ClinVar Miner

Submissions for variant NM_000384.3(APOB):c.2863C>T (p.Pro955Ser)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory of Genetics and Molecular Cardiology, University of São Paulo RCV000497045 SCV000588423 uncertain significance Hypercholesterolemia, familial, 1 2016-03-01 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV001837930 SCV000777052 likely benign Hypercholesterolemia, autosomal dominant, type B; Familial hypobetalipoproteinemia 1 2023-11-10 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001138062 SCV001298085 uncertain significance Hypercholesterolemia, autosomal dominant, type B 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV001138063 SCV001298086 uncertain significance Familial hypobetalipoproteinemia 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV001576522 SCV001803728 uncertain significance not provided 2022-01-11 criteria provided, single submitter clinical testing Reported as a single nucleotide polymorphism associated with high LDL-C levels in exome wide association studies and has been reported in association with hypertriglyceridemia (Yamada et al., 2019; Tada et al., 2019); 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: 30718733, 28473662, 30389453, 33020668, 30365130)
Ambry Genetics RCV002438204 SCV002752807 benign Cardiovascular phenotype 2016-08-09 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV004527603 SCV004106400 uncertain significance APOB-related disorder 2023-04-01 criteria provided, single submitter clinical testing The APOB c.2863C>T variant is predicted to result in the amino acid substitution p.Pro955Ser. This variant has been reported in individuals with dyslipidemia, although no further evidence was provided to determine its pathogenicity (Yamada et al. 2017. PubMed ID: 28473662; Yamada et al. 2019. PubMed ID: 30365130. Table VI; Tada et al. 2019. PubMed ID: 30389453). This variant is reported in 0.26% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-21242731-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
GENinCode PLC RCV004772941 SCV005387564 benign Familial hypercholesterolemia 2024-07-19 criteria provided, single submitter clinical testing BA1

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