ClinVar Genomic variation as it relates to human health

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Variant classified as Uncertain Significance - Favor Benign. The p.Leu15Gln vari ant in DSG2 has been reported in 1 Caucasian adult with "probable" ARVC (Bhuiyan 2009), and has been identified by our laboratory in 4 individuals: 1 child with HCM, 1 child with DCM who carried a disease-causing variant in another gene, an d 2 adults with DCM. This variant has also been identified in 0.4% (6/1706) of E uropean chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broad institute.org; dbSNP rs372174546). This variant is located in the last three bas es of the exon, which is part of the 5? splice region. Although computational to ols do not suggest an impact to the functionality of the 5' splice site, this in formation is not predictive enough to rule out pathogenicity. In summary, while the clinical significance of the p.Leu15Gln variant is uncertain, its frequency suggests that it is more likely to be benign.

The p.Leu15Gln variant (rs372174546) has been previously reported as an unclassified variant in one patient with probable arrhythmogenic right ventricular dysplasia / cardiomyopathy (Bhuiyan 2009), one from a cohort of cardiac arrest survivors (Mellor 2017), and has been reported to ClinVar (Variation ID: 44318). This variant is listed in the genome Aggregation Database with an overall population frequency of 0.02 percent (identified on 18 out of 56,058 chromosomes). The leucine at position 15 is weakly conserved (Alamut v2.8.1) and computational analyses of the effects of the p.Leu15Gln variant on protein structure and function indicate a neutral effect (SIFT: tolerated, MutationTaster: polymorphism, PolyPhen-2: benign). Altogether, there is not enough evidence to classify the p.Leu15Gln variant with certainty.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

Variant summary: DSG2 c.44T>A (p.Leu15Gln) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant also alters a conserved nucleotide in the exonic-splice region located at the second to last nucleotide of exon 1 before the canonical intron 1 splice donor site. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00032 in 56632 control chromosomes. The observed variant frequency is approximately 13 fold of the estimated maximal expected allele frequency for a pathogenic variant in DSG2 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is benign. c.44T>A has been reported in the literature in individuals affected with ARVD (Bhuyian_2009), ARVC (Mellor_2017, Ye_2019). These report(s) do not provide unequivocal conclusions about association of the variant with DSG2 associated Cardiomyopathy/ARVD/ARVC. One recent report proposes a categorization of this variant as a disease-modifier while acknowledging its prevalence greater than expected for a monogenic disease causation (Ye_2019). However, this is not supported by convincing data supporting its role as a disease modifier. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Ten clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (VUS, n=8, likely benign, n=2). Some submitters cite overlapping evidence utilized in the context of this evaluation. One submitter reports an unspecified co-occurence with a mutation in another gene that clearly explains a proband's phenotype. Based on the evidence outlined above, the variant was classified as likely benign.

This sequence change replaces leucine, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 15 of the DSG2 protein (p.Leu15Gln). This variant is present in population databases (rs372174546, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with DSG2-related conditions (PMID: 20031616, 31402444). ClinVar contains an entry for this variant (Variation ID: 44318). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

This variant is associated with the following publications: (PMID: 20031616, 18639457, 28600387, 31402444)

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3C. Following criteria are met: 0103 - Loss of function and gain of function are reported mechanisms of disease in this gene and are associated with arrhythmogenic right ventricular dysplasia 10 (ARVD 10; MIM#610193) and dilated cardiomyopathy 1BB (DCM; MIM#612877) (ClinVar, PMID: 23071725). (I) 0108 - This gene is associated with both recessive and dominant disease. It is commonly associated to dominant inheritance, however recessive has been reported in severe DCM patients (OMIM). (I) 0112 - The ARVD condition associated with this gene has incomplete penetrance (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from leucine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0308 - Population frequency for this variant is out of keeping with known incidence of ARVD 10 or DCM. (SB) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated signal sequence domain (PMID: 30885746). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported in a few ARVC related studies without proper classification (PMID: 20031616, 28600387, 30885746, 31402444). It has also been reported as VUS in individuals with ARVC and likely benign in individuals with cardiovascular phenotypes in ClinVar and various other databases (LOVD, ARVC genetic variant db). (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Given the weak case data, the number of cases with other pathogenic variants, gene constraint data and its presence in population databases, we consider this variant a variant of uncertain significance and we do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). This variant may alter RNA splicing. The variant has been seen in at least 33 unrelated cases of cardiomyopathy (not including this patient's family). There is weak case data. Some of these patients had additional pathogenic variants identified. This variant is present in ClinVar, classified as a variant of uncertain significance by 5 labs. It has been seen in at least 6 patients from 5 families. The Laboratory for Molecular Medicine has seen this variant in 5 individuals from 5 different families and they report the following cases: 1 child with HCM, 1 child with DCM who carried a disease-causing variant in another gene, and 2 adults with DCM. This variant is reported once in the literature: in a 55 year old male with "probable" ARVC. The diagnosis was based on the presence of epsilon eaves and left bundle branch ventricular tachycardia. Variant classification was based on physciocemical properties of the amino acids involved, the evolutionary conservation of the amino acid, and localization within a functionally important domain (Bhuiyan et al, 2009). There is weak evidence linking missense variants in DSG2 with DCM: Of note, Kapplinger et al. (2011) from Michael Ackerman’s group have reported a significant yield of rare missense variants in the ARVC genes of presumably healthy controls from various ethnicities. According to their data, 16% of 427 controls hosted missense variants—similar to the 21% yield in 175 Dutch and U.S. ARVC cases. This is a reminder that missense variants of unknown significance in ARVC-related genes need to be interpreted with caution. Kapplinger et al. also report a “hot spot” for DSG2 variants between amino acids 24-388 in patients with ARVC but not in controls. Furthermore, per the ExAC database's constraint data, DSG2 is tolerant of both missense (Z= -1.20) and loss of function variation (pLI=0.00). This constraint data is supported in a paper by Walsh and colleagues in 2016: in comparing the genetic variation between cases and controls, neither missense variants nor truncating variants in DSG2 were significantly enriched in cases versus controls. According to this data, missense variants in DSG2 are unlikely to significantly increase an individual's risk to develop DCM. Per the genetic testing report, "algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies." The leucine at codon 15 is moderately conserved across species, as are neighboring amino acids. Other variants reported in ClinVar at this codon and close by are called variants of uncertain significance, or likely benign. The variant was reported online in 18 of 28,029 individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. Specifically, the variant was observed in 12 of 12,221 individuals of European descent (MAF=0.07%). The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. Note that this is a low-quality site, with depth of coverage less than 20x.