CDK13 p.Lys1024=
c.3072G>A · rs2302341 · VCV1281139
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 30.9%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 6.906 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
30.9%
East Asian · 13,840/44,812 alleles
Filtering AF
30.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 30.3%
Overall
9.09%
146,586/1,613,122 alleles · common
exomes 132,795/1,461,494 · genomes 13,791/151,628 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 30.9% | 3 |
| South Asian | 24.9% | 4 |
| Admixed American | 15.7% | 6 |
| Finnishnot grpmax-eligible | 13.9% | 7 |
| Middle Eastern | 13.1% | 8 |
| Remaining individualsnot grpmax-eligible | 10.2% | 10 |
| Ashkenazi Jewishnot grpmax-eligible | 7.58% | 13 |
| European (non-Finnish) | 6.67% | 15 |
| African / African-American | 4.93% | 20 |
| Amishnot grpmax-eligible | 1.65% | 61 |
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.Lys1024=
- Coding
- c.3072G>A
- MANE Select
- NM_003718
- dbSNP
- rs2302341
- Type
- single nucleotide variant
- Location
- chr7:40088168 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
- Residue 1024
- 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-lys1024 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown