The CDH1 c.1901C>T Variant: A Founder Variant in the Portuguese Population with Severe Impact in mRNA Splicing

Abstract

Hereditary diffuse gastric cancer (HDGC) caused by CDH1 variants predisposes to early-onset diffuse gastric (DGC) and lobular breast cancer (LBC). In Northern Portugal, the unusually high number of HDGC cases in unrelated families carrying the c.1901C>T variant (formerly known as p.A634V) suggested this as a CDH1-founder variant. We aimed to demonstrate that c.1901C>T is a bona fide truncating variant inducing cryptic splicing, to calculate the timing of a potential founder effect, and to characterize tumour spectrum and age of onset in carrying families. The impact in splicing was proven by using carriers’ RNA for PCR-cloning sequencing and allelic expression imbalance analysis with SNaPshot. Carriers and noncarriers were haplotyped for 12 polymorphic markers, and the decay of haplotype sharing (DHS) method was used to estimate the time to the most common ancestor of c.1901C>T. Clinical information from 58 carriers was collected and analysed. We validated the cryptic splice site within CDH1-exon 12, which was preferred over the canonical one in 100% of sequenced clones. Cryptic splicing induced an out-of-frame 37bp deletion in exon 12, premature truncation (p.Ala634ProfsTer7), and consequently RNA mediated decay. The haplotypes carrying the c.1901C>T variant were found to share a common ancestral estimated at 490 years (95% Confidence Interval 445–10,900). Among 58 carriers (27 males (M)–31 females (F); 13–83 years), DGC occurred in 11 (18.9%; 4M–7F; average age 33 ± 12) and LBC in 6 females (19.4%; average age 50 ± 8). Herein, we demonstrated that the c.1901C>T variant is a loss-of-function splice-site variant that underlies the first CDH1-founder effect in Portugal. Knowledge on this founder effect will drive genetic testing of this specific variant in HDGC families in this geographical region and allow intrafamilial penetrance analysis and better estimation of variant-associated tumour risks, disease age of onset, and spectrum.

Genotype-first approach to identify associations between CDH1 germline variants and cancer phenotypes: a multicentre study by the European Reference Network on Genetic Tumour Risk Syndromes

“… 8 , 27 , 28 Indeed, the limited number of missense variants, that were initially deposited in VEP and ClinVar as pathogenic or likely pathogenic variants, have later been shown to affect splicing, generating premature truncation. 11 , 29 We should not, however, discard the possibility that some purely missense variants can cause HDGC. Large databases and increasingly robust clinical and functional studies are needed to show whether some missense variants of unknown significance could cause HDGC.…”

Case Series of 11 CDH1 Families (47 Carriers) Including Incidental Findings, Signet Ring Cell Colon Cancer and Review of the Literature

“…Germline pathogenic splice variant c.1901C>T (r.1900_1936del; p. Ala634Profs*7) was identified in one of these families (the proband had a nonspecific breast cancer at 39 years old and there was no other familial history of cancer, but her mother was adopted). This splice variant was recently reported as a founder variant in the Portuguese population with low penetrance (frequency of DGC and LBC was 18.9% and 19.4% in 58 carriers of CDH1 c.1901C>T) [ 39 ]. This reduced penetrance may explain the lack of familial cancer related to CDH1 , although to date there is no validated genotype–phenotype correlation to adapt follow-up recommendations [ 40 ].…”