ClinVar Miner

Submissions for variant NM_000155.4(GALT):c.626A>G (p.Tyr209Cys)

gnomAD frequency: 0.00002  dbSNP: rs111033744
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000022167 SCV000052471 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2011-08-18 criteria provided, single submitter curation Converted during submission to Pathogenic.
Eurofins Ntd Llc (ga) RCV000185918 SCV000110069 pathogenic not provided 2016-05-06 criteria provided, single submitter clinical testing
GeneDx RCV000185918 SCV000238871 pathogenic not provided 2022-02-28 criteria provided, single submitter clinical testing 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: 10399107, 25124065, 17876724, 27005423, 22975760, 20008339, 10960497, 24973740, 22693313, 17884932, 17079880, 16540753, 24045215, 27415407, 24718839, 11261429, 10408771, 29261178, 30172461, 31589614, 22743281, 34030713)
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000185918 SCV000281374 pathogenic not provided 2015-09-14 criteria provided, single submitter clinical testing
Invitae RCV000022167 SCV000952487 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2024-01-11 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 209 of the GALT protein (p.Tyr209Cys). This variant is present in population databases (rs111033744, gnomAD 0.003%). This missense change has been observed in individual(s) with galactosemia (PMID: 10399107, 11397328, 16540753). ClinVar contains an entry for this variant (Variation ID: 25231). 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%. Experimental studies have shown that this missense change affects GALT function (PMID: 22743281). This variant disrupts the p.Tyr209 amino acid residue in GALT. Other variant(s) that disrupt this residue have been observed in individuals with GALT-related conditions (PMID: 10399107), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000022167 SCV001163243 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000022167 SCV001193851 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2019-12-13 criteria provided, single submitter clinical testing NM_000155.3(GALT):c.626A>G(Y209C) is classified as likely pathogenic in the context of galactosemia. Sources cited for classification include the following: PMID 12595586, 10960497, 22693313, 11261429, 10399107 and 22743281. Classification of NM_000155.3(GALT):c.626A>G(Y209C) is based on the following criteria: This variant has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
Revvity Omics, Revvity RCV000022167 SCV002024170 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2019-02-13 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000022167 SCV002803322 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2021-08-04 criteria provided, single submitter clinical testing
GeneReviews RCV000022167 SCV000147998 not provided Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase no assertion provided literature only Severe classic pathogenic variant
Natera, Inc. RCV001831600 SCV002085223 pathogenic Galactosemia 2017-03-17 no assertion criteria provided clinical testing

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