CDH12 p.Thr260=
c.780C>T · rs76592602 · VCV786529
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.7%, afr)
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 -4.7 | GERP -3.7 |
| Overall | ||
| CADD | 2.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.7%
African / African-American · 2,019/74,912 alleles
Filtering AF
2.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.56%
Overall
0.156%
2,513/1,612,812 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.7% | 37 |
| Remaining individualsnot grpmax-eligible | 0.221% | 453 |
| Admixed American | 0.207% | 483 |
| Middle Eastern | 0.182% | 550 |
| European (non-Finnish) | 0.0178% | 5,616 |
| South Asian | 0.0121% | 8,259 |
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
- CDH12
- Protein
- p.Thr260=
- Coding
- c.780C>T
- MANE Select
- NM_004061
- dbSNP
- rs76592602
- Type
- single nucleotide variant
- Location
- chr5:21842195 (GRCh38)
- Gene constraint
- LOEUF 0.668 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.19
- Residue 260
- the cadherin 2 domain
Similar variants
- CDH12 c.1003-3C>T Benign ★★ same type
- CDH12 p.Asp780= Likely benign ★★ same type
- CDH12 p.Gln60= Benign ★★ same type
- CDH12 p.Glu349Asp Benign ★★ ⚠ same type
- CDH12 p.Glu34Gln Benign ★★ same type
- CDH12 p.Ile475Thr Benign ★★ ⚠ same type
- CDH12 p.Ile598= Likely benign ★★ same type
- CDH12 p.Pro213= Benign ★★ 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/cdh12-p-thr260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown