CDH1 p.Thr470fs
c.1408del · rs1131690821 · VCV428633
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.1408del (p.Thr470fs) variant is predicted to result in a premature stop codon that leads to a truncated or absent protein (PVS1, PM5_Supporting). The variant is absent in the gnomAD cohort (PM2_Supporting; http://https://gnomad.broadinstitute.org/). The variant has been reported in a family meeting clinical criteria for HDGC (PS4_Supporting; SCV000580711.3). 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, 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 | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 10 of 16 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.13 | GERP -2.5, phastCons 0.45 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CDH1
- Protein
- p.Thr470fs
- Coding
- c.1408del
- MANE Select
- NM_004360
- dbSNP
- rs1131690821
- Type
- Deletion
- Location
- chr16:68815602 (GRCh38)
- Gene constraint
- LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.13 · 22 PDB
- Residue 470
- the cadherin 3 domain; a β-strand; a UniProt-annotated variant site (in)
Similar variants
- CDH1 p.Thr470Ile Benign ★★★ ⚠ same residue
- CDH1 c.1137+1del Pathogenic ★★★ same condition
- CDH1 c.1565+1del Likely pathogenic ★★★ same condition
- CDH1 c.1711+2_1711+7del Likely pathogenic ★★★ same condition
- CDH1 p.Ala546fs Pathogenic ★★★ same condition
- CDH1 p.Arg800fs Pathogenic ★★★ same condition
- CDH1 p.Asn369fs Pathogenic ★★★ same condition
- CDH1 p.Asn390fs 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-thr470fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown