ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.870G>C (p.Glu290Asp)

gnomAD frequency: 0.00004  dbSNP: rs150358700
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000173100 SCV000224184 uncertain significance not provided 2015-05-11 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000330507 SCV000463356 uncertain significance Peroxisome biogenesis disorder 4A (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.
Labcorp Genetics (formerly Invitae), Labcorp RCV001852107 SCV002205533 uncertain significance Peroxisome biogenesis disorder 2022-07-12 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 290 of the PEX6 protein (p.Glu290Asp). This variant is present in population databases (rs150358700, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PEX6-related conditions. ClinVar contains an entry for this variant (Variation ID: 193076). 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 RCV003165359 SCV003899833 uncertain significance Inborn genetic diseases 2023-02-16 criteria provided, single submitter clinical testing The c.870G>C (p.E290D) alteration is located in exon 1 (coding exon 1) of the PEX6 gene. This alteration results from a G to C substitution at nucleotide position 870, causing the glutamic acid (E) at amino acid position 290 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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