ClinVar Miner

Submissions for variant NM_032119.4(ADGRV1):c.12586C>T (p.Pro4196Ser) (rs397517420)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000039517 SCV000063206 likely benign not specified 2012-08-28 criteria provided, single submitter clinical testing Pro4196Ser in Exon 62 of GPR98: This variant has not been reported in the litera ture nor previously identified by our laboratory. However, computational analyse s (biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SI FT) suggest that the Pro4196Ser variant may not impact the protein. In particula r, this variant occurs in another mammal (shrew) despite nearby conservation. Th erefore, this variant is likely benign.
Invitae RCV001042748 SCV001206449 uncertain significance not provided 2019-12-11 criteria provided, single submitter clinical testing This sequence change replaces proline with serine at codon 4196 of the ADGRV1 protein (p.Pro4196Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine. This variant is present in population databases (rs397517420, 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: 46261). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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 RCV001157422 SCV001318990 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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