CDK13 p.Ser184=
c.552C>T · rs1293078589 · VCV798668
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0068%, 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 2.5 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 13.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0068%
European (non-Finnish) · 68/1,000,292 alleles
Filtering AF
0.00545%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00498%
Overall
0.00568%
71/1,251,096 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0068% | 14,710 |
| Admixed American | 0.00424% | 23,606 |
| Remaining individualsnot grpmax-eligible | 0.00215% | 46,520 |
| African / African-American | 0.00156% | 64,252 |
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.Ser184=
- Coding
- c.552C>T
- MANE Select
- NM_003718
- dbSNP
- rs1293078589
- Type
- single nucleotide variant
- Location
- chr7:39951193 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
- Residue 184
- the 'disordered' region
Similar variants
- CDK13 p.Ser184Phe Uncertain significance ★ ⚠ same residue
- 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
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-ser184 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown