ClinVar Miner

Submissions for variant NM_017875.4(SLC25A38):c.199C>T (p.Arg67Cys)

gnomAD frequency: 0.00011  dbSNP: rs200791957
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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 RCV001150974 SCV001312070 uncertain significance Sideroblastic anemia 2 2018-01-13 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.
GeneDx RCV001555048 SCV001776399 uncertain significance not provided 2020-01-24 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect
Invitae RCV001555048 SCV003283479 uncertain significance not provided 2022-07-02 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 67 of the SLC25A38 protein (p.Arg67Cys). This variant is present in population databases (rs200791957, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with SLC25A38-related conditions. ClinVar contains an entry for this variant (Variation ID: 903565). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002557255 SCV003716885 uncertain significance Inborn genetic diseases 2021-06-11 criteria provided, single submitter clinical testing The c.199C>T (p.R67C) alteration is located in exon 3 (coding exon 3) of the SLC25A38 gene. This alteration results from a C to T substitution at nucleotide position 199, causing the arginine (R) at amino acid position 67 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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