CDH1 p.Lys314Ter
c.940A>T · rs1131690820 · VCV428632
ClinGen expert panel — CDH1 VCEP
Pathogenic for CDH1-related diffuse gastric and lobular breast cancer. Applied ACMG criteria (verbatim):
PVS1 PM2_Supporting PS4_Supporting PM5_Supporting
Curation rationale (ClinGen, verbatim)
The c.940A>T (p.Lys314Ter) variant is predicted to result in a premature termination codon in exon 7 (PVS1, PM5_Supporting). The variant is absent from the gnomAD population database (PM2_Supporting; https://gnomad.broadinstitute.org/). This variant has previously been reported in one individual meeting IGCLC criteria for HDGC (PS4_Supporting; PMID: 26182300). In summary, this variant meets criteria to be classified as pathogenic based on ACMP/AMP criteria as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PVS1, PM2_Supporting, PS4_Supporting, PM5_Supporting.
ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 16 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.9 | GERP -3.6 |
| Overall | ||
| CADD | 19.49 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDH1
- Protein
- p.Lys314Ter
- Coding
- c.940A>T
- MANE Select
- NM_004360
- dbSNP
- rs1131690820
- Type
- single nucleotide variant
- Location
- chr16:68811791 (GRCh38)
- Gene constraint
- LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.13 · 22 PDB
- Residue 314
- the cadherin 2 domain
Similar variants
- CDH1 p.Lys314Ile Uncertain significance ★★ ⚠ same residue
- CDH1 p.Lys314Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
- CDH1 c.1008+2T>C Likely pathogenic ★★★ same condition
- CDH1 c.1137+1G>A Pathogenic ★★★ same condition
- CDH1 c.1137+2T>C Likely pathogenic ★★★ same condition
- CDH1 c.1320+1G>C Likely pathogenic ★★★ same condition
- CDH1 c.1565+1G>A Pathogenic ★★★ same condition
- CDH1 c.1565+1G>C Pathogenic ★★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdh1-p-lys314ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown