Is CDH1 p.Val501= (c.1503G>A) pathogenic?

CDH1 p.Val501= (c.1503G>A) is classified Benign/Likely benign in CDH1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2024-09-19). Very rare (popmax 0.005%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with CDH1 p.Val501= (c.1503G>A)?

CDH1 p.Val501= (c.1503G>A) is associated with hereditary neoplastic syndrome, hereditary diffuse gastric adenocarcinoma (ClinVar).

How common is CDH1 p.Val501= (c.1503G>A) in the general population?

CDH1 p.Val501= (c.1503G>A) is very rare (popmax 0.005%, amr) (gnomAD).

CDH1 p.Val501=

c.1503G>A · rs775290153 · VCV819401

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

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	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1	GERP -2.5, phastCons 1
Overall
CADD	6.856	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/59,990 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000186% 3/1,614,076 alleles · very rare exomes 2/1,461,890 · genomes 1/152,186 · joint denominator

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.Val501=
Coding: c.1503G>A
MANE Select: NM_004360
dbSNP: rs775290153
Type: single nucleotide variant
Location: chr16:68815697 (GRCh38)
Gene constraint: LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.13 · 22 PDB
Residue 501: the cadherin 4 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.Val501Gly Uncertain significance ★ ⚠ same residue
CDH1 p.Val501Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
CDH1 p.Val501Met Conflicting classifications of pathogenicity ★ ⚠ same residue
CDH1 p.Val501fs 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-val501 (accessed [today's date]).

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