CDK13 p.Ser804=
c.2412A>G · rs768027976 · VCV2918095
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.109%, sas)
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 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 8.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.109%
South Asian · 99/91,048 alleles
Filtering AF
0.0914%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0849%
Overall
0.00849%
137/1,613,028 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.109% | 920 |
| Finnishnot grpmax-eligible | 0.0203% | 4,923 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,806 |
| East Asian | 0.00892% | 11,207 |
| European (non-Finnish) | 0.0011% | 90,711 |
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
- CDK13
- Protein
- p.Ser804=
- Coding
- c.2412A>G
- MANE Select
- NM_003718
- dbSNP
- rs768027976
- Type
- single nucleotide variant
- Location
- chr7:40045894 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
- Residue 804
- the protein kinase domain; an α-helix
Similar variants
- CDK13 p.Ala732Thr Likely pathogenic ★★ same type
- CDK13 p.Arg1025Ter Pathogenic/Likely pathogenic ★★ same type
- CDK13 p.Arg737Cys Pathogenic ★★ same type
- CDK13 p.Arg751Gln Pathogenic/Likely pathogenic ★★ same type
- CDK13 p.Arg860Gln Pathogenic/Likely pathogenic ★★ same type
- CDK13 p.Arg880Cys Pathogenic/Likely pathogenic ★★ same type
- CDK13 p.Asn842Asp Pathogenic/Likely pathogenic ★★ same type
- CDK13 p.Asn842Ser Pathogenic/Likely 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/cdk13-p-ser804 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown