CDH8 p.Pro510=
c.1530C>T · rs200934735 · VCV2646584
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0285%, amr)
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 3.4 | GERP -0.8, phastCons 1 |
| Overall | ||
| CADD | 15.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0285%
Admixed American · 17/59,662 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0148%
Overall
0.0064%
103/1,610,578 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0285% | 3,510 |
| Middle Eastern | 0.0166% | 6,042 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,792 |
| European (non-Finnish) | 0.00586% | 17,068 |
| South Asian | 0.0044% | 22,738 |
| African / African-American | 0.00402% | 24,896 |
| East Asian | 0.00223% | 44,800 |
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
- CDH8
- Protein
- p.Pro510=
- Coding
- c.1530C>T
- MANE Select
- NM_001796
- dbSNP
- rs200934735
- Type
- single nucleotide variant
- Location
- chr16:61727100 (GRCh38)
- Gene constraint
- LOEUF 0.369 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.26
- Residue 510
- the cadherin 5 domain
Similar variants
- CDH8 p.Arg666Cys Likely benign ★★ ⚠ same type
- CDH8 p.Ile429= Benign ★★ same type
- CDH8 p.Tyr667= Benign/Likely benign ★★ same type
- CDH8 p.Ala30Thr Uncertain significance ★ ⚠ same type
- CDH8 p.Ala332Thr Uncertain significance ★ ⚠ same type
- CDH8 p.Ala443Thr Uncertain significance ★ ⚠ same type
- CDH8 p.Ala502Gly Uncertain significance ★ ⚠ same type
- CDH8 p.Ala629Val 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/cdh8-p-pro510 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown