ClinVar Genomic variation as it relates to human health

The c.2167dupG (p.Asp723Glyfs*730) frameshift variant in the POMT1 gene has been previously reported as homozygous (Wallace SE et al., 2014; van Reeuwijk J et al., 2006) as well as compound heterozygous (Beltrán-Valero de Bernabé D et al., 2002; Wallace SE et al., 2014) in patients who were diagnosed with WWS. Functional studies using a skin biopsy from a WWS patient, who was heterozygous for variant, showed that the protein's molecular weight and binding to the basement membrane ligand, laminin were all affected. Furthermore, immunofluorescence staining of a muscle biopsy from a patient, who was homozygous for this variant, showed almost complete absence of α-dystroglycan expression (Wallace SE et al., 2014). The frequency of this variant is absent in the 1000Genome and Exome Sequencing Project databases and is very low in ExAC (<0.1%). Finally, reputable clinical databases have classified this variant as Pathogenic. In summary, the evidence meets our criteria for a Pathogenic classification. We have confirmed this finding in our laboratory using Sanger sequencing.

This variant was classified as: Pathogenic. This variant was inherited from a parent.

The heterozygous p.Asp723GlyfsTer8 variant in POMT1 was identified by our study, in the compound heterozygous state with a variant of uncertain significance (ClinVar Variation ID: 502200), in one individual with muscular dystrophy. This individual also carried a variant of uncertain significance (ClinVar Variation ID: 502200), however the phase of these variants are unknown at this time. The p.Asp723GlyfsTer8 variant in POMT1 has been previously reported in more than 24 unrelated individuals with POMT1-associated muscular dystrophy-dystroglycanopathy (PMID: 31311558, PMID: 24304607, PMID: 12369018, PMID: 17559086, PMID: 18752264, PMID: 18640039, PMID: 16575835, PMID: 24491487) and segregated with disease in 11 affected relatives from 4 families (PMID: 3131155, PMID: 18640039), but has been identified in 0.06% (2/3470) of Ashkenazi Jewish chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP: rs398124245). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. Of these 24 previously reported unrelated affected individuals (PMID: 31311558, PMID: 24304607, PMID: 12369018, PMID: 17559086, PMID: 18752264, PMID: 18640039, PMID: 16575835, PMID: 24491487), 3 were homozygotes (PMID: 24491487, PMID: 16575835, PMID: 31311558), 5 were compound heterozygotes who carried pathogenic or likely pathogenic variants in trans (PMID: 18640039, dbSNP ID: rs1402329255; PMID: 17559086, NC_000009.12:g.131515513_131515514del; PMID: 31311558, ClinVar Variation ID: 95452, PMID: 24491487, ClinVar Variation ID: 194962), and 5 were compound heterozygotes who carried pathogenic or likely pathogenic variants in unknown phase (PMID: 24491487, ClinVar Variation ID: 1458255, 194757, 2413915, 3250, NC_000009.12:g.131504299dup), which increases the likelihood that the p.Asp723GlyfsTer8 variant is pathogenic. This variant has also been reported in ClinVar (Variation ID: 3255) and has been interpreted as pathogenic by multiple submitters. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 723 and leads to a premature termination codon 8 amino acids downstream. This termination codon occurs within the terminal 50 bases of the last exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. Loss of function of the POMT1 gene is an established disease mechanism in autosomal recessive POMT1-associated muscular dystrophy-dystroglycanopathy. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive POMT1-associated muscular dystrophy-dystroglycanopathy. ACMG/AMP Criteria applied: PVS1_Moderate, PM3_VeryStrong, PP1_Strong (Richards 2015).

The POMT1 c.2167dupG (p.Asp723GlyfsTer8) variant results in a frameshift, and is predicted to result in premature termination of the protein. The p.Asp723GlyfsTer8 variant, also referred to as c.2163_2164insG, has been reported in seven studies in a total of 19 patients with POMT1-related disorders, including in two in a homozygous state, 15 in a compound heterozygous state, and two in a heterozygous state in whom a second variant was not identified (Beltran-Valero de Bernabe et al. 2002; van Reeuwijk et al. 2006; Bouchet et al. 2007; Vajsar et al. 2008; Manzini et al. 2008; Devisme et al. 2012; Wallace et al. 2014). The majority of patients were affected with Walker-Warburg syndrome or, more generally, congenital muscular dystrophy. The p.Asp723GlyfsTer8 variant was absent from 298 controls and is reported at a frequency of 0.001291 in the Ashkenazi Jewish population of the Genome Aggregation Database. Based on the evidence, the p.Asp723GlyfsTer8 variant is classified as pathogenic for POMT1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

Variant summary: POMT1 c.2167dupG (p.Asp723GlyfsX8) results in a premature termination codon in the last exon affecting the last 26 amino acids of the encoded POMT1 protein. Although nonsense mediated decay is not predicted to occur, variants downstream of this position have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 0.00016 in 248716 control chromosomes. c.2167dupG has been reported in the literature in individuals affected with muscular dystrophy including Walker-Warburg syndrome (e.g. BeltranValterodeBernabe_2002). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 12369018). 13 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change creates a premature translational stop signal (p.Asp723Glyfs*8) in the POMT1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 25 amino acid(s) of the POMT1 protein. This variant is present in population databases (rs767631573, gnomAD 0.1%). This premature translational stop signal has been observed in individuals with congenital muscular dystrophy and/or Walker-Warburg syndrome (PMID: 12369018, 16575835, 17559086, 22323514, 24304607, 24491487). This variant is also known as c.2167InsG, c.2167_2168insG, and p.G722fs. ClinVar contains an entry for this variant (Variation ID: 3255). For these reasons, this variant has been classified as Pathogenic.

The c.2167dupG (p.D723Gfs*8) alteration, located in exon 20 (coding exon 19) of the POMT1 gene, consists of a duplication of G at position 2167, causing a translational frameshift with a predicted alternate stop codon after 8 amino acids. This alteration occurs at the 3' terminus of the POMT1 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 25 amino acids of the protein. However, premature stop codons are typically deleterious in nature. This mutation has been reported in several individuals with POMT1-related dystroglycanopathies in the homozygous and compound heterozygous state (Beltr&aacute;n-Valero de Bernab&eacute;, 2002; van Reeuwijk, 2006; Manzini, 2008; Wallace, 2014; Geis, 2019). Based on the available evidence, this alteration is classified as pathogenic.

Frameshift variant predicted to result in abnormal protein length as the last 25 amino acids are replaced with 7 different amino acids, and other similar variants have been reported in HGMD; This variant is associated with the following publications: (PMID: 12369018, 30060766, 22323514, 28116189, 17559086, 16575835, 24304607, 31311558, 31980526, 31127727, 24491487, 31589614, 32528171, 32860008, 35229910)

The POMT1 c.2167dupG variant is predicted to result in a frameshift and premature protein termination (p.Asp723Glyfs*8). This variant has been reported in the homozygous and compound heterozygous states to be causative for Walker-Warburg syndrome (Beltrán-Valero et al. 2002. PubMed ID: 12369018; Devisme et al. 2012. PubMed ID: 22323514; Wallace et al. 2014. PubMed ID: 24491487). This variant has also been reported in many unrelated individuals to be causative for a spectrum of congenital muscular dystrophies (Johnson et al. 2018. PubMed ID: 30060766; Wallace et al. 2014. PubMed ID: 24491487). This variant is reported in 0.12% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Frameshift variants in POMT1 are expected to be pathogenic. This variant is interpreted as pathogenic.