ClinVar Miner

Submissions for variant NM_015046.7(SETX):c.7490G>A (p.Ser2497Asn)

gnomAD frequency: 0.00013  dbSNP: rs61735488
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000516539 SCV000615213 benign not specified 2020-11-16 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000531955 SCV000645289 likely benign Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 2024-09-05 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV001509372 SCV001716036 uncertain significance not provided 2021-06-17 criteria provided, single submitter clinical testing
GeneDx RCV001509372 SCV001776705 uncertain significance not provided 2024-10-21 criteria provided, single submitter clinical testing Observed in a child with cleft lip and palate who also harbored additional variants in genes related to the phenotype (PMID: 35385219); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 35385219)
Ambry Genetics RCV002395238 SCV002672706 uncertain significance Inborn genetic diseases 2020-11-25 criteria provided, single submitter clinical testing The p.S2497N variant (also known as c.7490G>A), located in coding exon 24 of the SETX gene, results from a G to A substitution at nucleotide position 7490. The serine at codon 2497 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the supporting evidence, this variant is unlikely to be causative of autosomal dominant juvenile amyotrophic lateral sclerosis 4; however, its contribution to the development of autosomal recessive spinocerebellar ataxia with axonal neuropathy 2 is uncertain.
PreventionGenetics, part of Exact Sciences RCV004541622 SCV004774721 likely benign SETX-related disorder 2022-11-28 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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