ClinVar Genomic variation as it relates to human health

Variant summary: GALT c.790_792delinsTAG (p.Leu264X) 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 was absent in 245500 control chromosomes. c.790_792delinsTAG has been reported in the literature in individuals affected with Galactosemia (example, Elsas_1998, Yang_2002, Demirbas_2019 and an external laboratory database). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic.

Observed in apparent homozygous state in a patient with a confirmed diagnosis of classic galactosemia (Elsas et al., 1998); Not observed in large population cohorts (Lek et al., 2016); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 11261429, 30718057, 11754113, 10408771)

This sequence change creates a premature translational stop signal ( p.Leu264*) in the GALT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GALT are known to be pathogenic (PMID: 22944367). This variant is present in population databases (no rsID available, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with galactosemia (PMID: 11261429, 11754113). ClinVar contains an entry for this variant (Variation ID: 1074150). For these reasons, this variant has been classified as Pathogenic.

PP4, PM2, PVS1

The GALT c.790_792inv; p.Leu264Ter variant (rs367543270), also known as L264X, is reported in the literature in individuals affected with galactosemia (Demirbas 2019, Elsas 1998, Yang 2002). This variant is also reported in ClinVar (Variation ID: 459627), and is only observed on two alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Additionally, several downstream truncating variants have been described in individuals with galactosemia and are considered pathogenic (Boutron 2012, Demirbas 2019, Tyfield 1999). Based on available information, this variant is considered to be pathogenic. References: Boutron A et al. Mutation spectrum in the French cohort of galactosemic patients and structural simulation of 27 novel missense variations. Mol Genet Metab. 2012 Nov;107(3):438-47. PMID: 22944367. Demirbas D et al. The ability of an LC-MS/MS-based erythrocyte GALT enzyme assay to predict the phenotype in subjects with GALT deficiency. Mol Genet Metab. 2019 Apr;126(4):368-376. PMID: 30718057. Elsas LJ 2nd and Lai K. The molecular biology of galactosemia. Genet Med. 1998 Nov-Dec;1(1):40-8. PMID: 11261429. Tyfield L et al. Classical galactosemia and mutations at the galactose-1-phosphate uridyl transferase (GALT) gene. Hum Mutat. 1999;13(6):417-30. PMID: 10408771. Yang YP et al. Molecular analysis in newborns from Texas affected with galactosemia. Hum Mutat. 2002 Jan;19(1):82-3. PMID: 11754113.