CDK12 p.Ala407=
c.1221A>T · VCV4224307
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 2.3 | GERP -0.13, phastCons 1 |
| Overall | ||
| CADD | 8.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,826 alleles
Overall
0.000657%
1/152,162 alleles · very 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.Ala407=
- Coding
- c.1221A>T
- MANE Select
- NM_016507
- Type
- single nucleotide variant
- Location
- chr17:39471053 (GRCh38)
- Gene constraint
- LOEUF 0.21 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.39 · 39 PDB
- Residue 407
- the 'disordered' region
Similar variants
- 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
- CDK12 c.3308-26A>G Likely 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-ala407 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown