ClinVar Genomic variation as it relates to human health

The p.Lys142Arg variant in COL7A1 has been reported in the homozygous or compoun d heterozygous state in >15 individuals with dystrophic epidermolysis bullosa ( DEB) (Gardella 1996, Gardella 2002, Csikos 2005). This variant has also been ide ntified in 0.01% (12/126664) of European chromosomes by the Genome Aggregation D atabase (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs121912856). Although this variant has been seen in the general population, its frequency is low enoug h to be consistent with a recessive carrier frequency. This variant is located w ithin the last three bases of exon 3, which is part of the 5' splice region. Com putational tools do suggest an impact to splicing, and functional studies have s hown that this variant impacts splicing of exon 3, leading to a truncated or abs ent protein (Gardella 1996). Loss of function of the COL7A1 gene is an establish ed disease mechanism in autosomal recessive DEB. In summary, this variant meets criteria to be classified as pathogenic for DEB in an autosomal recessive manner . ACMG/AMP Criteria applied: PM3_Very Strong; PS3; PP3; PP4.

Variant summary: COL7A1 c.425A>G (p.Lys142Arg) results in a conservative amino acid change located in the von Willebrand factor, type A domain (IPR002035) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 5' splicing donor site and three predict the variant also creates a 3' acceptor site. At least one publication reports experimental evidence that this variant indeed affects mRNA splicing, resulting in the creation of a premature termination codon (e.g. Gardella_1996). The variant allele was found at a frequency of 3.2e-05 in 251394 control chromosomes. c.425A>G has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with Recessive Dystrophic Epidermolysis Bullosa (eg. Gardella_1996, Jerabkova_2010). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 8755915, 20598510). ClinVar contains an entry for this variant (Variation ID: 29636). Based on the evidence outlined above, the variant was classified as pathogenic.

Across a selection of the available literature, the COL7A1 c.425A>G (p.Lys142Arg) missense variant has been identified in 42 individuals with dystrophic epidermolysis bullosa, including in a homozygous state in nine probands, in a compound heterozygous state in 30 probands, and in a heterozygous state in 3 probands with second alleles not identified (Gardella et al. 1996; Csikos et al. 2005; Jerabkova et al. 2010; Wertheim-Tysarowska et al. 2012). The p.Lys142Arg variant was found in a heterozygous state in one of 100 control alleles (Csikos et al. 2005) and is reported at a frequency of 0.000095 in the European (non-Finnish) population of the Genome Aggregation Database. RT-PCR found the p.Lys142Arg variant to have aberrant transcripts that indicate exon skipping (Gardella et al. 1996). Based on the evidence, the p.Lys142Arg variant is classified as pathogenic for dystrophic epidermolysis bullosa. 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: PS1,PS3,PM2,PM3,PP3,PP4. This variant was detected in homozygous state.

PM1, PM2, PP2, PP3, PP5

Non-canonical splice site variant predicted to damage or destroy the natural splice donor site for intron 3 and demonstrated to result in loss-of-function through cDNA analysis of cultured skin fibroblasts from a patient with c.425 A>G (Gardella et al., 1996); This variant is associated with the following publications: (PMID: 15888141, 12485454, 11781296, 8755915, 12787275, 22266148, 29080321, 26990548, 21448560, 34008892, 31589614, 16971478, 34426522, 33274474)

This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 142 of the COL7A1 protein (p.Lys142Arg). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs121912856, gnomAD 0.009%). This missense change has been observed in individuals with autosomal recessive epidermolysis bullosa dystrophica (PMID: 11781296, 12787275, 15888141, 16971478, 19681861, 22266148). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 29636). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Studies have shown that this missense change results in abnormal splicing and introduces a premature termination codon (PMID: 8755915, 10408773). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

This sequence change in COL7A1 is predicted to replace lysine with arginine at codon 142, p.(Lys142Arg). This variant also falls at the second last nucleotide of exon 3 of the COL7A1 coding sequence, which is part of the consensus donor splice site for this exon. The highest population minor allele frequency in gnomAD v2.1 is 0.007% (9/129,144 alleles) in the European (non-Finnish) population, which is consistent with recessive disease. This variant has been detected in at least 12 individuals with recessive dystrophic epidermolysis bullosa (RDEB). Of those individuals, two individuals were homozygous and 10 were compound heterozygous for the variant and a pathogenic or likely pathogenic variant confirmed in trans by parental testing. All these cases demonstrated loss or reduced expression of Collagen VII in the dermal-epidermal junction (PMID: 8755915, 10408773, 12787275, 15888141). The variant has been reported to segregate with RDEB in at least one family (PMID: 12787275). Multiple lines of computational evidence predict an impact on splicing (SpliceAI, MaxEntScan, NNSplice), and have conflicting predictions for the missense substitution (3/6 algorithms predict deleterious). The splicing prediction is confirmed by RT-PCR and allele-specific analyses in skin fibroblasts. The assay demonstrated that the variant impacts splicing by full expression of three aberrant transcripts (all expected to undergo nonsense-mediated decay), exon 3 skipping being the most prevalent (PMID: 8755915, 10408773). Based on the classification scheme RMH Modified ACMG Guidelines v1.4.0, this variant is classified as PATHOGENIC. Following criteria are met: PS3, PM3_VeryStrong, PM2_Supporting, PP1, PP3, PP4.

The COL7A1 c.425A>G variant is predicted to result in the amino acid substitution p.Lys142Arg. This variant has been frequently reported in the homozygous or compound heterozygous state in individuals with epidermolysis bullosa dystrophica (see for example Rossi et al. 2021. PubMed ID: 33274474; Zimmer et al. 2002. PubMed ID: 11781296; Table SII in Almaani et al. 2011. PubMed ID: 21448560; Kahofer et al. 2003. PubMed ID: 12787275; Drera et al. 2006. PubMed ID: 16965329; Gardella et al. 2002. PubMed ID: 12485454; Varki et al. 2007. PubMed ID: 16971478); and, it has been shown to disrupt the canonical splice donor site (Gardella et al. 1999. PubMed ID: 10408773). This variant is reported in 0.0070% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.