ClinVar Miner

Submissions for variant NM_032119.4(ADGRV1):c.7873C>T (p.Arg2625Cys) (rs201583659)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000155734 SCV000205444 uncertain significance not specified 2013-11-06 criteria provided, single submitter clinical testing The Arg2625Cys variant in GPR98 has not been previously reported in individuals with hearing loss, but has been identified in 0.2% (1/574) of European chromosom es by the ClinSeq Project (dbSNP rs201583659). Computational analyses (biochemic al amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) do not p rovide strong support for or against an impact to the protein. In summary, addit ional data is needed to determine the clinical significance of this variant.
Athena Diagnostics Inc RCV000710462 SCV000840687 uncertain significance not provided 2018-04-10 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000765844 SCV000897240 uncertain significance Usher syndrome, type 2C; Febrile seizures, familial, 4 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000710462 SCV001215713 uncertain significance not provided 2019-12-22 criteria provided, single submitter clinical testing This sequence change replaces arginine with cysteine at codon 2625 of the ADGRV1 protein (p.Arg2625Cys). The arginine residue is weakly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs201583659, ExAC 0.2%). This variant has not been reported in the literature in individuals with ADGRV1-related conditions. ClinVar contains an entry for this variant (Variation ID: 178958). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.
Illumina Clinical Services Laboratory,Illumina RCV001157105 SCV001318651 uncertain significance Usher syndrome, type 2C 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.

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