ClinVar Miner

Submissions for variant NM_015046.7(SETX):c.1670G>A (p.Arg557Gln)

gnomAD frequency: 0.00001  dbSNP: rs548433078
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV001663590 SCV001880501 uncertain significance not provided 2021-06-01 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV004771505 SCV005382497 uncertain significance Amyotrophic lateral sclerosis type 4 2023-05-20 criteria provided, single submitter clinical testing The missense c.1670G>A (p.Arg557Gln) variant in the SETX gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is reported with the allele frequency (0.005%) in the gnomAD Exomes. This variant has been reported to the ClinVar database as Uncertain Significance. However, no details are available for independent assessment. The amino acid Arginine at position 557 is changed to a Glutamine changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidence (Polyphen - Benign, SIFT - Tolerated and MutationTaster - Polymorphism) predict no damaging effect on protein structure and function for this variant. The reference amino acid Arginine in SETX is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV005225449 SCV005861926 benign Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 2024-07-31 criteria provided, single submitter clinical testing

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