CDH3 p.Ser115=
c.345T>C · rs138829996 · VCV285916
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.3%, afr)
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 -2.1 | GERP 2.2 |
| Overall | ||
| CADD | 8.159 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.3%
African / African-American · 225/75,044 alleles
Filtering AF
0.268%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.255%
Overall
0.0149%
241/1,614,170 alleles · rare
exomes 116/1,461,856 · genomes 125/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.3% | 334 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| Admixed American | 0.005% | 20,007 |
| South Asian | 0.0011% | 91,090 |
| European (non-Finnish) | 0.000169% | 590,002 |
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.Ser115=
- Coding
- c.345T>C
- MANE Select
- NM_001793
- dbSNP
- rs138829996
- Type
- single nucleotide variant
- Location
- chr16:68678232 (GRCh38)
- Gene constraint
- LOEUF 0.823 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.71 · 19 PDB
- Residue 115
- a β-strand; the cadherin 1 domain
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-ser115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown