DACT2 p.Ala595=
c.1785G>A · rs183650899 · VCV2657141
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.24%, mid)
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 -1.6 |
| Overall | ||
| CADD | 0.068 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.24%
Middle Eastern · 74/5,952 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.932%
Overall
0.364%
5,643/1,551,042 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.24% | 80 |
| Ashkenazi Jewishnot grpmax-eligible | 0.671% | 149 |
| European (non-Finnish) | 0.417% | 240 |
| Remaining individualsnot grpmax-eligible | 0.366% | 273 |
| Admixed American | 0.28% | 357 |
| South Asian | 0.163% | 614 |
| African / African-American | 0.0998% | 1,002 |
| Finnishnot grpmax-eligible | 0.0252% | 3,963 |
| East Asian | 0.00489% | 20,445 |
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
- DACT2
- Protein
- p.Ala595=
- Coding
- c.1785G>A
- MANE Select
- NM_214462
- dbSNP
- rs183650899
- Type
- single nucleotide variant
- Location
- chr6:168307972 (GRCh38)
- Gene constraint
- LOEUF 1.469 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.81
Similar variants
- DACT2 p.Ala595Glu Uncertain significance ★ ⚠ same residue
- DACT2 p.Ala595Val Uncertain significance ★ ⚠ same residue
- DACT2 p.Ala11Thr Uncertain significance ★ ⚠ same type
- DACT2 p.Ala162Thr Uncertain significance ★ ⚠ same type
- DACT2 p.Ala186Val Uncertain significance ★ ⚠ same type
- DACT2 p.Ala228Val Uncertain significance ★ ⚠ same type
- DACT2 p.Ala239Thr Uncertain significance ★ ⚠ same type
- DACT2 p.Ala283Val 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/dact2-p-ala595 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown