CDK10 p.Pro4=
c.12A>T · rs192221267 · VCV2570958
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.614%, 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 -1.8 | GERP -2.2 |
| Overall | ||
| CADD | 2.168 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.614%
European (non-Finnish) · 7,223/1,176,298 alleles
Filtering AF
0.602%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.597%
Overall
0.533%
8,565/1,605,928 alleles · rare
exomes 7,908/1,453,850 · genomes 657/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.614% | 163 |
| Ashkenazi Jewishnot grpmax-eligible | 0.564% | 177 |
| Finnishnot grpmax-eligible | 0.561% | 178 |
| Remaining individualsnot grpmax-eligible | 0.528% | 189 |
| Middle Eastern | 0.431% | 232 |
| Admixed American | 0.361% | 277 |
| South Asian | 0.227% | 441 |
| African / African-American | 0.0682% | 1,466 |
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
- CDK10
- Protein
- p.Pro4=
- Coding
- c.12A>T
- MANE Select
- NM_052988
- dbSNP
- rs192221267
- Type
- single nucleotide variant
- Location
- chr16:89686722 (GRCh38)
- Gene constraint
- LOEUF 1.344 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.27
Similar variants
- CDK10 p.Pro4Ala Likely benign ★ same residue
- CDK10 c.608+1G>A Pathogenic ★★ same type
- CDK10 c.609-1G>A Pathogenic/Likely pathogenic ★★ same type
- CDK10 c.87+5G>A Pathogenic/Likely pathogenic ★★ same type
- CDK10 p.Cys8Ter Pathogenic/Likely pathogenic ★★ same type
- CDK10 p.Arg205Gln Uncertain significance ★★ ⚠ same type
- CDK10 p.Arg345Gln Uncertain significance ★★ ⚠ same type
- CDK10 p.Arg57Gln 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/cdk10-p-pro4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown