ClinVar Miner

Submissions for variant NM_013322.3(SNX10):c.152G>A (p.Arg51Gln)

gnomAD frequency: 0.00001  dbSNP: rs398123011
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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 RCV002514140 SCV003439531 pathogenic not provided 2022-04-30 criteria provided, single submitter clinical testing 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 51 of the SNX10 protein (p.Arg51Gln). This variant is present in population databases (rs398123011, gnomAD 0.003%). This missense change has been observed in individuals with osteopetrosis (PMID: 22499339; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 40050). Experimental studies have shown that this missense change affects SNX10 function (PMID: 25212774). This variant disrupts the p.Arg51 amino acid residue in SNX10. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 23280965, 25212774). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000033149 SCV000056931 pathogenic Autosomal recessive osteopetrosis 8 2012-04-01 no assertion criteria provided literature only
Hereditary Research Laboratory, Bethlehem University RCV000033149 SCV001571689 pathogenic Autosomal recessive osteopetrosis 8 2021-04-24 no assertion criteria provided clinical testing

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