CDK10 p.Phe158=
c.474C>T · rs1233106178 · VCV3047147
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, afr)
Conditions
1
CDK10-related disorder
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 1.4 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 12.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
African / African-American · 1/73,272 alleles
Filtering AF
0.000547%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000432%
Overall
0.000816%
13/1,592,388 alleles · very rare
exomes 11/1,440,196 · genomes 2/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00136% | 73,272 |
| European (non-Finnish) | 0.00103% | 97,447 |
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.Phe158=
- Coding
- c.474C>T
- MANE Select
- NM_052988
- dbSNP
- rs1233106178
- Type
- single nucleotide variant
- Location
- chr16:89692505 (GRCh38)
- Gene constraint
- LOEUF 1.344 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.27
- Residue 158
- the protein kinase domain
Disease context
CDK10-related disorder
Similar variants
- CDK10 c.417+5G>A Likely benign same condition
- CDK10 c.609-7T>G Likely benign same condition
- CDK10 c.*82G>A Likely benign same condition
- CDK10 c.*90G>A Likely benign same condition
- CDK10 p.Phe182= Likely benign same condition
- CDK10 p.Ter361= Likely benign same condition
- CDK10 c.608+1G>A Pathogenic ★★ same type
- CDK10 c.609-1G>A Pathogenic/Likely pathogenic ★★ 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-phe158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown