CDH4 p.Asn450=
c.1350C>T · rs78259850 · VCV711082
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.439%, nfe)
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 -8.4 | GERP -4.2 |
| Overall | ||
| CADD | 6.631 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.439%
European (non-Finnish) · 5,177/1,179,916 alleles
Filtering AF
0.429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.425%
Overall
0.35%
5,647/1,613,630 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.439% | 228 |
| Remaining individualsnot grpmax-eligible | 0.317% | 316 |
| Admixed American | 0.128% | 779 |
| South Asian | 0.102% | 979 |
| Finnishnot grpmax-eligible | 0.0723% | 1,384 |
| African / African-American | 0.0693% | 1,443 |
| Middle Eastern | 0.066% | 1,516 |
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.Asn450=
- Coding
- c.1350C>T
- MANE Select
- NM_001794
- dbSNP
- rs78259850
- Type
- single nucleotide variant
- Location
- chr20:61910583 (GRCh38)
- Gene constraint
- LOEUF 0.533 · pLI 0.54 (gnomAD)
- Structure
- AlphaFold pLDDT 79.02
- Residue 450
- the cadherin 3 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.Ile691= 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-asn450 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown