ClinVar Genomic variation as it relates to human health

Published functional studies demonstrate a damaging effect; the mutated glycogenin-1 protein lost its ability to autoglucosylate, and was therefore unable to form the primer for normal glycogen synthesis (Malfatti et al., 2014; Hedberg-Oldfors et al., 2017); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29422440, 31791869, 34662886, 25272951, 27718144, 25741868, 32477874, 31980526, 34426522, 31589614, 32528171)

GYG1: PM3:Strong, PM2:Supporting, PP3

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PM2,PM3,PS1,PP3,PP4.

The GYG1 c.304G>C variant is predicted to result in the amino acid substitution p.Asp102His. This variant has been previously reported in the compound heterozygous state with a protein truncating variant in two different patients with polyglucosan body myopathy (Malfatti et al. 2014. PubMed ID: 25272951; Lefeuvre et al. 2020. PubMed ID: 32477874). The same variant was also found in the homozygous state via exome sequencing in three unrelated individuals who presented with cardiomyopathy (Hedberg-Oldfors et al. 2017. PubMed ID: 27718144). In all of these studies, morphological analysis revealed accumulation of glycogen and/or polyglucosan bodies in either skeletal or cardiac muscle. Furthermore, in vitro studies showed that the p.Asp102His change lead to the loss of GYG1 autoglucosylation, which would result in a non-functional GYG1 protein (Malfatti et al. 2014. PubMed ID: 25272951; Hedberg-Oldfors et al. 2017. PubMed ID: 27718144). This variant is reported in 0.18% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-148714249-G-C). This variant is interpreted as pathogenic.

PP3, PP4, PM3, PS4_moderate

This sequence change replaces aspartic acid, which is acidic and polar, with histidine, which is basic and polar, at codon 102 of the GYG1 protein (p.Asp102His). This variant is present in population databases (rs143137713, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with glycogenin 1 deficiency (PMID: 25272951, 27718144). ClinVar contains an entry for this variant (Variation ID: 162663). 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 GYG1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects GYG1 function (PMID: 25272951, 27718144). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

This sequence change in GYG1 is predicted to replace aspartic acid with histidine at codon 102, p.(Asp102His). The aspartic acid residue is highly conserved (100 vertebrates, UCSC), and is located in located in the highly conserved DxD motif, which is defined as a critical functional domain (PMID: 27718144). There is a moderate physicochemical difference between aspartic acid and histidine. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.18% (235/129,154 alleles) in the European (non-Finnish) population. This variant has been detected in at least six individuals with muscle glycogenin 1 deficiency. Of those individuals, three individuals were homozygous presenting with cardiomyopathy and three were compound heterozygous with a second pathogenic variant presenting with neuromuscular features (PMID: 25272951, 27718144, 31791869, 32477874). At least one patient with this variant displayed defective glycogenin-1 function in muscle biopsies after alpha-amylase treatment, which is highly specific for muscle glycogenin 1 deficiency (PMID: 27718144, 31791869). An in vitro functional assay with limited validation demonstrated the variant altered the autoglycosylation function of the protein (PMID: 27718144). Computational evidence predicts a deleterious effect for the missense substitution (REVEL = 0.942). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_Strong, PM1, PP3_Moderate, PP4, PS3_Supporting.

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 reported mechanism of disease in this gene and is associated with polyglucosan body myopathy 2 (MIM#616199) and glycogen storage disease XV (MIM#613507). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity. With multiple cases reporting abnormal glycogen storage, and varying muscular phenotypes, age of onset, and sometimes severe cardiac disorders (PMID: 31791869, PMID: 32477874). (I) 0200 - Variant is predicted to result in a missense amino acid change from aspartic acid to histidine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (290 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated glycosyl transferase family 8 domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been identified in at least six unrelated affected individuals (ClinVar, PMID:25272951, PMID:27718144, PMID: 31791869, PMID: 32477874). It has also been reported as a VUS in ClinVar, including one as a VUS favouring pathogenic and two without further information provided. (SP) 0906 - Segregation evidence for this variant is inconclusive. A homozygous sibling of an affected individual showed no clinical symptoms at 53 years of age (PMID:27718144). (I) 1001 - This variant has strong functional evidence supporting abnormal protein function. Functional studies from a homozygous individual demonstrated protein activity was abolished in cardiac muscle. (PMID:27718144). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Variant summary: GYG1 c.304G>C (p.Asp102His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.001 in 251340 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in GYG1 causing Polyglucosan Body Myopathy Type 2, allowing no conclusion about variant significance. c.304G>C has been reported in the literature as a biallelic homozygous or compound heterozygous genotype in multiple individuals affected with features of Polyglucosan Body Myopathy Type 2 (Malfatti_2014, Hedber-Oldfors_2017, Topf_2020). These data indicate that the variant is likely to be associated with disease. To our knowledge, no quantifiable variant specific experimental evidence demonstrating an impact on protein function has been reported. Although one study reported that an assay of autoglucosylation in vitro did not show any gel shift after the addition of UDP glucose, suggesting nonfunctional glycogenin-1 (Malfatti_2014). The following publications have been ascertained in the context of this evaluation (PMID: 32528171, 27718144, 25272951). ClinVar contains an entry for this variant (Variation ID: 162663). Based on the evidence outlined above, the variant was classified as likely pathogenic.

Variant classified as Uncertain Significance - Favor Pathogenic. The p.Asp102His variant in GYG1 has been reported in the compound heterozygous state in 1 individual with polyglucosan body myopathy and in the homozygous state in 3 individuals with cardiomyopathy and no muscle weakness but with abnormal glycogen storage as indicated by an endomyocardial biopsy (Malfatti 2014, Hedberg-Oldfors 2017). An in vitro functional study suggests that the p.Asp102His could cause defects in auto-glycosylation upon addition of UPD glucose, however, these types of assays may not accurately represent biological function (Malfatti 2014). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 162663) and has been identified in 0.18% (235/129154) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). 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: PM3, PP3, PS3_Supporting, BS1_Supporting.