CDK13 p.Pro952fs
c.2854_2858del · VCV3721620
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 10 of 14 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.3, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDK13
- Protein
- p.Pro952fs
- Coding
- c.2854_2858del
- MANE Select
- NM_003718
- Type
- Deletion
- Location
- chr7:40078075 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
- Residue 952
- the protein kinase domain
Similar variants
- CDK13 p.Pro952Leu Likely benign ★ same residue
- CDK13 p.Leu61fs Pathogenic/Likely pathogenic ★★ same type
- CDK13 p.Ser1048_Asp1052delinsTyr Uncertain significance ★★ same type
- CDK13 p.Ser662del Uncertain significance ★★ same type
- CDK13 p.Ala561fs Pathogenic ★ same type
- CDK13 p.Arg110fs Likely pathogenic ★ same type
- CDK13 p.Arg301fs Pathogenic ★ same type
- CDK13 p.Arg396fs 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-pro952fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown