CDK10 p.Phe182=
c.546C>T · rs376029099 · VCV3053513
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, 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 | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.6 | GERP -3.4 |
| Overall | ||
| CADD | 2.875 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,924 alleles
Filtering AF
0.00623%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00198%
32/1,614,036 alleles · ultra-rare
exomes 28/1,461,838 · genomes 4/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,325 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| East Asian | 0.00223% | 44,888 |
| Admixed American | 0.00167% | 60,008 |
| European (non-Finnish) | 0.00153% | 65,558 |
| South Asian | 0.0011% | 91,080 |
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.Phe182=
- Coding
- c.546C>T
- MANE Select
- NM_052988
- dbSNP
- rs376029099
- Type
- single nucleotide variant
- Location
- chr16:89693405 (GRCh38)
- Gene constraint
- LOEUF 1.344 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.27
- Residue 182
- the protein kinase domain
Disease context
CDK10-related disorder
Similar variants
- CDK10 p.Phe182Leu Uncertain significance ★ ⚠ same residue
- 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.Phe158= Likely benign same condition
- CDK10 p.Ter361= Likely benign same condition
- CDK10 c.608+1G>A 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-phe182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown