ClinVar Genomic variation as it relates to human health

The COL6A2 c.1970-9G>A splice region variant has been reported in at least six studies in which it was found in a total of seven affected individuals, including in one in a homozygous state, in five in a compound heterozygous state with a truncating variant on the second allele, and in one in a heterozygous state in whom the second allele was not detected. The individuals were affected with a range of phenotypes from a moderately severe form of Ullrich congenital muscular dystrophy through different intermediate phenotypes to a milder Bethlem myopathy (Martoni et al. 2009; Deconinck et al. 2010; Foley et al. 2011; Quijano-Roy et al. 2014; Deconinck et al. 2015; Stehlíková et al. 2017). Control data are unavailable for this variant, which is reported at a frequency of 0.000436 in the Latino population of the Genome Aggregation Database. The c.1970-9G>A variant was shown to create a cryptic splice site in intron 25, leading to a frameshift and premature termination of the protein and reduced transcript levels to 20% of normal (Martoni et al. 2009). RT-PCR experiments in patient fibroblasts showed the presence of some normally spliced transcript (Foley e al. 2011). Studies in patient fibroblast cultures demonstrated that the variant resulted in significantly reduced levels of collagen VI protein, decreased intracellular secretion, and abnormal deposition and organization of the protein in the extracellular matrix (Martoni et al. 2009; Deconinck et al. 2015). Based on the collective evidence, the c.1970-9G>A variant is classified as pathogenic for an autosomal recessive form of collagen type VI-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The c.1970-9G>A variant in COL6A2 has been reported in 3 individuals (two compou nd heterozygotes who had other disease-causing variants in trans and one homozyg ote) with Ullrich congenital muscular dystrophy (Martoni 2009, Foley 2011, Decon ninck 2014). This variant has also been identified in 7/113354 of chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP r s747900252). This frequency is low enough to be consistent with a recessive carr ier frequency. The c.1970-9G>A variant was demonstrated to cause altered splici ng, leading to a frameshift and a truncated or absent protein (Martoni 2009, Fol ey 2011). In summary, this variant meets our criteria to be classified as patho genic for collagen VI-related myopathy in an autosomal recessive manner based up on its segregation in affected individuals, low frequency in controls and functi onal impact.

The heterozygous c.1970-9G>A variant in COL6A2 was identified by our study, along with a variant of uncertain significance, in 2 unrelated individuals with either Bethlem myopathy 1 or Ullrich congenital muscular dystrophy 1. The variant has been reported in at least 11 individuals of Brazilian, European, and unknown ethnicity with Ullrich congenital muscular dystrophy 1 or Bethlem myopathy 1 (PMID: 27447704, 19309692, 28578317, 32065942, 21280092, 20576434, 25535305, 20976770, 24314752), and has been identified in 0.04% (15/35314) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs747900252). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID: 265506) as pathogenic by multiple submitters, as likely pathogenic by Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, and as likely benign by Illumina Clinical Services Laboratory. In vitro functional studies provide some evidence that the c.1970-9G>A variant may impact protein function (PMID: 19309692, 21280092). 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. The presence of this variant in at least 3 affected homozygotes, in combination with reported likely pathogenic variants, in combination with reported variants of uncertain significance, and in at least 11 individuals with Ullrich congenital muscular dystrophy 1 or Bethlem myopathy 1 increases the likelihood that the c.1970-9G>A variant is pathogenic (VariationID: 497233; PMID: 19309692, 28578317, 32065942, 21280092, 20576434, 25535305, 20976770, 24314752). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PM3_strong, PS3_moderate, PP3 (Richards 2015).

This sequence change falls in intron 25 of the COL6A2 gene. It does not directly change the encoded amino acid sequence of the COL6A2 protein. This variant is present in population databases (rs747900252, gnomAD 0.04%). This variant has been observed in individual(s) with autosomal recessive COL6A2-related conditions (PMID: 19309692, 20576434, 21280092, 25535305; Invitae). 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: 265506). Studies have shown that this variant alters COL6A2 gene expression (PMID: 19309692). 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.

Functional studies show this variant affects the deposition and organization of collagen VI in the extracellular matrix, and the collagen VI level is decreased (PMID: 19309692); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 21280092, 33441455, 37526466, 32363432, 20882040, 28578317, 25535305, 27447704, 20576434, 24314752, 20976770, 29774307, 30609409, 32065942, 31127727, 33250842, 34426522, 34106991, 19309692, 38374194)

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.010%). Functional studies provide moderate evidence of the variant having a damaging effect on the gene or gene product (PMID: 19309692, 21280092). In silico tools predict the variant to alter splicing and produce an abnormal transcript (SpliceAI: 0.85). It has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 2 similarly affected unrelated individuals (PMID: 21280092, 25535305). The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000265506 / PMID: 19309692). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

28-year-old female, born as a floppy baby with some improvement. At the moment, she has proximal and distal weakness, and myogenic electromyography.