Is CDH1 p.Arg151fs (c.451del) pathogenic?

CDH1 p.Arg151fs (c.451del) is classified Likely pathogenic in CDH1 (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD; Associated with breast carcinoma.

What condition is associated with CDH1 p.Arg151fs (c.451del)?

CDH1 p.Arg151fs (c.451del) is associated with breast carcinoma (ClinVar).

How common is CDH1 p.Arg151fs (c.451del) in the general population?

CDH1 p.Arg151fs (c.451del) is absent from gnomAD (gnomAD).

CDH1 p.Arg151fs

c.451del · rs2152129697 · VCV1264325

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

breast carcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.6	GERP 0.99, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Arg151fs
Coding: c.451del
MANE Select: NM_004360
dbSNP: rs2152129697
Type: Deletion
Location: chr16:68808486 (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

breast carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDH1 p.Arg151Ile Uncertain significance ★★ ⚠ same residue
CDH1 p.Arg151Lys Uncertain significance ★ ⚠ same residue
CDH1 p.Glu497Lys Uncertain significance ★★ ⚠ same condition
CDH1 c.1137+1del Pathogenic ★★★ same type
CDH1 c.1565+1del Likely pathogenic ★★★ same type
CDH1 c.1711+2_1711+7del Likely pathogenic ★★★ same type
CDH1 p.Ala546fs Pathogenic ★★★ same type
CDH1 p.Arg800fs Pathogenic ★★★ same type

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-arg151fs (accessed [today's date]).

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