ClinVar Miner

Submissions for variant NM_015046.7(SETX):c.5051C>G (p.Ser1684Cys)

gnomAD frequency: 0.00012  dbSNP: rs140116005
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000757760 SCV000886105 uncertain significance not provided 2018-01-12 criteria provided, single submitter clinical testing The SETX c.5051C>G p.Ser1684Cys variant (rs140116005), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.01 % (identified on 38 out of 277,110 chromosomes). The serine at position 1684 is weakly conserved, considering 12 species, and computational analyses of the effects of the p.Ser1684Cys variant on protein structure and function do not agree (SIFT: damaging, MutationTaster: polymorphism, PolyPhen-2: benign). Based on the available information, the clinical significance of the p.Ser1684Cys variant cannot be determined with certainty.
Athena Diagnostics RCV000757760 SCV001145555 uncertain significance not provided 2018-09-07 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001047649 SCV001211619 benign Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 2023-10-29 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000757760 SCV001747011 uncertain significance not provided 2021-03-01 criteria provided, single submitter clinical testing
GeneDx RCV000757760 SCV001814811 likely benign not provided 2021-05-30 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001849091 SCV002105165 uncertain significance Hereditary spastic paraplegia 2018-04-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002343608 SCV002645889 uncertain significance Inborn genetic diseases 2022-06-08 criteria provided, single submitter clinical testing The p.S1684C variant (also known as c.5051C>G), located in coding exon 8 of the SETX gene, results from a C to G substitution at nucleotide position 5051. The serine at codon 1684 is replaced by cysteine, an amino acid with dissimilar 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 (ALS4); however, its contribution to the development of autosomal recessive spinocerebellar ataxia with axonal neuropathy 2 (SCAN2) is uncertain.

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