CDK19 p.Leu131=
c.391T>C · VCV3349669
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0677%, eas)
Conditions
1
CDK19-related disorder
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 6.1 | GERP -0.71, phastCons 1 |
| Overall | ||
| CADD | 9.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0677%
East Asian · 30/44,294 alleles
Filtering AF
0.0487%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0422%
Overall
0.00194%
31/1,595,810 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0677% | 1,476 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,730 |
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
- CDK19
- Protein
- p.Leu131=
- Coding
- c.391T>C
- MANE Select
- NM_015076
- Type
- single nucleotide variant
- Location
- chr6:110667499 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 77.97
- Residue 131
- the protein kinase domain
Disease context
CDK19-related disorder
Similar variants
- CDK19 p.Pro341Ser Uncertain significance ⚠ same condition
- CDK19 p.Leu442= Likely benign same condition
- CDK19 c.316-10dup Likely benign same condition
- CDK19 p.Thr196Ala Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDK19 p.Lys47Asn Uncertain significance ★★ ⚠ same type
- CDK19 p.Pro495Thr Uncertain significance ★★ ⚠ same type
- CDK19 p.Trp198Cys Uncertain significance ★★ ⚠ same type
- CDK19 p.Arg200Gln 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/cdk19-p-leu131 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown