Is CDH1 p.Arg734Ile (c.2201G>T) pathogenic?

CDH1 p.Arg734Ile (c.2201G>T) is classified Uncertain significance in CDH1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-02). AlphaMissense: ambiguous (0.399); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with CDH1 p.Arg734Ile (c.2201G>T)?

CDH1 p.Arg734Ile (c.2201G>T) is associated with hereditary neoplastic syndrome, hereditary diffuse gastric adenocarcinoma (ClinVar).

How common is CDH1 p.Arg734Ile (c.2201G>T) in the general population?

CDH1 p.Arg734Ile (c.2201G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDH1 p.Arg734Ile (c.2201G>T)?

AlphaMissense predicts ambiguous (score 0.399) — an in-silico prediction, not a clinical call.

CDH1 p.Arg734Ile

c.2201G>T · rs587781859 · VCV141587

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.399 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,614,032)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.399	ambiguous
REVEL	0.363	indeterminate
SaProt	LLR -12.60	damaging
Splicing
SpliceAI	Δ0.54	acceptor gain · deltas
Pangolin	Δ0.22	gain · loss 0.06 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 3.4	GERP -2.3, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 25 kb · p 0.00015 · regional, not allelic
Overall
CADD	26.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,614,032). 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.Arg734Ile
Coding: c.2201G>T
MANE Select: NM_004360
dbSNP: rs587781859
Type: single nucleotide variant
Location: chr16:68828210 (GRCh38)
Gene constraint: LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.13 · 22 PDB

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.Arg734Ter Pathogenic ★★ same residue
CDH1 p.Arg734Ser Uncertain significance ★★ ⚠ same residue
CDH1 p.Arg734Thr Uncertain significance ★★ ⚠ same residue
CDH1 p.Arg734= Likely benign ★★ same residue
CDH1 p.Arg734Lys 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

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-arg734ile (accessed [today's date]).

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