CDH3 p.Ala34=
c.102T>C · rs1474198781 · VCV1555179
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0122%, eas)
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 -0.48 | GERP -1.1, phastCons 0.082 |
| Overall | ||
| CADD | 16.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0122%
East Asian · 5/40,900 alleles
Filtering AF
0.00479%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.00043%
6/1,394,068 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0122% | 8,180 |
| South Asian | 0.00119% | 83,930 |
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.Ala34=
- Coding
- c.102T>C
- MANE Select
- NM_004933 · reported on NM_001793
- dbSNP
- rs1474198781
- Type
- single nucleotide variant
- Location
- chr16:68645692 (GRCh38)
- Structure
- AlphaFold pLDDT 78.70
Similar variants
- CDH3 p.Ala34Thr Uncertain significance ★★ ⚠ same residue
- CDH3 p.Ala34Val Uncertain significance ★ ⚠ same residue
- CDH15 p.Trp34fs Uncertain significance ★★ same residue
- 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
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-ala34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown