ClinVar Miner

Submissions for variant NM_000155.4(GALT):c.772C>T (p.Arg258Cys)

gnomAD frequency: 0.00001  dbSNP: rs368166217
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000493672 SCV000110073 pathogenic not provided 2013-07-16 criteria provided, single submitter clinical testing
GeneDx RCV000493672 SCV000582974 pathogenic not provided 2023-06-09 criteria provided, single submitter clinical testing Identified in an individual with galactosemia who harbored a second variant in the GALT gene. This individual had >5% residual enzyme activity in erythrocytes and a Duarte-like isoelectric focusing banding pattern (Berry et al., 2000); Considered a milder GALT variant (Korner et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25087612, 30718057, 15633893, 30808388, 31194895, 10408771, 20008339, 23690308, 10960497, 17876724, 29350350, 11261429, 10384398, 31194252, 34426522, 35677809)
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000493672 SCV000885498 likely pathogenic not provided 2017-08-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000078235 SCV000931179 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2024-01-08 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 258 of the GALT protein (p.Arg258Cys). This variant is present in population databases (rs368166217, gnomAD 0.006%). This missense change has been observed in individual(s) with clinical features of galactosemia (PMID: 10960497, 30718057; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 92522). 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 with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000078235 SCV004198490 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2024-03-30 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000493672 SCV004226597 likely pathogenic not provided 2023-03-13 criteria provided, single submitter clinical testing PP3, PP4, PM2, PM3, PS4_moderate
Counsyl RCV000078235 SCV000800530 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2019-03-13 no assertion criteria provided clinical testing
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000078235 SCV001469241 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2020-10-11 no assertion criteria provided clinical testing
Revvity Omics, Revvity RCV000078235 SCV003808590 uncertain significance Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2021-04-09 flagged submission clinical testing

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