CDK13 p.Leu355=
c.1063C>T · rs758235150 · VCV2987311
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0204%, mid)
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 0.36 | GERP 0.62, phastCons 0.77 |
| Overall | ||
| CADD | 8.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0204%
Middle Eastern · 1/4,908 alleles
Filtering AF
0.00207%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00177%
Overall
0.00306%
45/1,470,052 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0204% | 4,908 |
| Remaining individualsnot grpmax-eligible | 0.0107% | 9,376 |
| South Asian | 0.00418% | 23,927 |
| African / African-American | 0.00292% | 34,233 |
| European (non-Finnish) | 0.00286% | 35,010 |
| Admixed American | 0.00254% | 39,300 |
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.Leu355=
- Coding
- c.1063C>T
- MANE Select
- NM_003718
- dbSNP
- rs758235150
- Type
- single nucleotide variant
- Location
- chr7:39951704 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
- Residue 355
- the 'disordered' region
Similar variants
- CDK13 p.Leu355Gln Benign/Likely benign ★★ 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-leu355 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown