CDK11A p.Asp683=
c.2049C>T · rs376339378 · VCV2638052
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.225%, nfe)
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 -0.026 | phastCons 0.31 |
| Overall | ||
| CADD | 5.142 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.225%
European (non-Finnish) · 2,580/1,145,866 alleles
Filtering AF
0.218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.215%
Overall
0.178%
2,711/1,524,866 alleles · rare
exomes 2,582/1,397,406 · genomes 129/127,460 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.225% | 444 |
| Remaining individualsnot grpmax-eligible | 0.123% | 815 |
| Admixed American | 0.0419% | 2,387 |
| African / African-American | 0.036% | 2,780 |
| Finnishnot grpmax-eligible | 0.0274% | 3,654 |
| Middle Eastern | 0.0184% | 5,428 |
| South Asian | 0.00121% | 82,598 |
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
- CDK11A
- Protein
- p.Asp683=
- Coding
- c.2049C>T
- MANE Select
- NM_024011
- dbSNP
- rs376339378
- Type
- single nucleotide variant
- Location
- chr1:1703487 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.94
Similar variants
- CDK11A p.Asp683Asn Likely benign ★ same residue
- CDK11A p.Arg247Gln Uncertain significance ★★ ⚠ same type
- CDK11A p.Ala196Val Uncertain significance ★ ⚠ same type
- CDK11A p.Ala558Thr Uncertain significance ★ ⚠ same type
- CDK11A p.Ala590Thr Uncertain significance ★ same type
- CDK11A p.Ala597Val Uncertain significance ★ ⚠ same type
- CDK11A p.Arg131Cys Uncertain significance ★ ⚠ same type
- CDK11A p.Arg132Gln 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/cdk11a-p-asp683 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown