CDHR2 p.Pro286=
c.858C>T · VCV4224077
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00709%, 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 -13 | GERP -2.7 |
| Overall | ||
| CADD | 0.039 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00709%
East Asian · 3/42,320 alleles
Filtering AF
0.00188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00102%
Overall
0.000635%
10/1,574,928 alleles · very rare
exomes 8/1,422,782 · genomes 2/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00709% | 14,107 |
| African / African-American | 0.00271% | 36,906 |
| Admixed American | 0.00186% | 53,908 |
| European (non-Finnish) | 0.000345% | 289,948 |
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
- CDHR2
- Protein
- p.Pro286=
- Coding
- c.858C>T
- MANE Select
- NM_017675
- Type
- single nucleotide variant
- Location
- chr5:176575737 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.84 · 2 PDB
- Residue 286
- the cadherin 3 domain
Similar variants
- CDHR2 p.Ala1162Thr Uncertain significance ★ ⚠ same type
- CDHR2 p.Ala121Thr Uncertain significance ★ ⚠ same type
- CDHR2 p.Ala13Val Uncertain significance ★ ⚠ same type
- CDHR2 p.Ala415Thr Uncertain significance ★ ⚠ same type
- CDHR2 p.Ala423Thr Uncertain significance ★ ⚠ same type
- CDHR2 p.Ala512Thr Uncertain significance ★ ⚠ same type
- CDHR2 p.Ala652Thr Uncertain significance ★ ⚠ same type
- CDHR2 p.Ala656Thr Uncertain significance ★ ⚠ 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/cdhr2-p-pro286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown