ClinVar Miner

Submissions for variant NM_002617.4(PEX10):c.821C>T (p.Thr274Ile)

gnomAD frequency: 0.00006  dbSNP: rs199683357
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001097464 SCV001253746 uncertain significance Peroxisome biogenesis disorder 6A (Zellweger) 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.
Invitae RCV002555994 SCV003519984 uncertain significance Peroxisome biogenesis disorder, complementation group 7 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 294 of the PEX10 protein (p.Thr294Ile). This variant is present in population databases (rs199683357, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with PEX10-related conditions. ClinVar contains an entry for this variant (Variation ID: 874477). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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 RCV002555993 SCV003760680 uncertain significance Inborn genetic diseases 2021-07-08 criteria provided, single submitter clinical testing The c.881C>T (p.T294I) alteration is located in exon 5 (coding exon 5) of the PEX10 gene. This alteration results from a C to T substitution at nucleotide position 881, causing the threonine (T) at amino acid position 294 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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