CDK13 p.Thr1271=
c.3813T>C · rs775368819 · VCV2756177
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
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 -0.77 | GERP -3.7, phastCons 0.017 |
| Overall | ||
| CADD | 4.456 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/59,832 alleles
Filtering AF
0.00775%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0058%
Overall
0.000682%
11/1,612,664 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,648 |
| South Asian | 0.0022% | 45,415 |
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.Thr1271=
- Coding
- c.3813T>C
- MANE Select
- NM_003718
- dbSNP
- rs775368819
- Type
- single nucleotide variant
- Location
- chr7:40094254 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59 · 2 PDB
- Residue 1271
- the 'disordered' region
Similar variants
- CDK13 p.Thr1271Ile 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-thr1271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown