CDK10 p.Glu331=
c.993G>A · VCV4822991
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.5e-05%, 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 1.4 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 7.921 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,176,752 alleles
Overall
6.24e-05%
1/1,603,780 alleles · very rare
exomes 1/1,451,440 · genomes 0/152,340 · joint denominator
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
- CDK10
- Protein
- p.Glu331=
- Coding
- c.993G>A
- MANE Select
- NM_052988
- Type
- single nucleotide variant
- Location
- chr16:89695602 (GRCh38)
- Gene constraint
- LOEUF 1.344 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.27
Similar variants
- CDK10 c.608+1G>A Pathogenic ★★ same type
- CDK10 c.609-1G>A Pathogenic/Likely pathogenic ★★ same type
- CDK10 c.87+5G>A Pathogenic/Likely pathogenic ★★ same type
- CDK10 p.Cys8Ter Pathogenic/Likely pathogenic ★★ same type
- CDK10 p.Arg205Gln Uncertain significance ★★ ⚠ same type
- CDK10 p.Arg345Gln Uncertain significance ★★ ⚠ same type
- CDK10 p.Arg57Gln Uncertain significance ★★ ⚠ same type
- CDK10 p.Arg57Trp 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/cdk10-p-glu331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown