CDH12 p.Pro213=
c.639C>G · rs112146213 · VCV790399
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1%, nfe)
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 0.63 | GERP -1.8, phastCons 0.99 |
| Overall | ||
| CADD | 7.777 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1%
European (non-Finnish) · 11,765/1,174,518 alleles
Filtering AF
0.987%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.98%
Overall
0.824%
13,223/1,605,602 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1% | 100 |
| Admixed American | 0.74% | 135 |
| Remaining individualsnot grpmax-eligible | 0.693% | 144 |
| Ashkenazi Jewishnot grpmax-eligible | 0.376% | 266 |
| Finnishnot grpmax-eligible | 0.225% | 444 |
| South Asian | 0.222% | 450 |
| African / African-American | 0.17% | 587 |
| Middle Eastern | 0.117% | 857 |
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.Pro213=
- Coding
- c.639C>G
- MANE Select
- NM_004061
- dbSNP
- rs112146213
- Type
- single nucleotide variant
- Location
- chr5:21854678 (GRCh38)
- Gene constraint
- LOEUF 0.668 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.19
- Residue 213
- the cadherin 2 domain
Similar variants
- CDH12 p.Pro213Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown