ClinVar Miner

Submissions for variant NM_014249.4(NR2E3):c.925C>T (p.Arg309Trp)

dbSNP: rs774102273
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001115329 SCV001273298 uncertain significance Retinitis pigmentosa 37 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina RCV001121911 SCV001280566 uncertain significance Enhanced S-cone syndrome 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001247193 SCV001420601 pathogenic not provided 2024-05-15 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 309 of the NR2E3 protein (p.Arg309Trp). This variant is present in population databases (rs774102273, gnomAD 0.005%). This missense change has been observed in individual(s) with clinical features of enhanced S-cone syndrome and/or Goldmann-Favre syndrome (PMID: 33781268; Invitae). ClinVar contains an entry for this variant (Variation ID: 884317). 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 NR2E3 protein function with a positive predictive value of 80%. This variant disrupts the p.Arg309 amino acid residue in NR2E3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10655056, 15459973, 19718767; Invitae). 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.
Natera, Inc. RCV001121911 SCV002085630 uncertain significance Enhanced S-cone syndrome 2020-04-15 no assertion criteria provided clinical testing

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