DAPK2 p.Pro287=
c.861G>A · rs149186606 · VCV788128
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.34%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.37 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.21 | gain · loss 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.1 |
| Overall | ||
| CADD | 0.077 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.34%
South Asian · 3,037/91,064 alleles
Filtering AF
3.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.2%
Overall
0.201%
3,240/1,614,012 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.34% | 30 |
| Remaining individualsnot grpmax-eligible | 0.213% | 470 |
| Middle Eastern | 0.0826% | 1,210 |
| African / African-American | 0.0107% | 9,379 |
| East Asian | 0.00891% | 11,218 |
| Admixed American | 0.00666% | 15,005 |
| European (non-Finnish) | 0.00415% | 24,082 |
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
- DAPK2
- Protein
- p.Pro287=
- Coding
- c.861G>A
- MANE Select
- NM_014326
- dbSNP
- rs149186606
- Type
- single nucleotide variant
- Location
- chr15:63912195 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.41 · 11 PDB
- Residue 287
- the 'calmodulin-binding' region
Similar variants
- DAPK2 c.632+8G>T Benign/Likely benign ★★ same type
- DAPK2 p.Arg60= Likely benign ★★ same type
- DAPK2 p.Arg60Gln Likely benign ★★ same type
- DAPK2 p.Arg68Gln Benign/Likely benign ★★ ⚠ same type
- DAPK2 p.Thr270= Benign ★★ same type
- DAPK2 p.Ala126Val Uncertain significance ★ ⚠ same type
- DAPK2 p.Ala175Pro Uncertain significance ★ ⚠ same type
- DAPK2 p.Ala175Val 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/dapk2-p-pro287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown