CDH3 p.Asp710=
c.2130C>T · rs977506327 · VCV1140193
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00509%, amr)
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 3.3 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 11.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00509%
Admixed American · 3/58,982 alleles
Filtering AF
0.00135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000674%
Overall
0.000412%
6/1,457,162 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00509% | 19,661 |
| European (non-Finnish) | 0.000255% | 392,656 |
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
- CDH3
- Protein
- p.Asp710=
- Coding
- c.2130C>T
- MANE Select
- NM_004933 · reported on NM_001793
- dbSNP
- rs977506327
- Type
- single nucleotide variant
- Location
- chr16:68695382 (GRCh38)
- Structure
- AlphaFold pLDDT 78.70
Similar variants
- CDH3 c.1796-2A>G Pathogenic ★★ same type
- CDH3 c.691+1G>A Pathogenic/Likely pathogenic ★★ same type
- CDH3 p.Arg103Ter Pathogenic ★★ same type
- CDH3 p.Arg221Ter Pathogenic ★★ same type
- CDH3 p.Arg503His Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDH3 p.Gln299Ter Pathogenic ★★ same type
- CDH3 p.Glu708Ter Likely pathogenic ★★ same type
- CDH3 p.Trp362Ter 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/cdh3-p-asp710 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown