ClinVar Genomic variation as it relates to human health

The c.1565+2dupT variant is a intronic variant in the donor region of intron 10 (PVS1_Strong, PM5_Supporting). This variant affects the same splice site as a well-characterized splice variant with similar or worse in silico/RNA predictions (PP3_Moderate). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). It has been reported in at least six families meeting HDGC clinical criteria (PS4; PMID: 18391748, 23709761, 25315765, 26072394, SCV000665426.2), and was also found to co-segregate with disease in multiple affected family members with 5 meioses observed (PP1_Moderate; PMID: 25315765, 22020549, SCV000665426.2). In summary, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PVS1_Strong, PS4, PM2_Supporting, PM5_Supporting, PP1_Moderate, PP3_Moderate.

This variant causes a single nucleotide insertion at the +3 position in the intron 10 splice acceptor site of the CDH1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. Although this prediction has not been confirmed in published RNA studies, this variant is expected to result in an absent or disrupted protein product. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in multiple individuals affected with diffused gastric cancer (PMID: 18391748, 22020549, 23709761, 25315765, 26072394, 26182300). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

Variant summary: CDH1 c.1565+2dupT alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251328 control chromosomes. c.1565+2dupT has been reported in the literature in multiple individuals affected with Hereditary Diffuse Gastric Cancer and Gastric Cancer (example, Rogers_2008, Kluijt_2011 and Nadauld_2014). These data strongly suggest variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories and an expert panel (ClinGen CDH1 Variant Curation Expert Panel) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory have classified the variant as likely pathogenic while two laboratories and the expert panel have classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The CDH1 c.1565+2dup; p.? variant (rs1555516200) is reported in the literature in at least five probands and multiple family members who were affected with diffuse gastric cancer (Benusiglio 2013, Kluijt 2012, Nadauld 2014, Rogers 2008, and van der Post 2015). This variant is also reported in ClinVar (Variation ID: 406624), but it is absent from general population databases (Exome Variant Server, Genome Aggregation Database), which indicates that it is not a common polymorphism. This is an intronic variant in a highly conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant abolishes the canonical splice donor site. Based on the available information, this variant is considered to be pathogenic.

For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 406624). This variant is also known as c.1565+2insT. This variant has been observed in individuals with diffuse gastric cancer and gastric cancer (PMID: 18391748, 22020549, 25315765). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 10 of the CDH1 gene. It does not directly change the encoded amino acid sequence of the CDH1 protein. It affects a nucleotide within the consensus splice site.

The c.1565+2dupT intronic pathogenic mutation results from a duplication of a T nucleotide two nucleotide positions after coding exon 10 of the CDH1 gene. This mutation has been reported in multiple individuals with hereditary diffuse gastric cancer (HDGC) as well as their affected family members (Rogers WM et al. Am. J. Surg. Pathol. 2008 Jun; 32(6):799-809; Nadauld LD et al. Genome Biol., 2014 Aug;15:428). This mutation has also been reported in a hereditary gastric cancer family in which gastric cancer occurred in at least four family members at ages 43 to 56. Authors note that of the 16 additional relatives who tested positive for this mutation, 14 underwent prophylactic gastrectomy. In six prophylactic treated patients, only subtle gastric abnormalities were observed, and in one patient a total absence of typical HDGC-related histological findings was observed; however, ages of prophylactic gastrectomies were not provided (Kluijt I et al. Int. J. Cancer 2012 Jul;131:367-76). In silico splice site analysis predicts that this alteration may weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). Based on the available evidence, this alteration is interpreted as a disease-causing mutation.

PS4; PM2; PP1_Moderate; PP3_Moderate (PMID: 30311375)

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 22020549, 18391748, 25315765, 23709761].

Intronic variant directly or indirectly altering the +5 splice site in a gene for which loss of function is a known mechanism of disease, and splice predictors support a deleterious effect; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31125277, 24389957, 33929593, 30745422, 34949788, 22020549, 23709761, 28688938, 26182300, 25315765, 35626031, 26072394, 36436516, 18391748)