ClinVar Miner

Submissions for variant NM_001142800.2(EYS):c.8779T>C (p.Cys2927Arg)

gnomAD frequency: 0.00001  dbSNP: rs373203896
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000762414 SCV000892729 likely pathogenic not provided 2018-07-01 criteria provided, single submitter clinical testing
Blueprint Genetics RCV001073470 SCV001239013 likely pathogenic Retinal dystrophy 2019-03-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000762414 SCV002232337 pathogenic not provided 2023-12-03 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 2927 of the EYS protein (p.Cys2927Arg). This variant is present in population databases (rs373203896, gnomAD 0.01%). This missense change has been observed in individual(s) with retinitis pigmentosa (PMID: 30718709, 31725169, 32728228; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 624249). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on EYS protein function. For these reasons, this variant has been classified as Pathogenic.
Mendelics RCV002249466 SCV002519630 pathogenic Retinitis pigmentosa 25 2022-05-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV002249466 SCV004195279 pathogenic Retinitis pigmentosa 25 2024-03-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000787601 SCV005380305 likely pathogenic Retinitis pigmentosa 2024-08-23 criteria provided, single submitter clinical testing Variant summary: EYS c.8779T>C (p.Cys2927Arg) results in a non-conservative amino acid change located in the EGF-like domain (IPR000742) of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.8e-05 in 157362 control chromosomes. c.8779T>C has been reported in the literature in individuals affected with Retinitis Pigmentosa (example, Colombo_2021, Hanany_2020, Pierrottet_ 2014, Soares_2023, Wang_2014 ). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 33576794, 31964843, 25366773, 36764454, 25097241). ClinVar contains an entry for this variant (Variation ID: 624249). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet RCV000787601 SCV000926584 likely pathogenic Retinitis pigmentosa 2018-04-01 no assertion criteria provided research

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