Is CDH1 p.Glu353= (c.1059G>A) pathogenic?

CDH1 p.Glu353= (c.1059G>A) is classified Benign/Likely benign in CDH1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-12-29). Ultra-rare (popmax 0.0285%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with CDH1 p.Glu353= (c.1059G>A)?

CDH1 p.Glu353= (c.1059G>A) is associated with hereditary neoplastic syndrome, hereditary diffuse gastric adenocarcinoma (ClinVar).

How common is CDH1 p.Glu353= (c.1059G>A) in the general population?

CDH1 p.Glu353= (c.1059G>A) is ultra-rare (popmax 0.0285%, sas) (gnomAD).

CDH1 p.Glu353=

c.1059G>A · rs537703872 · VCV463698

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0285%, sas)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.26	donor loss, 5 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -11	GERP -3.5
Overall
CADD	0.008	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0285% South Asian · 26/91,086 alleles

Filtering AF 0.0199% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0171%

Overall 0.00186% 30/1,614,188 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0285%	3,503
Remaining individualsnot grpmax-eligible	0.0032%	31,254
European (non-Finnish)	0.000169%	590,009

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDH1
Protein: p.Glu353=
Coding: c.1059G>A
MANE Select: NM_004360
dbSNP: rs537703872
Type: single nucleotide variant
Location: chr16:68812185 (GRCh38)
Gene constraint: LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.13 · 22 PDB
Residue 353: the cadherin 2 domain

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

Also linked: hereditary diffuse gastric adenocarcinoma

Similar variants

CDH1 p.Glu353Lys Likely pathogenic ★★★ ⚠ same residue
CDH1 p.Glu353Val Uncertain significance ★★ ⚠ same residue
CDH1 p.Glu353Gln Uncertain significance ★ ⚠ same residue
CDH1 p.Glu353fs Pathogenic ★ 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

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-glu353 (accessed [today's date]).

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