CDK19 p.Thr419=
c.1257C>T · rs148540500 · VCV2656845
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0801%, afr)
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 · G>C here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.5 | GERP -5.1 |
| Overall | ||
| CADD | 0.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0801%
African / African-American · 60/74,910 alleles
Filtering AF
0.0638%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.058%
Overall
0.00601%
97/1,613,270 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0801% | 1,249 |
| East Asian | 0.0134% | 7,481 |
| Admixed American | 0.01% | 10,000 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,609 |
| European (non-Finnish) | 0.00161% | 62,105 |
| Finnishnot grpmax-eligible | 0.00157% | 63,804 |
| South Asian | 0.0011% | 91,046 |
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.Thr419=
- Coding
- c.1257C>T
- MANE Select
- NM_015076
- dbSNP
- rs148540500
- Type
- single nucleotide variant
- Location
- chr6:110621224 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 77.97
- Residue 419
- the 'disordered' region
Similar variants
- 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
- CDK19 p.Arg200Trp Likely pathogenic ★ same type
- CDK19 c.1111-4A>G Uncertain significance ★ same type
- CDK19 c.456+5G>A 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/cdk19-p-thr419 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown