ClinVar Genomic variation as it relates to human health

The Q344K missense change has been reported in patients with the severe galactosemia phenotype (Berry et al. 2000; Berry et al. 2004). The Q344K variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The Q344K variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Missense variants in nearby residues (E340K, L342I, A345D) have been reported in the Human Gene Mutation Database in association with galactosemia (Stenson et al., 2014), supporting the functional importance of this region of the protein. In summary, we interpret Q344K to be likely pathogenic.

This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 344 of the GALT protein (p.Gln344Lys). This variant is present in population databases (rs111033814, gnomAD 0.01%). This missense change has been observed in individual(s) with galactosemia (PMID: 11397328, 11754113; Invitae). ClinVar contains an entry for this variant (Variation ID: 25320). 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. Experimental studies have shown that this missense change affects GALT function (PMID: 23319291). For these reasons, this variant has been classified as Pathogenic.

The GALT c.1030C>A; p.Gln344Lys variant (rs111033814) has been reported in patients diagnosed with hereditary galactosemia (Elsas 1998, Berry 2000, Yang 2002). This variant is also reported in ClinVar (Variation ID: 25320). It is only found on two alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. Codon 344 is located at the subunit interface and is predicted to be important for maintaining inter-subunit hydrogen bonds and stabilize the enzyme complex (Facchiano 2010). Functional characterization indicates that, when found in trans with another pathogenic GALT variant, the p.Gln344Lys variant abrogates GALT activity in erythrocytes (Berry 2000). Based on available information, this variant is considered to be pathogenic. References: Berry G et al. Galactose breath testing distinguishes variant and severe galactose-1-phosphate uridyltransferase genotypes. Pediatr Res. 2000; 48(3):323-8. PMID: 10960497. Elsas LJ et al. The molecular biology of galactosemia. Genet Med. 1998; 1(1):40-8. PMID: 11261429. Facchiano A et al. Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach. Protein Eng Des Sel. 2010; 23(2):103-13. PMID: 20008339. Yang Y et al. Molecular analysis in newborns from Texas affected with galactosemia. Hum Mutat. 2002; 19(1):82-3. PMID: 11754113.

Variant summary: GALT c.1030C>A (p.Gln344Lys) results in a conservative amino acid change located in the Galactose-1-phosphate uridyl transferase, C-terminal domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251468 control chromosomes. c.1030C>A has been reported in the literature in individuals affected with Galactosemia. These data indicate that the variant is 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 activity. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

NM_000155.3(GALT):c.1030C>A(Q344K) is a missense variant classified as likely pathogenic in the context of galactosemia. Q344K has been observed in cases with relevant disease (PMID: 27363831, 21779791, 14728988, 11754113, Dobrowlski_2017_(no PMID; abstract)). Functional assessments of this variant are available in the literature (PMID: 23319291). Q344K has been observed in population frequency databases (gnomAD: NFE 0.01%). In summary, NM_000155.3(GALT):c.1030C>A(Q344K) is a missense variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

PP3, PM2