ClinVar Miner

Submissions for variant NM_000155.4(GALT):c.502G>T (p.Val168Leu)

dbSNP: rs367543258
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000022125 SCV000220506 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2014-07-11 criteria provided, single submitter literature only
Labcorp Genetics (formerly Invitae), Labcorp RCV000022125 SCV001236618 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2023-05-12 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 168 of the GALT protein (p.Val168Leu). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects GALT function (PMID: 22461411). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GALT protein function. ClinVar contains an entry for this variant (Variation ID: 25189). This missense change has been observed in individual(s) with galactosemia (PMID: 22461411, 24045215). This variant is not present in population databases (gnomAD no frequency).
Baylor Genetics RCV000022125 SCV004198496 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2023-10-23 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000022125 SCV005184476 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2024-05-28 criteria provided, single submitter clinical testing Variant summary: GALT c.502G>T (p.Val168Leu) results in a conservative amino acid change located in the galactose-1-phosphate uridyl transferase, N-terminal domain (IPR005849) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251446 control chromosomes. c.502G>T has been reported in the literature in the the homozygous and compound heterozygous states in individuals affected with Galactosemia (e.g. Estrada_2013, Tang_2012). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence that this variant results in absent enzyme activity in vitro (e.g. Tang_2012). The following publications have been ascertained in the context of this evaluation (PMID: 24045215, 22461411). ClinVar contains an entry for this variant (Variation ID: 25189). Based on the evidence outlined above, the variant was classified as pathogenic.
Natera, Inc. RCV001826494 SCV002085213 likely pathogenic Galactosemia 2021-08-26 no assertion criteria provided clinical testing

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