan 17, 2026 |
Comment:
show
This is a nonsynonymous variant in the APOB gene (OMIM: 107730). Pathogenic variants in this gene have been associated with autosomal dominant familial hypercholesterolemia 2. This variant has been observed to segregate with disease in multiple families (PMID: 8254047, 9105560, 9104431, 21059979, 18325181, 18222178, 10388479, 23375686, 2563166, 21868016, 15797858, 9603795) (PP1_Strong). Functional studies have shown that this variant alters APOB protein function (PMID: 8254047, 9486979, 10388479, 11115503, 15797858) (PS3). An alternate amino acid change at this position (p.Arg3527Trp) has been previously reported in affected individuals (PMID: 26415676, 27765764, 27783906, 11238294, 10388479, 7627691, 9191540, 9702952, 22294733, 21376320, 16250003) (PM5). In addition, the CG dinucleotide in this codon is considered a hotspot for pathogenic variants (PMID: 2563166). Multiple computational algorithms predict a deleterious effect for this variant (REVEL score: 0.735) (PP3). This variant has a 0.04932% maximum allele frequency in non-founder control populations (https://gnomad.broadinstitute.org/). Based on the current evidence, this variant is classified as pathogenic for autosomal dominant familial hypercholesterolemia 2. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Likely pathogenic
(Dec 11, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Medical and Scientific Branch, Hong Kong Genome Institute
Accession: SCV007329994.1
First in ClinVar: Jan 17, 2026 Last updated: Jan 17, 2026 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Jan 27, 2026)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypobetalipoproteinemia 1
Hypercholesterolemia, autosomal dominant, type B
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. |
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000541940.12
First in ClinVar: Jan 07, 2017 Last updated: Feb 23, 2026 |
Comment:
show
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 3527 of the APOB protein (p.Arg3527Gln). This variant is present in population databases (rs5742904, gnomAD 0.06%). This missense change has been observed in individual(s) with autosomal dominant hypercholesterolemia (PMID: 2563166, 9105560, 10388479, 18222178, 18325181, 21059979, 21868016, 23375686, 24404629). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 17890). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on APOB protein function. Experimental studies have shown that this missense change affects APOB function (PMID: 11115503, 15797858). This variant disrupts the p.Arg3527 amino acid residue in APOB. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7627691). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Likely pathogenic
(Nov 30, 2015)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypobetalipoproteinemia |
Genetic Services Laboratory, University of Chicago
Accession: SCV000593263.1
First in ClinVar: Aug 28, 2017 Last updated: Aug 28, 2017 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(May 25, 2017)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Accession: SCV000839879.1
First in ClinVar: Oct 13, 2018 Last updated: Oct 13, 2018 |
Comment:
show
This c.10580G>A (p.Arg3527Gln) variant in the APOB gene has previously been reported in multiple patients with hypercholesterolemia [PMID 2563166, 23375686, 18325181, 27497240, 24956927, 21059979, 9603795 among others, reported as p.Arg3500Gln]. This variant is the most common cause of hypercholesterolemia due to an APOB variant and is common among Northern European populations. This change disrupts the binding of low density lipoproteins (LDL) onto the LDL receptor. The receptor mediated catabolism is thus disrupted and LDL accumulates in the plasma. The disorder caused by this specific variant is sometimes referred as hypercholesterolemia, due to ligand-defective apo B [MIM 144010]. This variant has been observed in 28 heterozygous individuals from the ExAC database (http://exac.broadinstitute.org/variant/2-21229160-C-T). Arginine at position 3527 of the APOB protein is highly conserved within mammals. While not validated for clinical use, the computer-based algorithms predict this p.Arg3527Gln change to be deleterious. It is thus interpreted as a pathogenic variant. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Aug 22, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, familial, 1
(Autosomal dominant inheritance)
|
Robarts Research Institute, Western University
Accession: SCV000484820.2
First in ClinVar: Dec 17, 2016 Last updated: Sep 14, 2019 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 20
|
|
|
Pathogenic
(May 23, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, familial, 1 |
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia
Accession: SCV001432581.1
First in ClinVar: Sep 19, 2020 Last updated: Sep 19, 2020 |
Observation:
13
Observation 1
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
6 (clinical Dutch Lipid Clinic Network Criteria score); 7.36 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 2
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
8 (clinical Dutch Lipid Clinic Network Criteria score); 8.58 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 3
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
NA (clinical Dutch Lipid Clinic Network Criteria score); 4.5 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 4
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
16 (clinical Dutch Lipid Clinic Network Criteria score); 6.8 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 5
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
6 (clinical Dutch Lipid Clinic Network Criteria score); 6.94 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 6
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
6 (clinical Dutch Lipid Clinic Network Criteria score); 7.12 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 7
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
8 (clinical Dutch Lipid Clinic Network Criteria score); 5.95 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 8
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
7 (clinical Dutch Lipid Clinic Network Criteria score); 6.6 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 9
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
7 (clinical Dutch Lipid Clinic Network Criteria score); 6.86 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 10
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
10 (clinical Dutch Lipid Clinic Network Criteria score); 5.6 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 11
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
21 (clinical Dutch Lipid Clinic Network Criteria score); 8.8 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 12
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
6 (clinical Dutch Lipid Clinic Network Criteria score); 4.65 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform type: next-gen sequencing
Platform name: MiSeq
Observation 13
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Dutch Lipid Clinic Network Criteria score (present) , low-density lipoprotein cholesterol level (present)
Comment on clinical features:
5 (clinical Dutch Lipid Clinic Network Criteria score); 6.34 mmol/L (calculated low-density lipoprotein cholesterol level)
Platform Type: next-gen sequencing
Platform Name: MiSeq
|
|
|
Pathogenic
(Mar 07, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Division of Medical Genetics, University of Washington
Study: CSER_CHARM
Accession: SCV001434274.1 First in ClinVar: Oct 03, 2020 Last updated: Oct 03, 2020 |
Comment:
show
This is a well-studied variant in the APOB gene and has been shown to cause hypercholesterolemia via apolipoprotein B deficiency (Soria 1989, Tybjaerg-Hansen 1998). This variant has bene observed in a number of individuals and families with FH (Garcia-Garcia 2011, Radovica-Splavina 2015, Shen 2010, Soria 1989) and functional studies have demonstrated that this variant results in decreased low density lipoprotein (LDL) binding affinity (Benn 2005, Boren 2001). Based on this evidence, we consider this variant to be pathogenic. PS4; PP1; PS3 (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Indication for testing: Family history of ovarian cancer
|
|
|
Pathogenic
(Oct 17, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
HYPERCHOLESTEROLEMIA, AUTOSOMAL DOMINANT, TYPE B |
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV001443719.1
First in ClinVar: Nov 21, 2020 Last updated: Nov 21, 2020 |
Comment:
show
This variant has been previously reported as heterozygous change in patients with hypercholesterolemia (PMID: 9105560, 21059979, 18325181, 18222178, 10388479, 23375686, 2563166, 21868016). Experimental studies have shown that this missense change disturbs the APOB protein conformation, therefore reducing its ability to act as inhibitor of the LDL receptor (PMID: 11115503, 15797858). This variant is also known in the literature as p.Arg3500Gln (PMID: 27919345). ClinVar contains an entry for this variant (Variation ID: 17890). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.03% (83/282162), and one homozygous individual is also reported. The c.10580G>A (p.Arg3527Gln) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.10580G>A (p.Arg3527Gln) variant is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Nov 11, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypobetalipoproteinemia 1 |
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001934310.1
First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
Observation:
2
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: yes
Observation 2
Collection method: clinical testing
Allele origin: unknown
Affected status: yes
|
|
|
Pathogenic
(Nov 18, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
AiLife Diagnostics, AiLife Diagnostics
Accession: SCV002502502.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 3
Secondary finding: no
Platform type: NGS
|
|
|
Pathogenic
(Aug 06, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia |
National Institute of Allergy and Infectious Diseases - Centralized Sequencing Program, National Institutes of Health
Accession: SCV002522177.1
First in ClinVar: Jun 05, 2022 Last updated: Jun 05, 2022 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(May 02, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Illumina Laboratory Services, Illumina
Accession: SCV000426986.3
First in ClinVar: Dec 06, 2016 Last updated: Jul 08, 2023 |
Comment:
show
The APOB c.10580G>A (p.Arg3527Gln) missense variant, also reported as p.Arg3500Gln, results in the substitution of arginine at amino acid position 3527 with glutamine. The c.10580G>A variant is well described in the literature and reported as one of the two most common variants associated with familial hypercholesterolemia, particularly in individuals of European ancestry (PMID: 24404629). Across a selection of the available literature, the c.10580G>A variant has been found in a heterozygous state in 42 individuals with the disorder (PMID: 2563166; PMID: 9603795; PMID: 10952765; PMID: 11494965; PMID: 11781700; PMID: 26036859). Four of the studies demonstrated segregation of the variant with disease (PMID: 2563166; PMID: 10952765; PMID: 11494965; PMID: 26036859). Control data are unavailable for this variant, which is reported at a frequency of 0.000591 in the European (non-Finnish) population of the Genome Aggregation Database, which includes one homozygote (version 2.1.1) and at a frequency of 0.06798 in the Amish population (version 3.1.2), which is high but consistent with the prevalence of familial hypercholesterolemia in this population. Functional studies in transgenic mice showed that the variant resulted in defective LDL receptor binding (PMID: 11115503). Based on the available evidence, the c.10580G>A (p.Arg3527Gln) variant is classified as pathogenic for familial hypercholesterolemia. (less)
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
|
Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
APOB-related disorders
|
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV004046030.1
First in ClinVar: Oct 21, 2023 Last updated: Oct 21, 2023 |
Comment:
show
This variant is also known in the literature as p.Arg3500Gln (PMID: 27919345). This variant has been previously reported as heterozygous change in patients with hypercholesterolemia (PMID: 9105560, 21059979, 18325181, 18222178, 10388479, 23375686, 2563166, 21868016). Experimental studies have shown that this missense change disturbs the APOB protein conformation, therefore reducing its ability to act as inhibitor of the LDL receptor (PMID: 11115503, 15797858). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.03% (83/282162), and one homozygous individual is also reported. The c.10580G>A (p.Arg3527Gln) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.10580G>A (p.Arg3527Gln) variant is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Jul 12, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
(Autosomal dominant inheritance)
|
Genetics and Molecular Pathology, SA Pathology
Accession: SCV002761491.2
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2023 |
Comment:
show
The APOB c.10580G>A variant is classified as Pathogenic (PS4, PS3, PP1_Strong, PP3) The APOB c.10580G>A variant is a single nucleotide change in exon 26/29 of the APOB gene, which is predicted to change the amino acid arginine at position 3527 in the protein to glutamine. This variant is a well-known cause of hypercholesterolemia due to defective ApoB mainly in people of European ancestry and is reported as an Amish founder variant (PMID: 24404629). This variant has been reported in multiple unrelated affected individuals (PMID: 21059979) and with low allele frequency in gnomAD population data, demonstrating that this variant is enriched in the disease population (PS4). Note that this variant has also been reported as R3500Q in the literature. A paper by Soria et. al, 1989 (PMID: 2563166) reports segregation with disease in 2 families (PP1_strong). Functional assays have demonstrated that this missense variant disturbs the APOB protein conformation preventing it from binding LDL, disturbing its normal function as inhibitor of the LDL receptor (PMID: 11115503) (PS3). Computational predictions (REVEL = 0.735) support a deleterious effect on the gene or gene product (PP3). The variant has been reported in dbSNP (rs5742904) and in the HGMD database: CM890006. It has been reported as Pathogenic/Likely pathogenic by other diagnostic laboratories (ClinVar Variation ID: 17890). (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Aug 08, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000887561.4
First in ClinVar: Dec 19, 2017 Last updated: Jan 06, 2024 |
Comment:
show
The APOB c.10580G>A (p.Arg3527Gln) variant has been reported in the published literature in several individuals and families affected with hypercholesterolemia (PMIDs: 2563166 (1989), 9603795 (1998), 10388479 (1999), 23375686 (2013), 24404629 (2016), 31345425 (2019)). It has been reported to be strongly associated with disease in families affected with hypercholesterolemia (PMIDs: 2563166 (1989), 21868016 (2011)) and has been reported as a founder mutation in the Amish community (PMID: 21059979 (2010)). Published functional studies demonstrate that this variant is damaging to LDL receptor binding (PMIDs: 10388479 (1999), 11115503 (2001)). Based on the available information, this variant is classified as pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
|
Pathogenic
(Mar 30, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Molecular Genetics, Royal Melbourne Hospital
Accession: SCV004812275.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
Comment:
show
This sequence change in APOB is predicted to replace arginine with glutamine at codon 3527, p.(Arg3527Gln). The arginine residue is highly conserved (100 vertebrates, UCSC), and is a critical residue for normal LDL receptor binding (PMID: 9486979). There is a small physicochemical difference between arginine and glutamine. The highest population minor allele frequency in gnomAD v2.1 is 0.06% (76/128,568 alleles, 1 homozygote) in the European (non-Finnish) population. This is the most commonly occurring variant identified in European APOB-related familial hypercholesterolaemia individuals (PMID: 24404629). The variant has been reported to segregate with familial hypercholesterolaemia in multiple families (PMID: 2563166, 26036859). Assessment of the whole LDL receptor cycle in heterologous cells showed defective LDL receptor-binding activity indicating that this variant impacts protein function (PMID: 9486979, 11115503 ). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (5/6 algorithms). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as PATHOGENIC. Following criteria are met: PS3, PP1_Strong, PM1, PP3. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Oct 12, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005199565.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Mar 21, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Institute of Immunology and Genetics Kaiserslautern
Accession: SCV005382161.1
First in ClinVar: Oct 26, 2024 Last updated: Oct 26, 2024 |
Comment:
show
ACMG Criteria: PS3, PS4, PM1, PM5, PP1, PP3, PP4, PP5; Variant was found in heterozygous state. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Clinical Features:
Hypercholesterolemia (present)
|
|
|
Pathogenic
(Sep 16, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
Familial hypobetalipoproteinemia 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. |
New York Genome Center
Accession: SCV003925306.2
First in ClinVar: May 20, 2023 Last updated: Dec 22, 2024 |
Comment:
show
The c.10580G>A variant has previously been reported in multiple individuals with familial hypercholesterolemia [PMID: 24404629] and has been shown to segregate with hypercholesterolemia in multiple families [PMID: 2563166, 8254047, 21868016]. This variant is reported as one of the two most common variants associated with familial hypercholesterolemia, particularly in individuals of European ancestry [PMID: 24404629]. Multiple independent laboratories have deposited this variant as Pathogenic/Likely Pathogenic in the ClinVar database (Variation ID: 17890). The c.10580G>A variant is observed in 328 alleles (0.0556% minor allele frequency with 5homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8). This frequency is low enough to be consistent with the frequency of familial hypercholesterolemia in the general population and pathogenic variants in APOB can have reduced penetrance and a less severe phenotype than disease-causingLDLR or PCSK9 variants [PMID: 24404629]. The c.10580G>A variant is located in exon 26 of this 29-exon gene and is predicted to replace an evolutionarilyconserved arginine amino acid with glutamine at position 3527 in the encoded protein. In silico predictions are in favor of damaging effect for p.(Arg3527Gln) variant [(CADD v1.6 = 28, REVEL = 0.735)]. Functional studies have demonstrated that this variant affects APOB protein conformation and impairs its binding to the LDLR protein [PMID: 8254047, 9486979, 10388479, 11115503, 15797858, 26643808]. A different amino acid change at this codon p.(Arg3527Gln) has been reported in ClinVar [ClinVar ID: 40223] as Pathogenic. Moreover, a different missense variant p.(Arg3527Leu) has been reported in individuals with familial hypercholesterolemia [PMID:16250003, 33269076]. Based on available evidence this c.10580G>A p.(Arg3527Gln) variant identified in APOB is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Clinical Features:
Hyperlipidemia (present)
Test name: whole genome sequencing
Zygosity: 1 Single Heterozygote
Secondary finding: no
Platform name: NovaSeq 6000
|
|
|
Pathogenic
(Jan 22, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B
Familial hypobetalipoproteinemia 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. |
Fulgent Genetics, Fulgent Genetics
Accession: SCV005655803.1
First in ClinVar: Jan 25, 2025 Last updated: Jan 25, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Oct 23, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided
(Unknown mechanism)
|
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001447186.2
First in ClinVar: Nov 28, 2020 Last updated: Apr 13, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Sex: female
|
|
|
Likely pathogenic
(Mar 22, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
see cases
|
Centre of Medical Genetics, University Hospital Muenster
Accession: SCV002578091.3
First in ClinVar: Oct 08, 2022 Last updated: Apr 13, 2025 |
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: yes
Number of individuals with the variant: 1
Clinical Features:
Stroke disorder (present)
Zygosity: 1 Single Heterozygote
Age: 0-9 years
Sex: male
Tissue: blood
Platform type: next-gen sequencing
Platform name: NextSeq 500
|
|
|
Pathogenic
(Jul 25, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Department of Pathology and Laboratory Medicine, Sinai Health System
Accession: SCV005913581.1
First in ClinVar: Apr 28, 2025 Last updated: Apr 28, 2025 |
Observation: 1
Collection method: research
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: research
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Apr 25, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Cardiovascular phenotype |
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
Accession: SCV000987576.2
First in ClinVar: Sep 06, 2019 Last updated: Apr 28, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Feb 03, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Familial hypercholesterolemia |
Color Diagnostics, LLC DBA Color Health
Accession: SCV000902821.6
First in ClinVar: May 20, 2019 Last updated: May 03, 2025 |
Comment:
show
This missense variant replaces arginine with glutamine at codon 3527 in the beta 2 domain of the APOB protein. This variant is also known as p.Arg3500Gln in the mature protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function. Functional studies have shown that the variant affects APOB protein conformation and impairs its binding to the LDLR protein (PMID: 8254047, 9486979, 10388479, 11115503, 15797858). This variant has been reported in numerous individuals with familial hypercholesterolemia in multiple populations (PMID: 1466657, 2563166, 8254047, 9104431, 9105560, 9603795, 10388479, 11137107, 11494965, 11781700, 18222178, 18325181, 1977310, 21059979, 21868016, 23375686, 24956927, 32591292, 34834584, 35052492, 35741760, 37593691) and has been shown to segregate with hypercholesterolemia in multiple families (PMID: 2563166, 8254047, 21868016). A different missense variant at the same position, p.Arg3527Trp, is known to be pathogenic (ClinVar variation ID 40223), indicating that arginine at this position is important for APOB protein function. This variant has been identified in 83/282162 chromosomes in the general population by the Genome Aggregation Database (gnomAD). APOB mutations show incomplete penetrance, and individuals with APOB mutations may show a less severe phenotype than familial hypercholesterolemia patients with LDLR mutations (PMID: 8141833, 21868016, 21513517; GeneReviews NBK174884). In summary, the mutant APOB protein harboring this variant is functionally defective and has shown significant clinical association with familial hypercholesterolemia. Based on the available evidence, this variant is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Platform type: NGS
|
|
|
Pathogenic
(Oct 30, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Revvity Omics, Revvity
Accession: SCV002018216.4
First in ClinVar: Nov 29, 2021 Last updated: Sep 06, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Aug 25, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
APOB-related disorder
|
Daryl Scott Lab, Baylor College of Medicine
Accession: SCV006555536.1
First in ClinVar: Oct 18, 2025 Last updated: Oct 18, 2025 |
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: yes
Zygosity: 1 Single Heterozygote
|
|
|
Pathogenic
(Feb 24, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV002048236.4
First in ClinVar: Jan 08, 2022 Last updated: Jan 24, 2026 |
Comment:
show
The APOB c.10580G>A; p.Arg3527Gln variant (rs5742904, ClinVar Variation ID: 17890), also reported as Arg3500Gln, is described in the literature in many affected individuals, reported to segregate with disease in affected families, and is one of the most common variants associated with familial hypercholesterolemia in individuals of European ancestry (Braenne 2016, Horvath 2001, Peloso 2014, Tybjaerg-Hansen 1998, Youngblom 2016). This variant is found in the non-Finnish European population with an allele frequency of 0.06% (76/128,568 alleles including 1 homozygote) in the Genome Aggregation Database (v2.1.1). Computational analyses predict that this variant is deleterious (REVEL:0.735), and functional studies show that the variant results in defective LDL binding (Boren 2001). Based on available information, this variant is considered to be pathogenic. References: Boren J et al. The molecular mechanism for the genetic disorder familial defective apolipoprotein B100. J Biol Chem. 2001 Mar 23;276(12):9214-8. PMID: 11115503. Braenne I et al. Systematic analysis of variants related to familial hypercholesterolemia in families with premature myocardial infarction. Eur J Hum Genet. 2016 Feb;24(2):191-7PMID: 26036859. Horvath A et al. High frequency of the ApoB-100 R3500Q mutation in Bulgarian hypercholesterolaemic subjects. J Med Genet. 2001 Aug;38(8):536-40. PMID: 11494965. Peloso GM et al. Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. Am J Hum Genet. 2014 Feb 6;94(2):223-32. PMID: 24507774. Tybjaerg-Hansen A et al. Association of mutations in the apolipoprotein B gene with hypercholesterolemia and the risk of ischemic heart disease. N Engl J Med. 1998 May 28;338(22):1577-84. PMID: 9603795. Youngblom E et al. Familial Hypercholesterolemia. 2014 Jan 2 (updated 2016 Dec 8). In: Adam MP et al, editors. GeneReviews (Internet). Seattle (WA): University of Washington, Seattle; 1993-2021. PMID: 24404629. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Apr 14, 2026)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Dasa
Accession: SCV007598703.1
First in ClinVar: May 30, 2026 Last updated: May 30, 2026 |
Comment:
show
NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln) is a missense variant that results in the substitution of arginine with glutamine. Functional evidence supports a deleterious effect on the gene or gene product (PMID: 11115503; PMID: 10388479; PMID: 37593691; PMID: 32591292; PMID: 24956927). This variant has been recurrently observed in individuals with related phenotype (PMID: 11115503; PMID: 10388479; PMID: 37593691; PMID: 32591292; PMID: 24956927). Segregation evidence has been reported in affected families. Multiple computational predictions support a deleterious effect on the gene or gene product. The variant is present at low frequency in population datasets. Based on the available data, this variant is classified as pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Oct 27, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Clinical Genetics Laboratory, Region Ostergotland
Accession: SCV005368671.2
First in ClinVar: Oct 13, 2024 Last updated: Jun 20, 2026 |
Comment:
show
The following ACMG/AMP criteria were applied in classifying this variant as Pathogenic: PS4, PP1, PP3, PS3 (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
pathogenic
(Apr 21, 2026)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001428664.20
First in ClinVar: Aug 17, 2020 Last updated: Jul 14, 2026 |
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: yes
Clinical Features:
Hypercholesterolemia (present)
Sex: female
|
|
|
Pathogenic
(Sep 11, 2023)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypercholesterolemia, autosomal dominant, type B |
Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital
Accession: SCV007615091.1
First in ClinVar: Jul 14, 2026 Last updated: Jul 14, 2026 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(-)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Familial hypercholesterolemia |
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum
Accession: SCV000605966.1
First in ClinVar: Sep 30, 2017 Last updated: Sep 30, 2017 |
Observation: 1
Collection method: research
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: research
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Nov 01, 2001)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
HYPERCHOLESTEROLEMIA, FAMILIAL, 2 |
OMIM
Accession: SCV000039775.3
First in ClinVar: Apr 04, 2013 Last updated: Jun 23, 2019 |
Observation: 1
Collection method: literature only
Allele origin: germline
Affected status: not provided
Observation 1
Collection method: literature only
Allele origin: germline
Affected status: not provided
Comment on evidence:
By extensive sequence analysis of the 2 alleles of the APOB gene in a man with moderate hypercholesterolemia (FHCL2; 144010), who was originally reported by … (more)
By extensive sequence analysis of the 2 alleles of the APOB gene in a man with moderate hypercholesterolemia (FHCL2; 144010), who was originally reported by Vega and Grundy (1986) and was found to be heterozygous for familial defective apolipoprotein by Innerarity et al. (1987), Soria et al. (1989) demonstrated a mutation in the codon for amino acid 3500 that results in the substitution of glutamine for arginine. This same mutant allele was found in 6 other, unrelated subjects and in 8 affected relatives in 2 of these families. A partial haplotype of this mutant apoB100 allele was constructed by sequence analysis and restriction enzyme digestion at positions where variations in the apoB100 are known to occur. This haplotype was found to be the same in 3 probands and 4 affected members of 1 family and lacks a polymorphic XbaI site whose presence has been correlated with high cholesterol levels. Thus, it appears that the mutation in the codon for amino acid 3500 (CGG-to-CAG), a CG mutation hotspot, defines a minor apoB100 allele associated with defective low density lipoproteins and hypercholesterolemia. Ludwig and McCarthy (1990) used 10 markers for haplotyping at the APOB locus in cases of familial defective apolipoprotein B100: 8 diallelic markers within the structural gene and 2 hypervariable markers flanking the gene. In 14 unrelated subjects heterozygous for the mutation, 7 of 8 unequivocally deduced haplotypes were identical, and 1 revealed only a minor difference at one of the hypervariable loci. The genotypes of the other 6 affected subjects was consistent with the same haplotype. Familial defective apolipoprotein B100 (FDB) results from a G-to-A transition at nucleotide 10708 in exon 26 of the APOB gene. Ludwig and McCarthy (1990) interpreted the data as consistent with the existence of a common ancestral chromosome. In a screening for the APOB3500 mutation by PCR amplification and hybridization with an allele-specific oligonucleotide, Loux et al. (1993) found only 1 case among 101 French subjects with familial hypercholesterolemia. The son of this individual, a 45-year-old man, was found also to have the mutation. Haplotype analysis revealed strict identity to that previously reported by Ludwig and McCarthy (1990), thus supporting a unique European ancestry. The family lived in the southwest of France and had no knowledge of Germanic origin. Rauh et al. (1992) stated that the frequency of the arg3500-to-gln mutation has been found to be approximately 1/500 to 1/700 in several Caucasian populations in North America and Europe. On the other hand, Friedlander et al. (1993) found no instance of this mutation in a large screening program in Israel. They pointed out that the mutation has also not been found in Finland (Hamalainen et al., 1990) and is said to be absent in Japan. Tybjaerg-Hansen and Humphries (1992) gave a review suggesting that the risk of premature coronary artery disease in the carriers of the mutation is increased to levels as high as those seen in patients with familial hypercholesterolemia; at age 50, about 40% of males and 20% of females heterozygous for the mutation have developed coronary artery disease. Marz et al. (1992) found only moderate hypercholesterolemia in a 54-year-old man who was homozygous for the arg3500-to-gln mutation and on a normal diet without lipid-lowering medication. There was no evidence of atherosclerosis and no history of cardiovascular complaints. The levels of apoE-containing lipoproteins were normal. Marz et al. (1992) suggested that the intact metabolism of apoE-containing particles decreases LDL production in this disorder, explaining the difference from familial hypercholesterolemia due to a receptor defect in which apoE levels are raised. Marz et al. (1993) investigated possible compensatory mechanisms that may have alleviated the consequences of the familial defective apoB100 (FDB). They showed that the receptor interaction of buoyant LDL is normal due to the presence of apoE in these particles. In addition, they provided evidence that the arg3500-to-gln substitution profoundly alters the conformation of the apoB receptor binding domain when apolipoprotein B resides on particles at the lower and upper limits of the LDL density range. They concluded that these mechanisms distinguish FDB from FH and account for the mild hypercholesterolemia in homozygous FDB. Among 43 patients with clinically and biochemically defined type III hyperlipoproteinemia (107741), Feussner and Schuster (1992) found no instance of the arg3500-to-gln mutation. In the course of investigating 2 unrelated French patients heterozygous for mutations in the LDLR gene (606945) who had aggravated hypercholesterolemia, Benlian et al. (1996) found that each carried the identical arg3500-to-gln mutation in the APOB gene, i.e., were double heterozygotes. One of the patients was a 10-year-old boy when he was referred for hypercholesterolemia discovered at the time of a cardiac arrest. He had no planar xanthomata, although he exhibited bilateral xanthomas of the Achilles and metacarpal phalangeal tendons. Peripheral arterial disease was demonstrated by the presence of arterial murmurs and by arterial wall irregularity on ultrasound analysis. Stenoses of coronary arteries necessitated surgical angioplasty. The second patient was a 39-year-old man with myocardial infarction and acute ischemia of the legs. Both families came from the Perche region from which many French Canadians originated. The LDLR mutations trp66-to-gly (606945.0003) and glu207-to-lys (606945.0007) had previously been described in French Canadians. Rubinsztein et al. (1993) described an Afrikaner family with 6 FH/FDB double heterozygotes carrying another LDLR mutation, asp206-to-glu (606945.0006). (Benlian et al. (1996), in the title of their article, correctly referred to these patients as double heterozygotes; in the paper itself they incorrectly referred to them as FH/FDB compound heterozygotes. The latter term is used for heterozygosity for alleles at the same locus.) In a patient homozygous for the R3500Q mutation, Schaefer et al. (1997) found LDL cholesterol and apoB concentrations approximately twice normal, whereas apoE plasma level was low. Using a stable-isotope labeling technique, they obtained data showing that the in vivo metabolism of apoB100-containing lipoproteins in FDB is different from that in familial hypercholesterolemia, in which LDL receptors are defective. Although the residence times of LDL apoB100 appeared to be increased to approximately the same degree, LDL apoB100 synthetic rate was increased in FH and decreased in FDB. The decreased production of LDL apoB100 in FDB may originate from enhanced removal of apoE-containing LDL precursors by LDL receptors, which may be upregulated in response to the decreased flux of LDL-derived cholesterol into hepatocytes. Almost all individuals with familial defective apoB100 are of European descent, and in almost all cases the mutation is on a chromosome with a rare haplotype at the apoB locus, suggesting that all probands are descended from a common ancestor in whom the original mutation occurred. Distribution of the mutation is consistent with an origin in Europe 6,000 to 7,000 years ago. Myant et al. (1997) estimated the amount of recombination between the APOB gene and markers on chromosome 2 in 34 FDB (R3500Q) probands in whom the mutation is on the usual 194 haplotype. Significant linkage disequilibrium was found between the APOB gene and marker D2S220. They identified 3 YACs that contained the APOB gene and D2S220. The shortest restriction fragment common to the 3 YACs that contain both loci was 240 kb long. No shorter fragments with both loci were identified. On the assumption that 1000 kb corresponds to 1 cM, Myant et al. (1997) deduced that the recombination distance between D2S220 and the APOB gene is about 0.24 cM. Combining this value with the linkage disequilibrium observed between the 2 loci in the probands, they estimated that the ancestral mutation occurred about 270 generations ago. They postulated that the original mutation occurred in the common ancestor of living FDB (R3500Q) probands, who lived in Europe about 6,750 years ago. Tybjaerg-Hansen et al. (1998) found that the R3500Q mutation in the APOB gene is present in approximately 1 in 1,000 persons in Denmark and causes severe hypercholesterolemia and increases the risk of ischemic heart disease. Heterozygous carriers of the arg3531-to-cys (107730.0017) mutation, which is present in the population in approximately the same frequency and also is associated with familial defective apolipoprotein B100, was not associated with higher-than-normal plasma cholesterol levels or an increased risk of ischemic heart disease. Saint-Jore et al. (2000) estimated the respective contributions of the LDLR gene defect, APOB gene defect, and other gene defects in autosomal dominant type IIa hypercholesterolemia by studying 33 well-characterized French families in which this disorder had been diagnosed over at least 3 generations. Using the candidate gene approach, they found that defects in the LDLR gene accounted for the disorder in about 50% of the families. The estimated contribution of an APOB gene defect was only 15%. This low estimation of involvement of the APOB gene defect was strengthened by the existence of only 2 probands carrying the R3500Q mutation. Surprisingly, 35% of the families were estimated to be linked to neither LDLR nor APOB. The results suggested that genetic heterogeneity in type IIa hypercholesterolemia had been underestimated and that at least 3 major groups of defects were involved. The authors were unable to estimate the contribution of the FH3 gene (603776). Boren et al. (2001) concluded that normal receptor binding of LDL involves an interaction between arginine-3500 and tryptophan-4369 in the carboxyl tail of apoB100. Trp4369 to tyr (W4369Y) LDL and arg3500 to gln (R3500Q) LDL isolated from transgenic mice had identically defective LDL binding and a higher affinity for a monoclonal antibody that has an epitope flanking residue 3500. Boren et al. (2001) concluded that arginine-3500 interacts with tryptophan-4369 and facilitates the conformation of apoB100 required for normal receptor binding of LDL. They developed a model that explained how the carboxyl terminus of apoB100 interacts with the backbone of apoB100 that enwraps the LDL particle. The model explained how all known ligand-defective mutations in apoB100, including a newly discovered R3480W mutation, cause defective receptor binding. Horvath et al. (2001) studied 130 unrelated individuals with hypercholesterolemia in Bulgaria. Four of these individuals were found to be carriers of this mutation. Horvath et al. (2001) concluded that this mutation accounts for 0.99 to 8.17% (95% CI) of cases of hypercholesterolemia in Bulgaria and therefore represents the most common single mutation associated with this condition in Bulgaria. Bednarska-Makaruk et al. (2001) found the arg3500-to-gln mutation in 2.5% (13/525) of unrelated patients with hypercholesterolemia in Poland. All the patients belonged to the type IIA hyperlipoproteinemia group. In 65 patients with the clinical characteristics of familial hypercholesterolemia, the frequency of the arg3500-to-gln mutation was 10.8% (7/65). The same haplotype at the APOB locus in the carriers of this mutation in Poland as in other populations from western Europe suggested its common origin. (less)
|
|
|
Pathogenic
(May 31, 2024)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
APOB-related condition
|
PreventionGenetics, part of Exact Sciences
Accession: SCV004105374.3
First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024 |
Comment:
show
The APOB c.10580G>A variant is predicted to result in the amino acid substitution p.Arg3527Gln. This variant was identified and characterized in the 1980s (aka p.Arg3500Gln, Innerarity et al. 1987. PubMed ID: 3477815; Soria et al. 1989. PubMed ID: 2563166). It is now recognized as the most common pathogenic variant in APOB for autosomal dominant familial hypercholesterolemia (reviewed by Varret et al. 2008. PubMed ID: 18028451). The p.Arg3527Gln substitution has been shown to reduce the binding affinity of LDL receptors to 30% of normal values (Innerarity et al. 1987. PubMed ID: 3477815). This variant is reported in 0.059% of alleles in individuals of European (non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(May 16, 2017)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
not provided |
Stanford Center for Inherited Cardiovascular Disease, Stanford University
Accession: SCV000924752.1
First in ClinVar: Jun 29, 2019 Last updated: Jun 29, 2019 |
Comment:
show
p.Arg3527Gln (c.10580G>A) in the APOB gene (NM_000384.2) Given the overwhelming case data and that this is a founder variant, we consider this variant pathogenic and we do feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). This variant is frequently reported in the literature as p.Arg3500Gln. Per the test report, this variant has been reported to be responsible for 2-6% of Western European FH cases and has been reported as an Amish founder mutation (Heath KE et al. Atherosclerosis. 1999;143(1):41-54; Lombardi et al. Clin Genet. 2000;57(2):116-24; Chmara M et al. J Appl Genet. 2010;51(1):95-106; Shen H et al. Arch Intern Med. 2010;170(20):1850-5). 1 in 500 to 1 in 700 Caucasian individuals have this specific variant per a 1992 report by Rauh and colleagues. Tybjaerg-Hansen et al. (1998) found that the R3500Q mutation in the APOB gene is present in approximately 1 in 1,000 persons in Denmark and causes severe hypercholesterolemia and increases the risk of ischemic heart disease. Bednarska-Makaruk et al. (2001) found the arg3500-to-gln mutation in 2.5% (13/525) of unrelated patients with hypercholesterolemia in Poland. All the patients belonged to the type IIA hyperlipoproteinemia group. In 65 patients with the clinical characteristics of familial hypercholesterolemia, the frequency of the arg3500-to-gln mutation was 10.8% (7/65). The same haplotype at the APOB locus in the carriers of this mutation in Poland as in other populations from western Europe suggested its common origin. Horvath et al. (2001) studied 130 unrelated individuals with hypercholesterolemia in Bulgaria. Four of these individuals were found to be carriers of this mutation. Horvath et al. (2001) concluded that this mutation accounts for 0.99 to 8.17% (95% CI) of cases of hypercholesterolemia in Bulgaria and therefore represents the most common single mutation associated with this condition in Bulgaria. Segregation data is strong: Soria et al. (1989) demonstrated that this variant was found in 6 other, unrelated subjects and in 8 affected relatives in 2 of these families. A partial haplotype of this mutant apoB100 allele was constructed by sequence analysis and restriction enzyme digestion at positions where variations in the apoB100 are known to occur. This haplotype was found to be the same in 3 probands and 4 affected members of 1 family and lacks a polymorphic XbaI site whose presence has been correlated with high cholesterol levels. Tybjaerg-Hansen and Humphries (1992) gave a review suggesting that the risk of premature coronary artery disease in the carriers of the mutation is increased to levels as high as those seen in patients with familial hypercholesterolemia; at age 50, about 40% of males and 20% of females heterozygous for the mutation have developed coronary artery disease. Boren et al. (2001) concluded that normal receptor binding of LDL involves an interaction between arginine-3500 and tryptophan-4369 in the carboxyl tail of apoB100. Trp4369 to tyr (W4369Y) LDL and arg3500 to gln (R3500Q) LDL isolated from transgenic mice had identically defective LDL binding. Marz et al 1993 found that he arg3500-to-gln substitution profoundly alters the conformation of the apoB receptor binding domain when apolipoprotein B resides on particles at the lower and upper limits of the LDL density range. Marz et al in 1992 found that higher levels of apoE may be a compensatory mechanism whereby an increase in apoE leads to a decrease in LDL. The arginine at codon 3527 is completely conserved across species. Two alterations at the same codon, p.R3527L and p.R3527W (reported as p.R3500L and p.R3500W), have also been associated with FH (Gaffney D et al. Arterioscler. Thromb. Vasc. Biol. 1995;15:1025-9; Fouchier SW et al. Hum. Mutat. 2005;26:550-6). The variant was reported online in 63 of 122,754 individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. Specifically, the variant was observed in 58 of 55,525 individuals of European descent (MAF=0.05%), 1 of 11,148 individuals of Finnish descent, 1 of 16,779 individuals of Latino descent and 1 of 2,738 individuals of other descent. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. There is a cohort of patients with coronary artery disease in gnomAD. Note that other variants with strong evidence for pathogenicity have been seen at similar frequencies in datasets like this so this does not necessarily rule out pathogenicity (Pan et al 2012). (less)
Observation: 1
Collection method: provider interpretation
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: provider interpretation
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(-)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
not provided |
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001743505.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(-)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
not provided |
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808570.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(-)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
not provided |
Clinical Genetics, Academic Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001922500.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Sep 30, 2021)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Hypercholesterolemia, autosomal dominant, type B |
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein
Accession: SCV002011728.1
First in ClinVar: Nov 06, 2021 Last updated: Nov 06, 2021 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Likely pathogenic
(Jul 21, 2023)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Hypercholesterolemia, autosomal dominant, type B |
deCODE genetics, Amgen
Accession: SCV004022243.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
Comment:
show
The variant NM_000384.3:c.10580G>A (chr2:21006288) in APOB was detected in 3 heterozygotes out of 58K WGS Icelanders (MAF= 0,003%). Following imputation in a set of 166K Icelanders (8 imputed heterozygotes) we observed an association with LDL cholesterol using measurements from 128289 individuals (Effect (SD)= 1.89, P= 1.93e-03) and Non-HDL cholesterol using measurements from 136901 individuals (Effect (SD)= 1.85, P= 2.08e-03). This variant has been reported in ClinVar previously as likely pathogenic, pathogenic and as a variant of uncertain significance. Based on ACMG criteria (PS4, PM5, PP5) this variant classifies as likely pathogenic. (less)
Observation 1
Collection method: research
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 8
Ethnicity/Population group: Icelandic
|
|
|
not provided
(-)
N
Not contributing to aggregate classification
|
no classification provided
|
Familial hypercholesterolemia
Familial hypobetalipoproteinemia 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. |
GenomeConnect - Invitae Patient Insights Network
Accession: SCV006556210.1
First in ClinVar: Oct 18, 2025 Last updated: Oct 18, 2025 |
Comment:
show
Variant classified as Pathogenic and reported on 06-16-2021 by Invitae. GenomeConnect-InvitaePIN assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. (less)
Observation: 1
Collection method: phenotyping only
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: phenotyping only
Allele origin: unknown
Affected status: unknown
Clinical Features:
Abnormality of vision (present) , Hypercholesterolemia (present) , Abnormal intestine morphology (present) , Abnormality of the liver (present)
Indication for testing: Diagnostic
Zygosity: 1 Single Heterozygote
Age: 60-69 years
Sex: female
Method: Gene Panel Sequencing
Testing laboratory: Labcorp Genetics (formerly Invitae), Labcorp
Date variant was reported to submitter: 2021-06-16
Testing laboratory interpretation: Pathogenic
|
|
|
not provided
(-)
N
Not contributing to aggregate classification
|
no classification provided
|
Hypercholesterolemia, autosomal dominant, type B |
GeneReviews
Accession: SCV000490148.2
First in ClinVar: Jan 07, 2017 Last updated: Oct 01, 2022 |
Observation 1
Collection method: literature only
Allele origin: germline
Affected status: yes
Geographic origin: Europe
|
|
|
not provided
(-)
N
Not contributing to aggregate classification
|
no classification provided
|
Hypercholesterolemia, autosomal dominant, type B |
GenomeConnect - Brain Gene Registry
Accession: SCV004176859.2
First in ClinVar: Dec 24, 2023 Last updated: Apr 13, 2025 |
Comment:
show
Variant classified as Pathogenic and reported on 02-16-2021 by The Children's Hospital of Philadelphia. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. (less)
Observation: 1
Collection method: phenotyping only
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: phenotyping only
Allele origin: unknown
Affected status: unknown
Clinical Features:
Hypotonia (present) , Abnormal heart morphology (present) , Microcephaly (present)
Indication for testing: Diagnostic
Zygosity: 1 Single Heterozygote
Age: 0-9 years
Sex: male
Secondary finding: yes
Method: Exome Sequencing
Testing laboratory: Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Date variant was reported to submitter: 2021-02-16
Testing laboratory interpretation: Pathogenic
|
|
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Familial Hypercholesterolemia. | Adam MP | - | 2025 | PMID: 24404629 |
| Familial Hyperlipidemia Caused by Apolipoprotein B Mutation in the Pediatric Amish Population: A Mini Review. | Snyder C | Interventional cardiology | 2023 | PMID: 37593691 |
| Identification of New Genetic Determinants in Pediatric Patients with Familial Hypercholesterolemia Using a Custom NGS Panel. | Rutkowska L | Genes | 2022 | PMID: 35741760 |
| Clinical characterization of familial hypercholesterolemia due to an amish founder mutation in Apolipoprotein B. | Williams KB | BMC cardiovascular disorders | 2022 | PMID: 35300601 |
| Establishing the Mutational Spectrum of Hungarian Patients with Familial Hypercholesterolemia. | Madar L | Genes | 2022 | PMID: 35052492 |
| Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia). | Shakhtshneider E | Journal of personalized medicine | 2021 | PMID: 34834584 |
| The first Japanese cases of familial hypercholesterolemia due to a known pathogenic APOB gene variant, c.10580 G>A: p.(Arg3527Gln). | Hori M | Journal of clinical lipidology | 2020 | PMID: 32591292 |
| Risk of Premature Atherosclerotic Disease in Patients With Monogenic Versus Polygenic Familial Hypercholesterolemia. | Trinder M | Journal of the American College of Cardiology | 2019 | PMID: 31345425 |
| Development of a Novel Next-Generation Sequencing Assay for Carrier Screening in Old Order Amish and Mennonite Populations of Pennsylvania. | Crowgey EL | The Journal of molecular diagnostics : JMD | 2019 | PMID: 31028937 |
| Genetic variations in familial hypercholesterolemia and cascade screening in East Asians. | Chan ML | Molecular genetics & genomic medicine | 2019 | PMID: 30592178 |
| Recall by genotype and cascade screening for familial hypercholesterolemia in a population-based biobank from Estonia. | Alver M | Genetics in medicine : official journal of the American College of Medical Genetics | 2019 | PMID: 30270359 |
| Effects of Genetic Variants Associated with Familial Hypercholesterolemia on Low-Density Lipoprotein-Cholesterol Levels and Cardiovascular Outcomes in the Million Veteran Program. | Sun YV | Circulation. Genomic and precision medicine | 2018 | PMID: 31106297 |
| Evaluation of Recipients of Positive and Negative Secondary Findings Evaluations in a Hybrid CLIA-Research Sequencing Pilot. | Sapp JC | American journal of human genetics | 2018 | PMID: 30122538 |
| Genetic testing for a patient with suspected familial hypercholesterolaemia. | Mudgundi V | BMJ case reports | 2018 | PMID: 30030251 |
| Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults. | Perkins BA | Proceedings of the National Academy of Sciences of the United States of America | 2018 | PMID: 29555771 |
| Homozygous Familial Hypercholesterolemia Patients With Identical Mutations Variably Express the LDLR (Low-Density Lipoprotein Receptor): Implications for the Efficacy of Evolocumab. | Thedrez A | Arteriosclerosis, thrombosis, and vascular biology | 2018 | PMID: 29284604 |
| Analysis of publicly available LDLR, APOB, and PCSK9 variants associated with familial hypercholesterolemia: application of ACMG guidelines and implications for familial hypercholesterolemia diagnosis. | Chora JR | Genetics in medicine : official journal of the American College of Medical Genetics | 2018 | PMID: 29261184 |
| Spectrum of mutations in Italian patients with familial hypercholesterolemia: New results from the LIPIGEN study. | Pirillo A | Atherosclerosis. Supplements | 2017 | PMID: 28965616 |
| Familial Hypercholesterolemia and Type 2 Diabetes in the Old Order Amish. | Xu H | Diabetes | 2017 | PMID: 28428224 |
| Molecular genetics of familial hypercholesterolemia in Israel-revisited. | Durst R | Atherosclerosis | 2017 | PMID: 28104544 |
| The molecular genetic background of familial hypercholesterolemia: data from the Slovak nation-wide survey. | Gabčová D | Physiological research | 2017 | PMID: 27824480 |
| Double-heterozygous autosomal dominant hypercholesterolemia: Clinical characterization of an underreported disease. | Sjouke B | Journal of clinical lipidology | 2016 | PMID: 27919364 |
| Multiethnic Exome-Wide Association Study of Subclinical Atherosclerosis. | Natarajan P | Circulation. Cardiovascular genetics | 2016 | PMID: 27872105 |
| Aggregate penetrance of genomic variants for actionable disorders in European and African Americans. | Natarajan P | Science translational medicine | 2016 | PMID: 27831900 |
| Homozygous Familial Hypercholesterolemia in Spain: Prevalence and Phenotype-Genotype Relationship. | Sánchez-Hernández RM | Circulation. Cardiovascular genetics | 2016 | PMID: 27784735 |
| Child-Parent Familial Hypercholesterolemia Screening in Primary Care. | Wald DS | The New England journal of medicine | 2016 | PMID: 27783906 |
| Polygenic Versus Monogenic Causes of Hypercholesterolemia Ascertained Clinically. | Wang J | Arteriosclerosis, thrombosis, and vascular biology | 2016 | PMID: 27765764 |
| Identification and molecular characterisation of Lausanne Institutional Biobank participants with familial hypercholesterolaemia - a proof-of-concept study. | Maurer F | Swiss medical weekly | 2016 | PMID: 27497240 |
| The genetic spectrum of familial hypercholesterolemia in south-eastern Poland. | Sharifi M | Metabolism: clinical and experimental | 2016 | PMID: 26892515 |
| Systematic analysis of variants related to familial hypercholesterolemia in families with premature myocardial infarction. | Brænne I | European journal of human genetics : EJHG | 2016 | PMID: 26036859 |
| Structural analysis of APOB variants, p.(Arg3527Gln), p.(Arg1164Thr) and p.(Gln4494del), causing Familial Hypercholesterolaemia provides novel insights into variant pathogenicity. | Fernández-Higuero JA | Scientific reports | 2015 | PMID: 26643808 |
| Evaluation of the Genetic Basis of Familial Aggregation of Pacemaker Implantation by a Large Next Generation Sequencing Panel. | Celestino-Soper PB | PloS one | 2015 | PMID: 26636822 |
| Next-generation-sequencing-based identification of familial hypercholesterolemia-related mutations in subjects with increased LDL-C levels in a latvian population. | Radovica-Spalvina I | BMC medical genetics | 2015 | PMID: 26415676 |
| Familial hypercholesterolemia in Brazil: cascade screening program, clinical and genetic aspects. | Jannes CE | Atherosclerosis | 2015 | PMID: 25461735 |
| Whole exome sequencing of familial hypercholesterolaemia patients negative for LDLR/APOB/PCSK9 mutations. | Futema M | Journal of medical genetics | 2014 | PMID: 24987033 |
| Targeted genetic testing for familial hypercholesterolaemia using next generation sequencing: a population-based study. | Norsworthy PJ | BMC medical genetics | 2014 | PMID: 24956927 |
| Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. | Peloso GM | American journal of human genetics | 2014 | PMID: 24507774 |
| Novel functional APOB mutations outside LDL-binding region causing familial hypercholesterolaemia. | Alves AC | Human molecular genetics | 2014 | PMID: 24234650 |
| Decreased bone mineral density in subjects carrying familial defective apolipoprotein B-100. | Yerges-Armstrong LM | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 24106285 |
| Spectrum of mutations and phenotypic expression in patients with autosomal dominant hypercholesterolemia identified in Italy. | Bertolini S | Atherosclerosis | 2013 | PMID: 23375686 |
| Mutation detection in Croatian patients with familial hypercholesterolemia. | Pećin I | Annals of human genetics | 2013 | PMID: 23130880 |
| Low prevalence of mutations in known loci for autosomal dominant hypercholesterolemia in a multiethnic patient cohort. | Ahmad Z | Circulation. Cardiovascular genetics | 2012 | PMID: 23064986 |
| Use of targeted exome sequencing as a diagnostic tool for Familial Hypercholesterolaemia. | Futema M | Journal of medical genetics | 2012 | PMID: 23054246 |
| Genetic analysis of familial hypercholesterolaemia in Western Australia. | Hooper AJ | Atherosclerosis | 2012 | PMID: 22883975 |
| The molecular basis of familial hypercholesterolemia in the Czech Republic: spectrum of LDLR mutations and genotype-phenotype correlations. | Tichý L | Atherosclerosis | 2012 | PMID: 22698793 |
| Microfluidic amplification as a tool for massive parallel sequencing of the familial hypercholesterolemia genes. | Hollants S | Clinical chemistry | 2012 | PMID: 22294733 |
| Molecular characterization of familial hypercholesterolemia in Spain. | Palacios L | Atherosclerosis | 2012 | PMID: 22244043 |
| Correlation between common genetic variants and risk factors associated with prediction of cardiovascular diseases in dyslipidemic patients. | Kotaska K | Genetic testing and molecular biomarkers | 2012 | PMID: 21919778 |
| Reduced penetrance of autosomal dominant hypercholesterolemia in a high percentage of families: importance of genetic testing in the entire family. | Garcia-Garcia AB | Atherosclerosis | 2011 | PMID: 21868016 |
| Familial hypercholesterolemia: epidemiology, Neolithic origins and modern geographic distribution. | Liyanage KE | Critical reviews in clinical laboratory sciences | 2011 | PMID: 21657943 |
| Familial hypercholesterolemia: the lipids or the genes? | Fahed AC | Nutrition & metabolism | 2011 | PMID: 21513517 |
| Molecular basis of autosomal dominant hypercholesterolemia: assessment in a large cohort of hypercholesterolemic children. | van der Graaf A | Circulation | 2011 | PMID: 21382890 |
| Array-based resequencing for mutations causing familial hypercholesterolemia. | Chiou KR | Atherosclerosis | 2011 | PMID: 21376320 |
| An APEX-based genotyping microarray for the screening of 168 mutations associated with familial hypercholesterolemia. | Dušková L | Atherosclerosis | 2011 | PMID: 21310417 |
| Familial defective apolipoprotein B-100 and increased low-density lipoprotein cholesterol and coronary artery calcification in the old order amish. | Shen H | Archives of internal medicine | 2010 | PMID: 21059979 |
| Molecular spectrum of autosomal dominant hypercholesterolemia in France. | Marduel M | Human mutation | 2010 | PMID: 20809525 |
| A double heterozygote for familial hypercholesterolaemia and familial defective apolipoprotein B-100. | Taylor A | Annals of clinical biochemistry | 2010 | PMID: 20736250 |
| Mutation detection rate and spectrum in familial hypercholesterolaemia patients in the UK pilot cascade project. | Taylor A | Clinical genetics | 2010 | PMID: 20236128 |
| Molecular characterization of Polish patients with familial hypercholesterolemia: novel and recurrent LDLR mutations. | Chmara M | Journal of applied genetics | 2010 | PMID: 20145306 |
| Multiplex MassARRAY spectrometry (iPLEX) produces a fast and economical test for 56 familial hypercholesterolaemia-causing mutations. | Wright WT | Clinical genetics | 2008 | PMID: 18700895 |
| High-resolution melting analysis for detection of familial ligand-defective apolipoprotein B-100 mutations. | Liyanage KE | Annals of clinical biochemistry | 2008 | PMID: 18325181 |
| Detection of familial defective apoB (FDB) mutations in hypercholesterolemic children and adolescents by denaturing high performance liquid chromatography (DHPLC). | Nelken J | Clinical biochemistry | 2008 | PMID: 18222178 |
| Femoral atherosclerosis in heterozygous familial hypercholesterolemia: influence of the genetic defect. | Junyent M | Arteriosclerosis, thrombosis, and vascular biology | 2008 | PMID: 18096825 |
| Genetic heterogeneity of autosomal dominant hypercholesterolemia. | Varret M | Clinical genetics | 2008 | PMID: 18028451 |
| Familial hypercholesterolaemia in Portugal. | Bourbon M | Atherosclerosis | 2008 | PMID: 17765246 |
| Multiplex ARMS analysis to detect 13 common mutations in familial hypercholesterolaemia. | Taylor A | Clinical genetics | 2007 | PMID: 17539906 |
| ApoB-100 R3500Q mutation in the Lebanese population: prevalence and historical review of the literature. | Sabbagh AS | Molecular biology reports | 2007 | PMID: 17160438 |
| Genetic causes of familial hypercholesterolaemia in patients in the UK: relation to plasma lipid levels and coronary heart disease risk. | Humphries SE | Journal of medical genetics | 2006 | PMID: 17142622 |
| Update of the molecular basis of familial hypercholesterolemia in The Netherlands. | Fouchier SW | Human mutation | 2005 | PMID: 16250003 |
| Mutation in apolipoprotein B associated with hypobetalipoproteinemia despite decreased binding to the low density lipoprotein receptor. | Benn M | The Journal of biological chemistry | 2005 | PMID: 15797858 |
| Influence of LDL receptor gene mutations and the R3500Q mutation of the apoB gene on lipoprotein phenotype of familial hypercholesterolemic patients from a South European population. | Real JT | European journal of human genetics : EJHG | 2003 | PMID: 14508510 |
| The molecular basis of familial hypercholesterolemia in The Netherlands. | Fouchier SW | Human genetics | 2001 | PMID: 11810272 |
| Familial defective apolipoprotein B-100 in a group of hypercholesterolaemic patients in Poland. Identification of a new mutation Thr3492Ile in the apolipoprotein B gene. | Bednarska-Makaruk M | European journal of human genetics : EJHG | 2001 | PMID: 11781700 |
| High frequency of the ApoB-100 R3500Q mutation in Bulgarian hypercholesterolaemic subjects. | Horvath A | Journal of medical genetics | 2001 | PMID: 11494965 |
| Compound heterozygous familial hypercholesterolemia and familial defective apolipoprotein B-100 produce exaggerated hypercholesterolemia. | Tai ES | Clinical chemistry | 2001 | PMID: 11238294 |
| Frequency of the R3500Q mutation of the apolipoprotein B-100 gene in a sample screened clinically for familial hypercholesterolemia in Hungary. | Kalina A | Atherosclerosis | 2001 | PMID: 11137107 |
| The molecular mechanism for the genetic disorder familial defective apolipoprotein B100. | Borén J | The Journal of biological chemistry | 2001 | PMID: 11115503 |
| Autosomal dominant type IIa hypercholesterolemia: evaluation of the respective contributions of LDLR and APOB gene defects as well as a third major group of defects. | Saint-Jore B | European journal of human genetics : EJHG | 2000 | PMID: 10952765 |
| Molecular genetic testing for familial hypercholesterolemia: spectrum of LDL receptor gene mutations in The Netherlands. | Lombardi MP | Clinical genetics | 2000 | PMID: 10735632 |
| Mutations in the apolipoprotein (apo) B-100 receptor-binding region: detection of apo B-100 (Arg3500-->Trp) associated with two new haplotypes and evidence that apo B-100 (Glu3405-->Gln) diminishes receptor-mediated uptake of LDL. | Fisher E | Clinical chemistry | 1999 | PMID: 10388479 |
| The type of mutation in the low density lipoprotein receptor gene influences the cholesterol-lowering response of the HMG-CoA reductase inhibitor simvastatin in patients with heterozygous familial hypercholesterolaemia. | Heath KE | Atherosclerosis | 1999 | PMID: 10208479 |
| Identification and haplotype analysis of apolipoprotein B-100 Arg3500-->Trp mutation in hyperlipidemic Chinese. | Tai DY | Clinical chemistry | 1998 | PMID: 9702952 |
| LDL-R and Apo-B-100 gene mutations in Polish familial hypercholesterolemias. | Górski B | Human genetics | 1998 | PMID: 9654205 |
| Association of mutations in the apolipoprotein B gene with hypercholesterolemia and the risk of ischemic heart disease. | Tybjaerg-Hansen A | The New England journal of medicine | 1998 | PMID: 9603795 |
| Identification of the low density lipoprotein receptor-binding site in apolipoprotein B100 and the modulation of its binding activity by the carboxyl terminus in familial defective apo-B100. | Boren J | The Journal of clinical investigation | 1998 | PMID: 9486979 |
| Estimation of the age of the ancestral arginine3500-->glutamine mutation in human apoB-100. | Myant NB | Genomics | 1997 | PMID: 9339363 |
| Familial ligand-defective apolipoprotein B-100: simultaneous detection of the ARG3500-->GLN and ARG3531-->CYS mutations in a French population. | Rabès JP | Human mutation | 1997 | PMID: 9259199 |
| Denaturing gradient-gel electrophoresis screening of familial defective apolipoprotein B-100 in a mixed Asian cohort: two cases of arginine3500-->tryptophan mutation associated with a unique haplotype. | Choong ML | Clinical chemistry | 1997 | PMID: 9191540 |
| Familial ligand-defective apolipoprotein B-100: detection, biochemical features and haplotype analysis of the R3531C mutation in the UK. | Wenham PR | Atherosclerosis | 1997 | PMID: 9105560 |
| Molecular genetics of familial hypercholesterolaemia in Norway. | Leren TP | Journal of internal medicine | 1997 | PMID: 9104431 |
| Homozygous familial defective apolipoprotein B-100. Enhanced removal of apolipoprotein E-containing VLDLs and decreased production of LDLs. | Schaefer JR | Arteriosclerosis, thrombosis, and vascular biology | 1997 | PMID: 9081691 |
| Rapid testing for three mutations causing familial defective apolipoprotein B100 in 562 patients with familial hypercholesterolaemia. | Talmud PJ | Atherosclerosis | 1996 | PMID: 8831935 |
| Phenotypic expression in double heterozygotes for familial hypercholesterolemia and familial defective apolipoprotein B-100. | Benlian P | Human mutation | 1996 | PMID: 8723684 |
| Familial ligand-defective apolipoprotein B. Identification of a new mutation that decreases LDL receptor binding affinity. | Pullinger CR | The Journal of clinical investigation | 1995 | PMID: 7883971 |
| Independent mutations at codon 3500 of the apolipoprotein B gene are associated with hyperlipidemia. | Gaffney D | Arteriosclerosis, thrombosis, and vascular biology | 1995 | PMID: 7627691 |
| Absence of familial defective apolipoprotein B-100 in Israeli patients with dominantly inherited hypercholesterolemia and in offspring with parental history of myocardial infarction. | Friedlander Y | Human genetics | 1993 | PMID: 8478017 |
| A unique haplotype of the apolipoprotein B-100 allele associated with familial defective apolipoprotein B-100 in a Chinese man discovered during a study of the prevalence of this disorder. | Bersot TP | Journal of lipid research | 1993 | PMID: 8371062 |
| Identification of the haplotype associated with the APOB-3500 mutation in a French hypercholesterolemic subject: further support for a unique European ancestral mutation. | Loux N | Human mutation | 1993 | PMID: 8318993 |
| Characterization of six patients who are double heterozygotes for familial hypercholesterolemia and familial defective apo B-100. | Rubinsztein DC | Arteriosclerosis and thrombosis : a journal of vascular biology | 1993 | PMID: 8318509 |
| Accumulation of "small dense" low density lipoproteins (LDL) in a homozygous patients with familial defective apolipoprotein B-100 results from heterogenous interaction of LDL subfractions with the LDL receptor. | März W | The Journal of clinical investigation | 1993 | PMID: 8254047 |
| Familial defective apolipoprotein B-100: a review, including some comparisons with familial hypercholesterolaemia. | Myant NB | Atherosclerosis | 1993 | PMID: 8141833 |
| Familial defective apolipoprotein B-100: a common cause of primary hypercholesterolemia. | Rauh G | The Clinical investigator | 1992 | PMID: 1600334 |
| Screening for the apolipoprotein B-100 arginine3500-->glutamine mutation in patients with type III hyperlipoproteinemia. | Feussner G | Clinical genetics | 1992 | PMID: 1493642 |
| Familial defective apolipoprotein B-100: a single mutation that causes hypercholesterolemia and premature coronary artery disease. | Tybjaerg-Hansen A | Atherosclerosis | 1992 | PMID: 1466657 |
| Familial defective apolipoprotein B-100: mild hypercholesterolaemia without atherosclerosis in a homozygous patient. | März W | Lancet (London, England) | 1992 | PMID: 1360085 |
| Rapid screening for specific mutations in patients with a clinical diagnosis of familial hypercholesterolaemia. | Talmud P | Atherosclerosis | 1991 | PMID: 1793440 |
| Absence of familial defective apolipoprotein B-100 in Finnish patients with elevated serum cholesterol. | Hämäläinen T | Atherosclerosis | 1990 | PMID: 2375782 |
| Familial defective apolipoprotein B-100: a mutation of apolipoprotein B that causes hypercholesterolemia. | Innerarity TL | Journal of lipid research | 1990 | PMID: 2280177 |
| Haplotype analysis of the human apolipoprotein B mutation associated with familial defective apolipoprotein B100. | Ludwig EH | American journal of human genetics | 1990 | PMID: 1977310 |
| Association between a specific apolipoprotein B mutation and familial defective apolipoprotein B-100. | Soria LF | Proceedings of the National Academy of Sciences of the United States of America | 1989 | PMID: 2563166 |
| Familial defective apolipoprotein B-100: low density lipoproteins with abnormal receptor binding. | Innerarity TL | Proceedings of the National Academy of Sciences of the United States of America | 1987 | PMID: 3477815 |
| In vivo evidence for reduced binding of low density lipoproteins to receptors as a cause of primary moderate hypercholesterolemia. | Vega GL | The Journal of clinical investigation | 1986 | PMID: 3771801 |
| https://erepo.clinicalgenome.org/evrepo/ui/interpretation/57bcc7e1-22cc-4f98-98a3-7333c896048c | - | - | - | - |
| click to load more citations click to collapse | ||||
Text-mined citations for rs5742904 ...
HelpRecord last updated Jul 15, 2026
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
