ClinVar Genomic variation as it relates to human health

NM_017739.3(POMGNT1):c.1539+1G>A is classified as pathogenic in the context of POMGNT-related disorders. Sources cited for classification include the following: PMID 15466003 and 11709191. Classification of NM_017739.3(POMGNT1):c.1539+1G>A is based on the following criteria: The variant is located at a canonical splice site, is expected to disrupt gene function and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening.

Variant summary: POMGNT1 c.1539+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5 splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing and caused skipping of the upstream exon 17 (Predicted effect: p.Leu472_His513del, Yoshida_2001). The variant allele was found at a frequency of 0.00063 in 251850 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in POMGNT1 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive (0.00063 vs 0.0011), allowing no conclusion about variant significance. c.1539+1G>A has been reported in the literature in multiple individuals affected with Muscle-eye-brain disease including homozygotes (Yoshida_2001, ,Taniguchi_2003, Diesen_2004). These data indicate that the variant is very likely to be associated with disease. 11 ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (1x) and pathogenic (10x). Based on the evidence outlined above, the variant was classified as pathogenic.

The c.1539+1G>A variant in POMGNT1 has been reported in many individuals with muscular dystrophy-dystroglycanopathy (PMID: 17559086, 12588800, 22323514, 26013959, 1790688, 16427280, 11709191), and has been identified in 0.2% (49/25102) of European (Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: dbSNP ID rs138642840). 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. This variant has also been reported in ClinVar (Variation ID #56582) and has been interpreted as pathogenic by multiple labs and of uncertain significance by Institute of Human Genetics (University of Leipzig Medical Center). Of the multiple affected individuals, at least 2 were homozygotes, and multiple were compound heterozygotes that carried reported pathogenic/likely pathogenic variants in trans, which increases the likelihood that the c.1539+1G>A variant is pathogenic (PMID: 17559086, 11709191, 6427280, 12588800, 26013959, 17906881). RT-PCR analysis performed on patient skeletal muscle showed altered splicing with transcripts having exon 17 skipping or intron retention leading to premature termination (PMID: 11709191). In vitro functional studies provide some evidence that the c.1539+1G>A variant may impact protein function (PMID: 11709191). However, these types of assays may not accurately represent biological function. This variant is located in the 5' splice region. Computational tools predict a splicing impact, though this information is not predictive enough to determine pathogenicity. This variant is adjacent to an in-frame exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. In summary, this variant meets criteria to be classified as pathogenic for POMGNT1-associated muscular dystrophy-dystroglycanopathy. ACMG/AMP Criteria applied: PVS1_Moderate, PS3, PM3_VeryStrong (Richards 2015).

The c.1539+1 G>A variant is reported as a common Finnish founder mutation (Diesen et al., 2004); Published functional studies demonstrate a damaging effect as c.1539+1 G>A causes read-through of intronic sequences, resulting in introduction of a premature termination codon (Yoshida et al., 2001); Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Deletions involving coding exons in this gene are frequently reported as pathogenic, regardless of frame prediction (HGMD); This variant is associated with the following publications: (PMID: 15466003, 11709191, 22323514, 23326386, 25525159, 26990548, 29555514, 30961548, 27604308, 31980526, 31589614, 33144682)

The POMGNT1 c.1539+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. Across a selection of available literature, the c.1539+1G>A variant has been identified in at least 35 individuals with POMGNT1-related disorders, including in a homozygous state in 25 individuals and in a compound heterozygous state in six individuals and five fetuses (Yoshida et al. 2001; Taniguchi et al. 2003; Deisen et al. 2004; Vajsar et al. 2006; Hehr et al. 2007; Bouchet et al. 2007; Godfrey et al. 2007; Teber et al. 2008; Devisme et al. 2012; Amir et al. 2016). The c.1539+1G>A variant was reported in three of 1000 control alleles in a heterozygous state and at a frequency of 0.00240 in the European (Finnish) population of the Exome Aggregation Consortium. RT-PCR analysis confirmed that the variant disrupts splicing resulting in the skipping of exon 17 and premature truncation of the protein (Yoshida et al. 2001). Functional studies using targeted expression in HEK293 cells or fibroblasts from patients demonstrated that the POMGNT1 enzyme activity was significantly reduced (Yoshida et al. 2001; Vajsar et al. 2006). Based on the collective evidence, the c.1539+1G>A variant is classified as pathogenic for POMGNT1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PM2.

Based on the classification scheme VCGS_Germline_v1.3.3, 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 POMGNT-related disorders. (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0209 - Splice site variant proven to affect splicing of the transcript with uncertain effect on protein sequence. RT-RNA analysis has shown this variant causes two aberrant splicing outcomes; a read-through of intronic sequences resulting in a premature stop codon, and exon-skipping leading to an in-frame deletion of 42 amino acids. (PMID: 11709191). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 178 heterozygotes, 0 homozygotes). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals with POMGNT1-related disorders (ClinVar; VCGS). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

This sequence change affects a donor splice site in intron 17 of the POMGNT1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in POMGNT1 are known to be pathogenic (PMID: 19299310, 20816175, 21447391, 26908613, 27391550). This variant is present in population databases (rs138642840, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individuals with muscle-eye-brain disease and congenital muscular dystrophy (PMID: 11709191, 23326386). This variant is also known as IVS17+1G>A. ClinVar contains an entry for this variant (Variation ID: 56582). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

Converted during submission to Likely pathogenic.