CDK13 p.235HS[1]
c.703CACAGC[1] · rs1309927319 · VCV2868023
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00594%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.3 | GERP 0.57, phastCons 1 |
| Overall | ||
| CADD | 17.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00594%
African / African-American · 4/67,300 alleles
Filtering AF
0.00291%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00258%
Overall
0.00322%
47/1,460,102 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00594% | 16,825 |
| European (non-Finnish) | 0.00386% | 25,927 |
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.235HS[1]
- Coding
- c.703CACAGC[1]
- MANE Select
- NM_003718
- dbSNP
- rs1309927319
- Type
- Microsatellite
- Location
- chr7:39951342 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
Similar variants
- CDK13 p.Ile708del Likely pathogenic ★★ same type
- CDK13 p.Leu1418del Uncertain significance ★★ same type
- CDK13 c.3029+33_3029+45del Likely benign ★★ same type
- CDK13 p.Ala76_Ser77insAla Benign/Likely benign ★★ same type
- CDK13 p.Thr1143fs Likely pathogenic ★ same type
- CDK13 p.Gly256_Arg257insGly Uncertain significance ★ same type
- CDK13 p.Gly380_Asp381insGly Uncertain significance ★ same type
- CDK13 p.Leu159_Gly160insLeu Uncertain significance ★ 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-235hs-1 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown