CDK13 p.Arg751Ter
c.2251C>T · rs1295790880 · VCV1028145
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 14 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.53 | GERP -0.96, phastCons 0.99 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,552 |
| Finnishnot grpmax-eligible | 0.00156% | 63,968 |
| European (non-Finnish)grpmax | 8.5e-05% | 1,176,354 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Arg751Ter
- Coding
- c.2251C>T
- MANE Select
- NM_003718
- dbSNP
- rs1295790880
- Type
- single nucleotide variant
- Location
- chr7:40001929 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
- Residue 751
- the protein kinase domain; a UniProt-annotated variant site (in chdfidd); an α-helix
Disease context
congenital heart defects, dysmorphic facial features, and intellectual developmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor CDK13-related developmental delay-intellectual disability-facial dysmorphism-congenital heart defects syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Childhood, Infancy
Similar variants
- CDK13 p.Arg751Gln Pathogenic/Likely pathogenic ★★ same residue
- CDK13 p.Ala732Thr Likely pathogenic ★★ same condition
- CDK13 p.Arg737Cys Pathogenic ★★ same condition
- CDK13 p.Arg860Gln Pathogenic/Likely pathogenic ★★ same condition
- CDK13 p.Arg880Cys Pathogenic/Likely pathogenic ★★ same condition
- CDK13 p.Asn842Asp Pathogenic/Likely pathogenic ★★ same condition
- CDK13 p.Asn842Ser Pathogenic/Likely pathogenic ★★ same condition
- CDK13 p.Asp855Asn Likely pathogenic ★★ same condition
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-arg751ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown