DACT2 p.Pro473=
c.1419G>A · rs201301805 · VCV2657142
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, 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 -2.1 | GERP -1.8 |
| Overall | ||
| CADD | 6.795 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,016 alleles
Filtering AF
0.00439%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00399%
Overall
0.00451%
70/1,551,892 alleles · ultra-rare
exomes 51/1,399,702 · genomes 19/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,016 |
| European (non-Finnish) | 0.00549% | 18,207 |
| African / African-American | 0.00548% | 18,263 |
| Finnishnot grpmax-eligible | 0.00166% | 60,066 |
| South Asian | 0.00119% | 84,066 |
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.Pro473=
- Coding
- c.1419G>A
- MANE Select
- NM_214462
- dbSNP
- rs201301805
- Type
- single nucleotide variant
- Location
- chr6:168308338 (GRCh38)
- Gene constraint
- LOEUF 1.469 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.81
- Residue 473
- the 'disordered' region
Similar variants
- DACT2 p.Pro473Ala Uncertain significance ★ ⚠ same residue
- DACT2 p.Pro473Leu Likely benign ★ 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-pro473 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown