CDK16 p.Leu243=
c.727C>T · rs145117961 · VCV93666
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.283%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.93 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -0.28, phastCons 0.98 |
| Overall | ||
| CADD | 11.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.283%
European (non-Finnish) · 2,514/887,063 alleles
Filtering AF
0.274%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.27%
Overall
0.223%
2,682/1,201,151 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.283% | 353 |
| Remaining individualsnot grpmax-eligible | 0.226% | 443 |
| Admixed American | 0.0589% | 1,697 |
| African / African-American | 0.0544% | 1,838 |
| Middle Eastern | 0.0231% | 4,329 |
| Finnishnot grpmax-eligible | 0.00214% | 46,629 |
| South Asian | 0.00177% | 56,584 |
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
- CDK16
- Protein
- p.Leu243=
- Coding
- c.727C>T
- MANE Select
- NM_006201
- dbSNP
- rs145117961
- Type
- single nucleotide variant
- Location
- chrX:47225864 (GRCh38)
- Structure
- AlphaFold pLDDT 72.92 · 3 PDB
- Residue 243
- the protein kinase domain
Similar variants
- CDK16 c.1376-10C>T Benign ★★ same type
- CDK16 c.793-5C>T Benign ★★ same type
- CDK16 c.-6-279C>T Benign ★★ same type
- CDK16 p.Gly347= Likely benign ★★ same type
- CDK16 p.Leu15Phe Likely pathogenic ★ ⚠ same type
- CDK16 c.-5T>G Uncertain significance ★ same type
- CDK16 c.-6-245C>T Uncertain significance ★ same type
- CDK16 c.-6-264A>G 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/cdk16-p-leu243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown