ClinVar Genomic variation as it relates to human health

Variant summary: C2 c.841_849+19del28 involves the deletion of a canonical 5' donor splice-site and is therefore predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Accordingly, several computational tools predict a significant impact on normal splicing, with three predicting the variant abolishes the canonical 5' splicing donor site. At least one publication reports experimental evidence that this variant indeed affects mRNA splicing, resulting in the skipping of exon 6, which causes a frameshift and premature termination codon that is expected to be affected by nonsense mediate decay. The variant allele was found at a frequency of 0.0046 in 251134 control chromosomes in the gnomAD database, including 2 homozygotes and is found at a high frequency (0.011) in the Ashkenazi Jewish subpopulation, providing supporting evidence for a benign role. However, c.841_849+19del28 has been reported in the literature in multiple homozygous individuals affected with Complement Component 2 Deficiency and has been found to segregate with the disease phenotype in more than one family (e.g. Johnson_1992, Rice_2016, Morup_2022). These data indicate that the variant is very likely to be associated with disease, but may exhibit reduced penetrance. The following publications have been ascertained in the context of this evaluation (PMID: 1577763, 27943079, 35874679). Ten submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic (n=9)/likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.

The c.841_849+19del variant in C2 is the most common pathogenic variant for C2 deficiency (Johnson 1992, Truedsson 1993), accounting for about 90% of cases (Truedsson 2015). It has been identified in 1.2% (123/10162) of Ashkenazi Jewish chromosomes and 0.8% (1001/126816) of European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs572361305); however, this frequency is low enough to be consistent with the frequency of C2 deficiency in the general population. This variant is a deletion of 28 bp, including the invariant region of the splice consensus sequence, and has been shown to cause skipping of exon 6, leading to a frameshift (Johnson 1992). In summary, the c.841_849+19del meets criteria to be classified as pathogenic for C2 deficiency in an autosomal recessive manner.

This sequence variant is a 28 nucleotide deletion spanning positions 841 through 849+19 of the C2 gene that removes part of the coding sequence of exon 6 and the canonical donor splice site of intron 6. This is a previously reported variant (ClinVar 50634) that has been observed in homozygous and compound heterozygous individuals affected by type 1 complement C2 deficiency (PMID: 1577763, 9616367, 27943079, 31440263, 35874679). In the heterozygous state, this variant was observed in an individual affected by a pathogen-specific immunodeficiency (PMID: 35874679). This variant is present in 1927 of 403284 alleles (0.4778%) in the gnomAD population dataset. Predictions from bioinformatic tools are inconclusive for this variant. RNA studies have indicated that this variant disrupts the intron 6 donor splice site leading to the exclusion of exon 6 from the transcript and the introduction of a novel stop codon 12 bases downstream of the deletion (PMID: 1577763). The introduction of this premature stop codon likely causes a loss of C2 expression as a result of nonsense mediated decay (PMID: 9616367). Based upon the evidence, we consider this a pathogenic variant. ACMG Criteria: PS3, PVS1

Functional studies demonstrate that this variant results in skipping of exon 6 (Johnson et al., 1992); Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 1577763, 31440263, 25454804, 33726816, 27535533)

This variant results in the deletion of part of exon 6 (c.841_849+19del) of the C2 gene. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs572361305, gnomAD 1.2%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with C2 deficiency (PMID: 1577763, 9616367, 31440263). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 50634). Studies have shown that this variant results in skipping of exon 6 and introduces a premature termination codon (PMID: 1577763). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

C2: PM3:Very Strong, PVS1, PM2:Supporting, PS3:Supporting

The C2 c.841_849+19del28 variant is predicted to result in a deletion affecting a canonical splice site. This variant is predicted to result in a deletion encompassing the splice donor site at the exon 6/intron 6 boundary and has been reported to result in exon 6 skipping, with splicing prediction programs also indicating splicing alterations (Johnson et al. 1992. PubMed ID: 1577763; Alamut Visual Plus v1.6.1). This variant has been reported in many homozygous and compound heterozygous individuals with complement C2 deficiency (Zhu et al. 1998. PubMed ID: 9670930; Johnson et al. 1992. PubMed ID: 1577763; Liphaus et al. 2015. PubMed ID: 26017655; Blazina et al. 2018. PubMed ID: 29619023). Of note, heterozygous carriers of the c.841_849+19del were also found to have clinical features of C2 deficiency, including purulent meningitis, recurrent sinusitis, recurrent impetigo, pneumonia, and recurrent otitis (Blazina et al. 2018. PubMed ID: 29619023). This variant is reported in 1.18% of alleles in individuals of Ashkenazi Jewish descent in gnomAD; however, the allele balance is skewed for many heterozygous individuals indicating this data may not be reliable. In the ClinVar database, this variant has been reported as pathogenic or likely pathogenic by several outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/50634/). Of note, alternative transcripts have been reported for the C2 gene including two which have alternative splicing omitting exon 6 (NM_001178063.2 and NM_001282457.1; Cheng and Volanakis. 1994. PubMed ID: 8120386). Taken together, we interpret this variant as likely pathogenic.

NM_001282459.1:c.841_868del in the C2 gene has an allele frequency of 0.012 in Ashkenazi Jewish subpopulation in the gnomAD database. This variant also known as NM_000063.6(C2):c.841_849+19del has been reported in homozygosity in 6 probands with C2-deficiency, and segregated with disease in 2 affected homozygous relatives in one family (PMID: 1577763). The 28bp deletion leads to skipping of exon 6 and a premature stop-codon. Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PVS1, PM3, PP4, PP1.