Is CDH1 p.Val391= (c.1173C>T) pathogenic?

CDH1 p.Val391= (c.1173C>T) is classified Benign/Likely benign in CDH1 (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-01-31). Ultra-rare (popmax 0.0121%, sas); Associated with Breast and/or ovarian cancer.

What condition is associated with CDH1 p.Val391= (c.1173C>T)?

CDH1 p.Val391= (c.1173C>T) is associated with Breast and/or ovarian cancer, hereditary diffuse gastric adenocarcinoma, hereditary neoplastic syndrome (ClinVar).

How common is CDH1 p.Val391= (c.1173C>T) in the general population?

CDH1 p.Val391= (c.1173C>T) is ultra-rare (popmax 0.0121%, sas) (gnomAD).

CDH1 p.Val391=

c.1173C>T · rs148080550 · VCV136056

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0121%, sas)

Conditions

Breast and/or ovarian cancer

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -10	GERP -3.9
Overall
CADD	0.296	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0121% South Asian · 11/91,078 alleles

Filtering AF 0.00676% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00522%

Overall 0.00285% 46/1,614,030 alleles · ultra-rare exomes 42/1,461,874 · genomes 4/152,156 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0121%	8,280
Remaining individualsnot grpmax-eligible	0.0048%	20,828
Admixed American	0.00333%	30,000
European (non-Finnish)	0.00237%	42,144
East Asian	0.00223%	44,894
African / African-American	0.00133%	74,910

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.Val391=
Coding: c.1173C>T
MANE Select: NM_004360
dbSNP: rs148080550
Type: single nucleotide variant
Location: chr16:68813348 (GRCh38)
Gene constraint: LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.13 · 22 PDB
Residue 391: the cadherin 3 domain

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

Disease context

Breast and/or ovarian cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary diffuse gastric adenocarcinoma hereditary neoplastic syndrome

Similar variants

CDH1 p.Val391Gly Uncertain significance ★★ ⚠ same residue
CDH1 p.Val391Phe Uncertain significance ★★ ⚠ same residue
CDH1 p.Val391Ala Uncertain significance ★ ⚠ same residue
CDH1 p.Val391Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
CDH1 p.Val391Leu Likely benign ★ 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-val391 (accessed [today's date]).

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