CDH2 p.Gln663=
c.1989G>A · rs772715062 · VCV1783912
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.972%, mid)
Conditions
1
Inborn genetic diseases
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 0.11 | GERP -3.2, phastCons 0.93 |
| Overall | ||
| CADD | 5.124 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.972%
Middle Eastern · 59/6,068 alleles
Filtering AF
0.774%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.702%
Overall
0.00537%
86/1,601,850 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.972% | 103 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,754 |
| African / African-American | 0.00402% | 24,871 |
| Admixed American | 0.00334% | 29,958 |
| South Asian | 0.0022% | 45,375 |
| European (non-Finnish) | 0.00103% | 97,441 |
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
- CDH2
- Protein
- p.Gln663=
- Coding
- c.1989G>A
- MANE Select
- NM_001792
- dbSNP
- rs772715062
- Type
- single nucleotide variant
- Location
- chr18:27985220 (GRCh38)
- Gene constraint
- LOEUF 0.336 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.68
- Residue 663
- the cadherin 5 domain
Similar variants
- CDH2 p.Gln663Glu Uncertain significance ★★ ⚠ same residue
- CDH2 p.Ala21Val Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala294Gly Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala299Thr Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala415Ser Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala418Ser Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala418Thr Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala610Thr Uncertain significance ★★ ⚠ same condition
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/cdh2-p-gln663 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown