ClinVar Genomic variation as it relates to human health

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 26133662) - PS3_supporting. The c.860G>A;p.(Arg287Gln) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (PMID: 30257713; 29437916; 28877744; 27766311; 26310427; 26133662) - PS4. The variant is present at low allele frequencies population databases (rs202160208 - gnomAD 0.001905%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Arg287Gln) was detected in trans with a pathogenic variant (PMID: 30257713; 29437916; 28877744; 26310427; 26133662) - PM3_strong. Pathogenic missense variant in this residue have been reported (Clinvar ID: 225925) - PM5. Multiple lines of computational evidence suggest no impact on gene orgene product - BP4. In summary, the currently available evidence indicates that the variant is pathogenic.

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.028%). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 23768512). Same nucleotide change resulting in same amino acid change (ClinVar ID: VCV000060545) and a different missense change at the same codon (p.Arg287Trp / ClinVar ID: VCV000225925) have been previously reported as pathogenic/likely pathogenic with strong evidence. Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

The c.860G>A (p.R287Q) alteration is located in coding exon 8 of the GMPPB gene. This alteration results from a G to A substitution at nucleotide position 860, causing the arginine (R) at amino acid position 287 to be replaced by a glutamine (Q). Based on data from gnomAD, the A allele has an overall frequency of 0.028% (78/281352) total alleles studied. The highest observed frequency was 0.425% (44/10356) of Ashkenazi Jewish alleles. This variant has been reported in trans with a second alteration in the GMPPB gene in multiple individuals with clinical features of GMPPB-related dystroglycanopathies (Carss, 2013; Raphael, 2014; Belaya, 2015; Cabrera-Serrano, 2015; Jensen, 2015; Harris, 2017; Astrea, 2018; Sarkozy, 2018; Marinakis, 2021). In two families, both variants segregated with disease (Belaya, 2015; Raphael, 2014). In addition, this variant has been observed in homozygous individuals without clinical features of GMPPB-related dystroglycanopathies, suggesting it may be a mild allele (Ambry internal data). This amino acid position is not well conserved in available vertebrate species. Functional studies indicate this alteration mildly impairs enzymatic activity of GMPPB compared to other pathogenic alterations (Liu, 2021). In another study, functional analysis demonstrated that the p.R287Q alteration aggregated in the cytoplasm in transfected cells as well as decreased glycosylation of α-dystroglycan in muscle biopsies; however, a later study found that this variant had no effect on protein expression levels (Belaya, 2015; Carss, 2013). This alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

Published functional studies demonstrate a damaging effect, as C2C12 myoblast cell lines transfected with R287Q showed abnormal subcellular localization of GMPPB resulting in cytoplasmic protein aggregates (PMID: 23768512); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34758253, 24780531, 23768512, 28456886, 28433477, 27766311, 28478914, 27874200, 30684953, 34426522, 35006422, 31980526, 26133662, 28554332, 34008892, 28877744, 26310427, 25681410)

PM2, PM5, PP2, PP5

BP4, PP1, PM3, PM5, PS3, PS4_moderate

Variant summary: GMPPB c.860G>A (p.Arg287Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00029 in 249958 control chromosomes (gnomAD). c.860G>A has been reported in the literature in multiple individuals affected with congenital muscular dystrophy/alpha-dystroglycanopathy, including at least one family in which it segregated with the disease phenotype (e.g. Carrs_2013, Raphael_2014, Jensen_2015). These data indicate that the variant is very likely to be associated with disease. Functional experiments have shown that the variant has approximately 50% activity compared to the WT protein in an enzymatic activity assay and in vitro, results in the formation of aggregates, affecting the cellular localization of the protein (e.g. Carrs_2013, Liu_2021). Twelve submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. The majority classified the variant as either pathogenic (n=10) or likely pathogenic (n=1), and one classified it as VUS. Based on the evidence outlined above, the variant was classified as pathogenic.

Criteria applied: PM3_VSTR,PM5,PS3_SUP,PM2_SUP; Identified as compund heterozygous with NM_021971.4:c.79G>C

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 287 of the GMPPB protein (p.Arg287Gln). This variant is present in population databases (rs202160208, gnomAD 0.5%). This missense change has been observed in individual(s) with congenital muscular dystrophy-dystroglycanopathy and congenital myasthenic syndrome (PMID: 24780531, 26133662). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 60545). 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 not expected to disrupt GMPPB protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects GMPPB function (PMID: 23768512). This variant disrupts the p.Arg287 amino acid residue in GMPPB. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27766311, 27874200, 28478914). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 (MIM#615350), muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 14 (MIM#615351), and muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 (MIM#615352). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0252 - This variant is homozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (78 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (28 heterozygotes, 0 homozygotes). (I) 0503 - Missense variant consistently predicted to be tolerated by multiple in silico tools or not conserved in placental mammals with a minor amino acid change. (SB) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as pathogenic, and observed in compound heterozygous individuals with limb girdle muscular dystrophy (MD), congenital MD with intellectual disability or MD dystroglycanopathy (PMID: 30684953, ClinVar). (SP) 1209 - This variant has been shown to be both maternally and paternally inherited (biallelic, by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

The GMPPB c.860G>A variant is predicted to result in the amino acid substitution p.Arg287Gln. This variant has been reported in the compound heterozygous state in many unrelated individuals with GMPBB-related disorders (see for examples, Carss et al. 2013. PubMed ID: 23768512; Belaya et al. 2015. PubMed ID: 26133662; Jensen et al. 2015. PubMed ID: 26310427). This variant is reported in 0.42% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Given the evidence, we interpret c.860G>A (p.Arg287Gln) as pathogenic.