ClinVar Miner

Submissions for variant NM_001278431.2(C1QTNF5):c.489C>G (p.Ser163Arg)

dbSNP: rs111033578
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
UCLA Clinical Genomics Center, UCLA RCV000002208 SCV000255333 likely pathogenic Late-onset retinal degeneration 2012-06-12 criteria provided, single submitter clinical testing
Blueprint Genetics RCV001074679 SCV001240272 pathogenic Retinal dystrophy 2019-03-20 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001245416 SCV001418703 pathogenic not provided 2024-07-08 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 163 of the C1QTNF5 protein (p.Ser163Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with late-onset retinal degeneration (PMID: 12944416, 23289492, 29847639). It has also been observed to segregate with disease in related individuals. This variant is also known as c.686C>G. ClinVar contains an entry for this variant (Variation ID: 2126). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects C1QTNF5 function (PMID: 24531000). For these reasons, this variant has been classified as Pathogenic.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001245416 SCV001762129 pathogenic not provided 2021-06-17 criteria provided, single submitter clinical testing
GeneDx RCV001245416 SCV001787252 pathogenic not provided 2020-01-29 criteria provided, single submitter clinical testing Most common pathogenic variant associated with late-onset retinal degeneration (Hayward et al., 2003; Stanton et al., 2017); Published functional studies demonstrate a damaging effect with aggregate formation in vitro and pathological effects in mice that were similar to patients with late-onset retinal degeneration (Hayward et al., 2003; Dinculescu et al., 2015); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 29721928, 31385385, 29555955, 12944416, 26513502, 26197217, 22110650, 24531000, 22892318, 21349921, 23289492)
Institute of Human Genetics, University of Leipzig Medical Center RCV000002208 SCV004032299 pathogenic Late-onset retinal degeneration 2023-08-17 criteria provided, single submitter clinical testing Criteria applied: PS1,PS3,PS4_MOD,PM1_SUP,PM2_SUP,PP3
OMIM RCV000002208 SCV000022366 pathogenic Late-onset retinal degeneration 2003-10-15 no assertion criteria provided literature only
Genomics England Pilot Project, Genomics England RCV000002208 SCV001760265 pathogenic Late-onset retinal degeneration no assertion criteria provided clinical testing

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