ClinVar Miner

Submissions for variant NM_000155.4(GALT):c.610C>T (p.Arg204Ter) (rs111033737)

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Total submissions: 5
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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 RCV000022164 SCV000052470 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2020-08-20 criteria provided, single submitter clinical testing Variant summary: GALT c.610C>T (p.Arg204X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 1.2e-05 in 251502 control chromosomes (gnomAD and publication data). c.610C>T has been reported in the literature in multiple individuals affected with Galactosemia (Tyfield_1999, Webb_2003, Gort_2006, Chhay_2008, Carney_2009). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal GLAT activity (Chhay_2008). One ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000723395 SCV000202785 pathogenic not provided 2014-04-23 criteria provided, single submitter clinical testing
Counsyl RCV000022164 SCV000220666 likely pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2014-09-03 criteria provided, single submitter literature only
Invitae RCV000022164 SCV000818515 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2020-09-17 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg204*) in the GALT gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs111033737, ExAC 0.003%). This variant has been reported as homozygous or in combination with other variants in the GALT gene in several individuals affected with galactosemia (PMID: 12595586, 17041746, 18210213, 19224951, 19375122, 20213376, 22944367). ClinVar contains an entry for this variant (Variation ID: 25228). Loss-of-function variants in GALT are known to be pathogenic (PMID: 22944367). For these reasons, this variant has been classified as Pathogenic.
Research and Development, ARUP Laboratories RCV000022164 SCV000042846 pathogenic Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2012-12-04 no assertion criteria provided clinical testing Converted during submission to Pathogenic.

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