CDK12 p.His1413=
c.4239C>T · VCV3489397
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
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 0.61 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 5.841 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,820 alleles
Filtering AF
0.00727%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00515%
Overall
0.000688%
11/1,599,796 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,403 |
| South Asian | 0.00225% | 44,487 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,774 |
| European (non-Finnish) | 8.52e-05% | 1,174,133 |
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.His1413=
- Coding
- c.4239C>T
- MANE Select
- NM_016507
- Type
- single nucleotide variant
- Location
- chr17:39531082 (GRCh38)
- Gene constraint
- LOEUF 0.21 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.39 · 39 PDB
Similar variants
- CDK12 p.His1413Gln 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-his1413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown