CDH12 p.Pro190=
c.570G>A · rs545844887 · VCV719673
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0388%, 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 -9.4 | GERP -3.9 |
| Overall | ||
| CADD | 1.886 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0388%
African / African-American · 29/74,674 alleles
Filtering AF
0.0278%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0239%
Overall
0.0028%
45/1,608,908 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0388% | 2,575 |
| East Asian | 0.00447% | 22,354 |
| Admixed American | 0.00335% | 29,826 |
| South Asian | 0.00331% | 30,249 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,212 |
| European (non-Finnish) | 0.00068% | 147,075 |
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.Pro190=
- Coding
- c.570G>A
- MANE Select
- NM_004061
- dbSNP
- rs545844887
- Type
- single nucleotide variant
- Location
- chr5:21854747 (GRCh38)
- Gene constraint
- LOEUF 0.668 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.19
- Residue 190
- 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-pro190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown