DACH2 p.Pro439=
c.1317C>T · rs772992214 · VCV3079927
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0266%, sas)
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 -0.15 | GERP -0.48, phastCons 0.067 |
| Overall | ||
| CADD | 5.051 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0266%
South Asian · 15/56,438 alleles
Filtering AF
0.0163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0132%
Overall
0.00282%
34/1,205,998 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0266% | 3,763 |
| East Asian | 0.00594% | 16,822 |
| Remaining individualsnot grpmax-eligible | 0.00211% | 47,481 |
| African / African-American | 0.00175% | 57,004 |
| European (non-Finnish) | 0.00168% | 59,500 |
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
- DACH2
- Protein
- p.Pro439=
- Coding
- c.1317C>T
- MANE Select
- NM_053281
- dbSNP
- rs772992214
- Type
- single nucleotide variant
- Location
- chrX:86812932 (GRCh38)
- Structure
- AlphaFold pLDDT 62.69
Similar variants
- DACH2 p.Arg539His Uncertain significance ★★ ⚠ same type
- DACH2 p.Ala219Val Conflicting classifications of pathogenicity ★ ⚠ same type
- DACH2 p.Ala221Asp Uncertain significance ★ ⚠ same type
- DACH2 p.Ala221Ser Uncertain significance ★ ⚠ same type
- DACH2 p.Ala223Val Uncertain significance ★ ⚠ same type
- DACH2 p.Ala285Glu Uncertain significance ★ ⚠ same type
- DACH2 p.Ala296Val Uncertain significance ★ ⚠ same type
- DACH2 p.Ala362Gly 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/dach2-p-pro439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown