ClinVar Miner

Submissions for variant NM_015046.7(SETX):c.3200C>T (p.Thr1067Ile)

gnomAD frequency: 0.00002  dbSNP: rs374091487
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000393561 SCV000477850 uncertain significance Amyotrophic lateral sclerosis type 4 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000304137 SCV000477851 uncertain significance Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001810866 SCV001471688 uncertain significance not provided 2019-09-13 criteria provided, single submitter clinical testing The SETX c.3200C>T; p.Thr1067Ile variant (rs374091487), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 365360). This variant is found in the non-Finnish European population with an overall allele frequency of 0.005% (6/128938 alleles) in the Genome Aggregation Database. The threonine at codon 1067 is weakly conserved, and computational analyses (SIFT: damaging, PolyPhen-2: benign) predict conflicting effects of this variant on protein structure/function. However, due to limited information, the clinical significance of the p.Thr1067Ile variant is uncertain at this time.
GeneDx RCV001810866 SCV002552898 uncertain significance not provided 2022-07-19 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV002323570 SCV002609182 uncertain significance Inborn genetic diseases 2023-09-13 criteria provided, single submitter clinical testing The c.3200C>T (p.T1067I) alteration is located in exon 10 (coding exon 8) of the SETX gene. This alteration results from a C to T substitution at nucleotide position 3200, causing the threonine (T) at amino acid position 1067 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV002523743 SCV002944647 likely benign Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 2023-09-06 criteria provided, single submitter clinical testing

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