CDK10 p.Val190=
c.570C>T · rs779845266 · VCV2647127
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0661%, mid)
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 -0.43 | GERP -3.4, phastCons 0.069 |
| Overall | ||
| CADD | 2.221 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0661%
Middle Eastern · 4/6,056 alleles
Filtering AF
0.0226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.00031%
5/1,614,158 alleles · ultra-rare
exomes 5/1,461,834 · genomes 0/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0661% | 1,514 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
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.Val190=
- Coding
- c.570C>T
- MANE Select
- NM_052988
- dbSNP
- rs779845266
- Type
- single nucleotide variant
- Location
- chr16:89693429 (GRCh38)
- Gene constraint
- LOEUF 1.344 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.27
- Residue 190
- the protein kinase domain
Similar variants
- 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
- CDK10 p.Arg57Trp 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-val190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown