DAPK1 p.Asp11=
c.33T>C · rs200015695 · VCV793439
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0713%, eas)
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 -0.17 | GERP -1.7, phastCons 0.67 |
| Overall | ||
| CADD | 10.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0713%
East Asian · 32/44,862 alleles
Filtering AF
0.0519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0452%
Overall
0.00254%
41/1,613,964 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0713% | 1,402 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| European (non-Finnish) | 8.47e-05% | 1,179,972 |
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.Asp11=
- Coding
- c.33T>C
- MANE Select
- NM_004938
- dbSNP
- rs200015695
- Type
- single nucleotide variant
- Location
- chr9:87499110 (GRCh38)
- Gene constraint
- LOEUF 0.383 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.74 · 79 PDB
- Residue 11
- an α-helix
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-asp11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown