ClinVar Miner

Submissions for variant NM_000155.4(GALT):c.265T>G (p.Tyr89Asp)

gnomAD frequency: 0.00001  dbSNP: rs111033666
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000482282 SCV000567775 pathogenic not provided 2015-08-26 criteria provided, single submitter clinical testing The Y89D variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Missense variants in nearby residues (Y89H, N86D and F95L) have been reported in the Human Gene Mutation Database in association with galactosemia (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, we interpret Y89D to be a pathogenic variant.
Eurofins Ntd Llc (ga) RCV000482282 SCV000854788 pathogenic not provided 2017-11-28 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003330397 SCV004037674 uncertain significance not specified 2023-08-29 criteria provided, single submitter clinical testing Variant summary: GALT c.265T>G (p.Tyr89Asp) results in a non-conservative amino acid change located in the Galactose-1-phosphate uridyl transferase, N-terminal (IPR005849) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251492 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.265T>G in individuals affected with Galactosemia and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Both submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance.
Mayo Clinic Laboratories, Mayo Clinic RCV000482282 SCV004226583 likely pathogenic not provided 2022-12-06 criteria provided, single submitter clinical testing PP3, PP4, PM2, PS4_moderate
Revvity Omics, Revvity RCV003485523 SCV004235108 uncertain significance Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2023-02-03 criteria provided, single submitter clinical testing

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