ClinVar Miner

Submissions for variant NM_004589.4(SCO1):c.673G>A (p.Val225Ile)

gnomAD frequency: 0.00001  dbSNP: rs886052595
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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 RCV000314682 SCV000400536 uncertain significance Mitochondrial complex IV deficiency, nuclear type 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000314682 SCV000400537 uncertain significance Mitochondrial complex IV deficiency, nuclear type 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000407936 SCV000400538 uncertain significance Leigh syndrome 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.
Invitae RCV002521089 SCV003242949 uncertain significance not provided 2022-08-22 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 321793). This variant has not been reported in the literature in individuals affected with SCO1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 225 of the SCO1 protein (p.Val225Ile).

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