DAPK1 p.Pro1133=
c.3399C>T · rs559897885 · VCV2659291
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, amr)
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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.142 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
Admixed American · 8/59,948 alleles
Filtering AF
0.00662%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00483%
Overall
0.00335%
54/1,613,284 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0133% | 7,493 |
| African / African-American | 0.00668% | 14,966 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,822 |
| European (non-Finnish) | 0.00314% | 31,880 |
| East Asian | 0.00223% | 44,834 |
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
- DAPK1
- Protein
- p.Pro1133=
- Coding
- c.3399C>T
- MANE Select
- NM_004938
- dbSNP
- rs559897885
- Type
- single nucleotide variant
- Location
- chr9:87706470 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.74 · 79 PDB
Similar variants
- DAPK1 c.1131+9C>T Benign ★★ same type
- DAPK1 c.1231-6C>G Benign ★★ same type
- DAPK1 c.285-6T>C Benign ★★ same type
- DAPK1 c.919-10T>A Benign ★★ same type
- DAPK1 c.919-9A>T Likely benign ★★ same type
- DAPK1 p.Asn1347= Benign ★★ same type
- DAPK1 p.Gln122= Benign ★★ same type
- DAPK1 p.Gly1348Val Likely benign ★★ 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/dapk1-p-pro1133 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown