CDK19 p.Leu442=
c.1326A>G · VCV3357327
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -9.3 | GERP -5.4 |
| Overall | ||
| CADD | 0.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,950 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000186%
3/1,614,094 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,475 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
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.Leu442=
- Coding
- c.1326A>G
- MANE Select
- NM_015076
- Type
- single nucleotide variant
- Location
- chr6:110621155 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 77.97
- Residue 442
- the 'disordered' region
Disease context
CDK19-related disorder
Similar variants
- CDK19 p.Pro341Ser Uncertain significance ⚠ same condition
- CDK19 p.Leu131= 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-leu442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown