CDK13 p.Ala557=
c.1671C>T · rs139716678 · VCV709785
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.228%, afr)
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 -0.9 | GERP -3.6 |
| Overall | ||
| CADD | 6.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.228%
African / African-American · 171/75,010 alleles
Filtering AF
0.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.189%
Overall
0.0273%
440/1,614,060 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.228% | 439 |
| Middle Eastern | 0.099% | 1,010 |
| Admixed American | 0.0483% | 2,069 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,718 |
| European (non-Finnish) | 0.0179% | 5,592 |
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.Ala557=
- Coding
- c.1671C>T
- MANE Select
- NM_003718
- dbSNP
- rs139716678
- Type
- single nucleotide variant
- Location
- chr7:39988058 (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.Ala557Val Uncertain significance ★ ⚠ 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-ala557 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown