CDH15 p.Ala37=
c.111G>A · rs373216025 · VCV3025587
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.1%, 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 -5.1 | GERP -2.5 |
| Overall | ||
| CADD | 0.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.1%
European (non-Finnish) · 1,180/1,179,880 alleles
Filtering AF
0.0952%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0933%
Overall
0.078%
1,258/1,613,368 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.1% | 1,000 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,231 |
| Finnishnot grpmax-eligible | 0.0394% | 2,541 |
| South Asian | 0.0165% | 6,072 |
| African / African-American | 0.0107% | 9,368 |
| East Asian | 0.00446% | 22,446 |
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
- CDH15
- Protein
- p.Ala37=
- Coding
- c.111G>A
- MANE Select
- NM_004933
- dbSNP
- rs373216025
- Type
- single nucleotide variant
- Location
- chr16:89179484 (GRCh38)
- Gene constraint
- LOEUF 1.41 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.70
Similar variants
- CDH15 p.Ala37Ser Benign ★★ same residue
- CDH15 p.Ala37Val Uncertain significance ★ ⚠ same residue
- CDH3 p.Thr37Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- CDH3 p.Thr37= Likely benign ★ 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
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/cdh15-p-ala37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown