CDK12 p.Ile989=
c.2967T>C · VCV3830696
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, 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 3.5 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 9.557 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,058 alleles
Overall
6.84e-05%
1/1,461,634 alleles · ultra-rare
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
- CDK12
- Protein
- p.Ile989=
- Coding
- c.2967T>C
- MANE Select
- NM_016507
- Type
- single nucleotide variant
- Location
- chr17:39519959 (GRCh38)
- Gene constraint
- LOEUF 0.21 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.39 · 39 PDB
- Residue 989
- the protein kinase domain
Similar variants
- CDK12 p.Ile989Val Uncertain significance ★ ⚠ same residue
- CDK12 c.2108+56T>A Benign/Likely benign ★★ same type
- CDK12 c.2666+17A>C Benign ★★ same type
- CDK12 c.2769-74G>A Benign ★★ same type
- CDK12 c.2846+157G>T Benign ★★ same type
- CDK12 c.2963+111T>A Benign ★★ same type
- CDK12 c.2963+133G>A Benign ★★ same type
- CDK12 c.3308-116C>T Benign ★★ 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/cdk12-p-ile989 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown