DAPK2 p.Phe129Leu
c.385T>C · VCV4237593
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9898 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9898 | likely pathogenic |
|---|---|---|
| REVEL | 0.48 | indeterminate |
| SaProt | LLR -5.92 | tolerated |
| ⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 0.88, phastCons 1 |
| Overall | ||
| CADD | 28.8 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DAPK2
- Protein
- p.Phe129Leu
- Coding
- c.385T>C
- MANE Select
- NM_014326
- Type
- single nucleotide variant
- Location
- chr15:63971491 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.41 · 11 PDB
- Residue 129
- the protein kinase domain; an α-helix
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-phe129leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown