ClinVar Miner

Submissions for variant NM_032520.5(GNPTG):c.8C>T (p.Ala3Val)

gnomAD frequency: 0.00026  dbSNP: rs867217705
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000815830 SCV000956302 uncertain significance not provided 2022-10-18 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 3 of the GNPTG protein (p.Ala3Val). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with non-syndromic stuttering (PMID: 26130485). ClinVar contains an entry for this variant (Variation ID: 658914). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Illumina Laboratory Services, Illumina RCV001119136 SCV001277482 uncertain significance GNPTG-mucolipidosis 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Genome-Nilou Lab RCV001119136 SCV002045563 uncertain significance GNPTG-mucolipidosis 2021-11-07 criteria provided, single submitter clinical testing
Natera, Inc. RCV001119136 SCV001462083 uncertain significance GNPTG-mucolipidosis 2020-09-16 no assertion criteria provided clinical testing

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