ClinVar Miner

Submissions for variant NM_016938.5(EFEMP2):c.874C>T (p.His292Tyr)

gnomAD frequency: 0.00005  dbSNP: rs532989312
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001106761 SCV001263856 uncertain significance Cutis laxa, autosomal recessive, type 1B 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001106761 SCV001545677 uncertain significance Cutis laxa, autosomal recessive, type 1B 2022-07-26 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 292 of the EFEMP2 protein (p.His292Tyr). This variant is present in population databases (rs532989312, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with EFEMP2-related conditions. This variant is also known as rs532989312. ClinVar contains an entry for this variant (Variation ID: 879337). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV003380848 SCV004097806 likely benign Cardiovascular phenotype 2023-07-03 criteria provided, single submitter clinical testing This alteration is classified as likely 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.

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