CDH15 p.Asp88=
c.264T>C · rs59865771 · VCV128651
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 78.3%, eas) — too common for a highly-penetrant pathogenic allele
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 -4 | GERP -3.4 |
| Overall | ||
| CADD | 3.819 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
78.3%
East Asian · 34,924/44,584 alleles
Filtering AF
77.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 77.4%
Overall
28.9%
464,239/1,608,416 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 78.3% | 1 |
| South Asian | 45.7% | 2 |
| Finnishnot grpmax-eligible | 34.9% | 3 |
| Middle Eastern | 33.1% | 3 |
| Remaining individualsnot grpmax-eligible | 31.4% | 3 |
| Admixed American | 30.3% | 3 |
| African / African-American | 29.9% | 3 |
| European (non-Finnish) | 25.2% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 25.2% | 4 |
| Amishnot grpmax-eligible | 21.1% | 5 |
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.Asp88=
- Coding
- c.264T>C
- MANE Select
- NM_004933
- dbSNP
- rs59865771
- Type
- single nucleotide variant
- Location
- chr16:89180262 (GRCh38)
- Gene constraint
- LOEUF 1.41 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.70
- Residue 88
- the cadherin 1 domain
Similar variants
- CDH15 p.Asp88Asn 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
- CDH3 p.Gln299Ter Pathogenic ★★ same type
- CDH3 p.Glu708Ter 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/cdh15-p-asp88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown