ClinVar Miner

Submissions for variant NM_001029883.3(PCARE):c.3044C>A (p.Ser1015Tyr) (rs202196567)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000352886 SCV000429860 uncertain significance Retinitis pigmentosa 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000732357 SCV000860307 uncertain significance not provided 2018-04-03 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001000401 SCV001157194 uncertain significance not specified 2019-05-22 criteria provided, single submitter clinical testing The C2orf71 (PCARE) c.3044C>A; p.Ser1015Tyr variant (rs202196567), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 335642). This variant is found in the general population with an overall allele frequency of 0.03% (76/275818 alleles) in the Genome Aggregation Database. The serine at codon 1015 is moderately conserved and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. However, due to limited information, the clinical significance of the p.Ser1015Tyr variant is uncertain at this time.
Invitae RCV000732357 SCV001213536 uncertain significance not provided 2020-01-08 criteria provided, single submitter clinical testing This sequence change replaces serine with tyrosine at codon 1015 of the PCARE protein (p.Ser1015Tyr). The serine residue is moderately conserved and there is a large physicochemical difference between serine and tyrosine. This variant is present in population databases (rs202196567, ExAC 0.05%). This variant has not been reported in the literature in individuals with PCARE-related conditions. ClinVar contains an entry for this variant (Variation ID: 335642). 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: "Probably 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.

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