CDH4 p.Pro260=
c.780C>T · rs567022284 · VCV751029
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0285%, sas)
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 1.7 | GERP -0.99, phastCons 1 |
| Overall | ||
| CADD | 12.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0285%
South Asian · 26/91,076 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0171%
Overall
0.00254%
41/1,614,088 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0285% | 3,503 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| European (non-Finnish) | 0.00119% | 84,285 |
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
- CDH4
- Protein
- p.Pro260=
- Coding
- c.780C>T
- MANE Select
- NM_001794
- dbSNP
- rs567022284
- Type
- single nucleotide variant
- Location
- chr20:61852801 (GRCh38)
- Gene constraint
- LOEUF 0.533 · pLI 0.54 (gnomAD)
- Structure
- AlphaFold pLDDT 79.02
- Residue 260
- the cadherin 1 domain
Similar variants
- CDH4 p.Thr396Met Uncertain significance ★★ ⚠ same type
- CDH4 p.Val580Ile Uncertain significance ★★ ⚠ same type
- CDH4 c.1629-8C>T Benign ★★ same type
- CDH4 c.2240-4A>G Benign ★★ same type
- CDH4 p.Ala33Thr Benign ★★ same type
- CDH4 p.Ala344= Benign/Likely benign ★★ same type
- CDH4 p.Asn283= Benign/Likely benign ★★ same type
- CDH4 p.Asn450= Benign/Likely benign ★★ 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/cdh4-p-pro260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown