ClinVar Genomic variation as it relates to human health

Variant summary: GAA c.533G>A (p.Arg178His) results in a non-conservative amino acid change located in the Galactose mutarotase, N-terminal barrel domain (IPR031727) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.7e-05 in 238840 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.533G>A has been reported in the literature as a VUS in compound heterozygous genotype with a reportedly Asian pseudodeficiency allele (example, Chien_2011) or as a homozygous genotype in another newborn with an unknown phenotype (example, Burlina_2017) for Glycogen Storage Disease, Type 2 (Pompe Disease). These report(s) do not provide unequivocal conclusions about association of the variant with Glycogen Storage Disease, Type 2 (Pompe Disease). A mutational update as of 2021 lists this variant among the VUS found through NBS programs (de Farla_2021). At least one publication reports experimental evidence evaluating an impact on protein function in vitro (Chien_2013). The most pronounced variant effect results in approximately 10%-<30% of normal activity of the mutant form transfected into COS-1 cells measured using 4-MU as a substrate. Four 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 uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

The p.Arg178His variant in GAA has been reported in one Taiwanese individual with glycogen storage disease II (PMID: 21232767), and has been identified in 0.004% (1/23728) of African chromosomes and 0.003% (4/122358) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs762267535). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar as a VUS by Counsyl (VariationID: 554969). In vitro functional studies using COS-1 and fibroblast cells provide some evidence that the p.Arg178His variant may slightly impact protein function (PMID: 23632029). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2, PP3, PS3_Supporting (Richards 2015).

PP3, PP4, PM2, PM3

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 178 of the GAA protein (p.Arg178His). This variant is present in population databases (rs762267535, gnomAD 0.004%). This missense change has been observed in individual(s) with Pompe disease (PMID: 21232767, 29143201, 33202836). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 554969). 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 GAA protein function with a positive predictive value of 95%. Studies have shown that this missense change does not affect mRNA splicing (PMID: 31301153). For these reasons, this variant has been classified as Pathogenic.

The p.R178H variant (also known as c.533G>A), located in coding exon 1 of the GAA gene, results from a G to A substitution at nucleotide position 533. The arginine at codon 178 is replaced by histidine, an amino acid with highly similar properties. This alteration has been reported as homozygous and in trans with additional alterations in GAA; however, clinical details were limited (Chien YH et al. J Pediatr, 2011 Jun;158:1023-1027.e1; Burlina AB et al. J Inherit Metab Dis, 2018 Mar;41:209-219; Ficicioglu C et al. Int J Neonatal Screen, 2020 Nov;6:[ePub ahead of print]). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this alteration remains unclear.