DAPK1 p.Ser403=
c.1209G>A · rs17053276 · VCV780817
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.6%, afr) — too common for a highly-penetrant pathogenic allele
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>T here scores Δ0.46 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.73 | GERP -3.6, phastCons 0.95 |
| Overall | ||
| CADD | 10.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.6%
African / African-American · 4,200/74,954 alleles
Filtering AF
5.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4%
Overall
0.315%
5,077/1,611,578 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.6% | 18 |
| Admixed American | 0.597% | 168 |
| Remaining individualsnot grpmax-eligible | 0.457% | 219 |
| Middle Eastern | 0.297% | 336 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,932 |
| European (non-Finnish) | 0.0172% | 5,802 |
| South Asian | 0.00549% | 18,203 |
| East Asian | 0.00446% | 22,435 |
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.Ser403=
- Coding
- c.1209G>A
- MANE Select
- NM_004938
- dbSNP
- rs17053276
- Type
- single nucleotide variant
- Location
- chr9:87646538 (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-ser403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown