ClinVar Miner

Submissions for variant NM_000273.3(GPR143):c.413C>T (p.Ala138Val)

dbSNP: rs62635762
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000084933 SCV002146369 pathogenic not provided 2024-03-25 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 138 of the GPR143 protein (p.Ala138Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with congenital nystagmus and/or ocular albinism (PMID: 9529334; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 98634). 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) performed at Invitae indicates that this missense variant is expected to disrupt GPR143 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change does not substantially affect GPR143 function (PMID: 11115845). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000084933 SCV005325040 likely pathogenic not provided 2024-03-11 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function, but is inconclusive as to whether the variant alters gene splicing; in the absence of RNA/functional studies, the actual effect of this sequence change is unknown; This variant is associated with the following publications: (PMID: 9529334, 11115845)
Retina International RCV000084933 SCV000117069 not provided not provided no assertion provided not provided

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