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NM_000384.3(APOB):c.12310C>A (p.Leu4104Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 29, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000334079.6
Variation ID:
334079
Description:
single nucleotide variant
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NM_000384.3(APOB):c.12310C>A (p.Leu4104Met)

Allele ID
285073
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p24.1
Genomic location
2: 21003112 (GRCh38) GRCh38 UCSC
2: 21225984 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.21225984G>T
NC_000002.12:g.21003112G>T
NG_011793.1:g.45962C>A
NM_000384.3:c.12310C>A MANE Select NP_000375.3:p.Leu4104Met missense
Protein change
L4104M
Other names
-
Canonical SPDI
NC_000002.12:21003111:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00067
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00075
1000 Genomes Project 0.00060
Links
ClinGen: CA049887
dbSNP: rs199668351
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jan 2, 2018 RCV000343227.2
Benign 1 criteria provided, single submitter May 24, 2019 RCV000461857.4
Likely benign 1 criteria provided, single submitter Aug 6, 2017 RCV000771140.1
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV001087962.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
APOB Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2209 2326

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Familial Hypercholesterolemia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000426920.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Hypobetalipoproteinemia, familial, 1
Familial hypercholesterolemia 2
Allele origin: germline
Invitae
Accession: SCV000554832.4
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Jan 02, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia 1
(Autosomal dominant inheritance)
Allele origin: germline
Robarts Research Institute,Western University
Accession: SCV000782804.1
Submitted: (Apr 09, 2018)
Evidence details
Likely benign
(Aug 06, 2017)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemias
Allele origin: germline
Color Health, Inc
Accession: SCV000902948.1
Submitted: (Nov 06, 2018)
Evidence details
Benign
(May 24, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001133390.1
Submitted: (Oct 16, 2019)
Evidence details

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs199668351...

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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 Oct 08, 2021