ACMG classification criteria: PS3, PS4, PM2, PM3, PP3

This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 135 of the GALT protein (p.Ser135Leu). This variant is present in population databases (rs111033690, gnomAD 0.4%). This missense change has been observed in individual(s) with galactosemia (PMID: 7887417, 8551426, 12350230, 22461411, 22944367, 27176039, 28065439). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 3618). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) 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: 7887417, 11152465, 12208137). For these reasons, this variant has been classified as Pathogenic.

The c.404C>T variant in GALT is a missense variant predicted to cause substitution of serine to leucine at amino acid 135. This variant is rare in the general population with a frequency below the threshold expected for the associated phenotype(s). This variant has been observed in one or more individuals affected with the associated recessive disease, as either homozygous or compound heterozygous with a second variant (PMID: 9635294). Functional studies show that this variant may disrupt protein function (PMID: 8551426, 10070616, 11592823). Computational prediction algorithms indicate this variant is likely to affect gene or protein function. Given the available evidence, this variant is classified as Pathogenic.

This variant is interpreted as a Likely Pathogenic, for Galactosemia, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PM2 => Present at frequency compatible with disease prevalence in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:11754113) (PMID:22461411). PS3 => Well-established functional studies show a deleterious effect (PMID:7887417,25614870).

NM_000155.3(GALT):c.404C>T(S135L) is classified as pathogenic in the context of galactosemia. Sources cited for classification include the following: PMID 10070616, 11754113, 19418241, 8551426, 7887417, 12208137, 1610789 and 11152465. Classification of NM_000155.3(GALT):c.404C>T(S135L) is based on the following criteria: This is a well-established pathogenic variant in the literature that 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.

PS3, PP3, PM3_Strong

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.025%). Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.92; 3Cnet: 0.97). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000003618). Different missense changes at the same codon (p.Ser135Pro, p.Ser135Trp) have been reported to be associated with GALT related disorder (ClinVar ID: VCV000025172 / PMID: 15841485, 22944367). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

Functional analysis found S135L is associated with significantly reduced enzyme activity (Fridovich-Keil et al., 1995; Coelho et al., 2014); In silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect; This variant is associated with the following publications: (PMID: 1610789, 9323558, 12552079, 22975760, 25614870, 25087612, 11754113, 12208137, 12350230, 29302074, 34391645, 8551426, 11152465, 7887417, 20008339, 10070616, 19418241, 28065439, 27176039, 22944367, 22461411, 1373122, 31954591, 30275481, 34030713, 31589614)

The c.404C>T (p.S135L) alteration is located in exon 5 (coding exon 5) of the GALT gene. This alteration results from a C to T substitution at nucleotide position 404, causing the serine (S) at amino acid position 135 to be replaced by a leucine (L). Based on data from the Genome Aggregation Database (gnomAD) database, the GALT c.404C>T alteration was observed in 0.03% (94/282882) of total alleles studied, with a frequency of 0.35% (87/24960) in the African subpopulation. This mutation has been reported in multiple individuals in the homozygous and compound heterozygous states with galactosemia (Henderson, 2002; Boutron, 2012; Garcia, 2016; Welsink-Karssies, 2020). In yeast and E. coli, GALT activity was reduced compared to wild type (Fridovich-Keil, 1995; Riehman, 2001; Coelho, 2014). The p.S135L alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

The c.404C>T;p.(Ser135Leu) missense change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 3618; PMID: 20301691; 28065439; 27176039; 10070616; 7887417) - PS4.Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 9323558) - PS3_supporting. The variant is present at low allele frequencies population databases (rs111033690– gnomAD 0.009002%; ABraOM 0.000427 frequency - http://abraom.ib.usp.br/) -PM2_supporting. The p.(Ser135Leu) was detected in trans with a Pathogenic variant (PMID: 28065439; 27176039; 10070616) - PM3_strong. Pathogenic missense variant in this residue have been reported and classified as Pathogenic by ACMG criteria (Clinvar ID: 25172) -PM5. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is Pathogenic

Converted during submission from pathogenic to Pathogenic.

The GALT c.404C>T; p.Ser135Leu variant (rs111033690) has been reported in multiple individuals with GALT deficiency (Fridovich-Keil 1995, Lai 1996). Functional characterization of the variant protein indicates strongly reduced enzymatic activity and thermostability (Coelho 2014, Fridovich-Keil 1995, Lai 1996, Riehman 2001). This variant is also reported in ClinVar (Variation ID: 3618). It is observed in the general population with an overall allele frequency of 0.03% (94/282882 alleles) in the Genome Aggregation Database. The serine at codon 135 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.921). Based on available information, this variant is considered to be pathogenic. References: Coelho AI et al. Functional and structural impact of the most prevalent missense mutations in classic galactosemia. Mol Genet Genomic Med. 2014 Nov;2(6):484-96. PMID: 25614870. Fridovich-Keil JL et al. Identification and functional analysis of three distinct mutations in the human galactose-1-phosphate uridyltransferase gene associated with galactosemia in a single family. Am J Hum Genet. 1995 Mar;56(3):640-6. PMID: 7887417. Lai K et al. A prevalent mutation for galactosemia among black Americans. J Pediatr. 1996 Jan;128(1):89-95. PMID: 8551426. Riehman K et al. Relationship between genotype, activity, and galactose sensitivity in yeast expressing patient alleles of human galactose-1-phosphate uridylyltransferase. J Biol Chem. 2001 Apr 6;276(14):10634-40. PMID: 11152465.

This is a nonsynonymous variant in the GALT gene (OMIM: 606999). Pathogenic variants in this gene have been associated with autosomal recessive galactosemia. This variant has been reported in multiple individuals in the homozygous and compound heterozygous states with galactosemia (PMID: 28065439, 27176039, 10070616) (PM3). More than three variants classified as either LP or P were reported within the 30 bp surrounding this variant without benign variants (PM1). Multiple computational algorithms predict a deleterious effect for this variant (REVEL score: 0.921) (PP3) and independently conducted functional studies report a significantly negative effect on protein function (PMID: 7887417, 10070616, 11152465, 12208137) (PS3). Based on this evidence, this variant is classified as pathogenic for autosomal recessive galactosemia.

PS4_moderate, PP3_supporting, PM5_moderate, PS3_supporting, PP4_strong

The GALT c.404C>T variant is predicted to result in the amino acid substitution p.Ser135Leu. This variant has been well documented to be causative for galactosemia and is particularly common among individuals of African descent (Fridovich-Keil et al. 1995. PubMed ID: 7887417; Ya et al. 2002. PubMed ID: 11754113). Consistent with this observation, the c.404C>T variant has been observed at an allele frequency of ~0.35% in an African population in a large database, whereas it is present at <0.02% in other populations in the same database (http://gnomad.broadinstitute.org/variant/9-34647855-C-T). In functional assays, the activity of the GALT enzyme carrying the p.Ser135Leu substitution has been shown to be significantly reduced (Fridovich-Keil et al. 1995. PubMed ID: 7887417; Ya et al. 2002. PubMed ID: 11754113). In red blood cells from patients homozygous for the c.404C>T (p.Ser135Leu) variant, GALT enzyme activity is typically absent. However, ~10% enzyme activity remains in other tissues. As a result, patients homozygous for this variant may go undetected by newborn screening (Crushell et al. 2009. PubMed ID: 19418241). For these reasons, the p.Ser135Leu substitution has been associated with a form of galactosemia referred to as clinical variant galactosemia (see Berry 2017. PubMed ID: 20301691 for further details on clinical variant galactosemia). We classify this variant as pathogenic.

Most common clinical pathogenic variant in African Americans & South Africans