CDK9 p.Ala63=
c.189C>A · rs34238383 · VCV3050549
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.545%, amr)
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 0.18 | GERP -2.4, phastCons 0.092 |
| Overall | ||
| CADD | 10.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.545%
Admixed American · 327/60,008 alleles
Filtering AF
0.499%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.494%
Overall
0.425%
6,850/1,612,634 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.545% | 184 |
| European (non-Finnish) | 0.51% | 196 |
| Remaining individualsnot grpmax-eligible | 0.386% | 259 |
| Ashkenazi Jewishnot grpmax-eligible | 0.145% | 688 |
| Middle Eastern | 0.116% | 865 |
| South Asian | 0.108% | 929 |
| African / African-American | 0.0933% | 1,071 |
| Finnishnot grpmax-eligible | 0.0891% | 1,123 |
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
- CDK9
- Protein
- p.Ala63=
- Coding
- c.189C>A
- MANE Select
- NM_001261
- dbSNP
- rs34238383
- Type
- single nucleotide variant
- Location
- chr9:127787532 (GRCh38)
- Gene constraint
- LOEUF 1.139 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 28 PDB
- Residue 63
- the protein kinase domain; an α-helix
Similar variants
- CDK9 p.Arg225Cys Pathogenic/Likely pathogenic ★★ same type
- CDK9 c.175-7C>T Benign ★★ same type
- CDK9 p.Ala173= Benign/Likely benign ★★ same type
- CDK9 p.Ile292= Likely benign ★★ same type
- CDK9 p.Ala288Thr Uncertain significance ★ ⚠ same type
- CDK9 p.Ala36Gly Uncertain significance ★ ⚠ same type
- CDK9 p.Arg273Trp Uncertain significance ★ ⚠ same type
- CDK9 p.Arg303Gly 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/cdk9-p-ala63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown