Is CDH1 p.Glu463= (c.1389G>A) pathogenic?

CDH1 p.Glu463= (c.1389G>A) is classified Likely benign in CDH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-06). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with CDH1 p.Glu463= (c.1389G>A)?

CDH1 p.Glu463= (c.1389G>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDH1 p.Glu463= (c.1389G>A) in the general population?

CDH1 p.Glu463= (c.1389G>A) is absent from gnomAD v4.1 (gnomAD).

CDH1 p.Glu463=

c.1389G>A · rs2152134807 · VCV1771479

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.46 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.35	GERP -3.8
Overall
CADD	7.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

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.Glu463=
Coding: c.1389G>A
MANE Select: NM_004360
dbSNP: rs2152134807
Type: single nucleotide variant
Location: chr16:68815583 (GRCh38)
Gene constraint: LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.13 · 22 PDB
Residue 463: the cadherin 3 domain; a UniProt-annotated variant site (in a gastric carcinoma sample)

Full CDH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDH1 p.Glu463Lys Uncertain significance ★★ ⚠ same residue
CDH1 p.Glu463Ter Pathogenic ★ same residue
CDH1 p.Glu463Ala Uncertain significance ★ ⚠ 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.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-glu463 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown