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NM_000527.4(LDLR):c.694+2T>C

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jul 9, 2020)
Last evaluated:
Jun 15, 2020
Accession:
VCV000003738.4
Variation ID:
3738
Description:
single nucleotide variant
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NM_000527.4(LDLR):c.694+2T>C

Allele ID
18777
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.2
Genomic location
19: 11105602 (GRCh38) GRCh38 UCSC
19: 11216278 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_274t1:c.694+2T>C
NM_000527.5:c.694+2T>C MANE Select splice donor
NM_001195798.2:c.694+2T>C splice donor
... more HGVS
Protein change
-
Other names
IVS4, T-C, +2
Canonical SPDI
NC_000019.10:11105601:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA023753
LDLR-LOVD, British Heart Foundation: LDLR_000500
OMIM: 606945.0056
dbSNP: rs200238879
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts Mar 30, 2017 RCV000003936.8
Pathogenic 1 criteria provided, single submitter Jun 15, 2020 RCV001201185.1

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LDLR Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3093 3293

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Mar 25, 2016)
criteria provided, single submitter
Method: literature only
Familial hypercholesterolemia
(Autosomal dominant inheritance)
Allele origin: germline
LDLR-LOVD, British Heart Foundation
Accession: SCV000294919.2
Submitted: (Apr 20, 2016)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Dec 16, 2016)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia 1
Allele origin: germline
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies,APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix
Accession: SCV000503226.1
Submitted: (Jan 23, 2017)
Evidence details
Comment:
subject mutated among 2600 FH index cases screened = 1 , family member = 1
Pathogenic
(Mar 30, 2017)
criteria provided, single submitter
Method: clinical testing
Familial Hypercholesterolemia
Allele origin: germline
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille
Accession: SCV000583730.1
Submitted: (Mar 31, 2017)
Comment:
ACMG Guidelines: Pathogenic (i)
Evidence details
Pathogenic
(Mar 01, 2016)
criteria provided, single submitter
Method: research
Familial hypercholesterolemia
(Autosomal dominant inheritance)
Allele origin: germline
Fundacion Hipercolesterolemia Familiar
Study: SAFEHEART
Accession: SCV000607495.1
Submitted: (Apr 20, 2017)
Evidence details
Pathogenic
(Jun 15, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001372245.1
Submitted: (Jul 09, 2020)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: LDLR c.694+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Pathogenic
(Jan 01, 1997)
no assertion criteria provided
Method: literature only
FH ICELAND
Allele origin: germline
OMIM
Accession: SCV000024101.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Global molecular analysis and APOE mutations in a cohort of autosomal dominant hypercholesterolemia patients in France. Wintjens R Journal of lipid research 2016 PMID: 26802169
Common founder mutation in the LDL receptor gene causing familial hypercholesterolaemia in the Icelandic population. Gudnason V Human mutation 1997 PMID: 9222758

Text-mined citations for rs200238879...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021