DACH2 p.Val71=
c.213C>T · rs199943928 · VCV2661007
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0534%, eas)
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 -0.033 | GERP -2.6, phastCons 0.71 |
| Overall | ||
| CADD | 6.252 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0534%
East Asian · 18/33,704 alleles
Filtering AF
0.0345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0284%
Overall
0.00198%
24/1,209,549 alleles · ultra-rare
exomes 22/1,098,188 · genomes 2/111,361 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0534% | 1,872 |
| South Asian | 0.00706% | 14,172 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,614 |
| European (non-Finnish) | 0.000112% | 895,183 |
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.Val71=
- Coding
- c.213C>T
- MANE Select
- NM_053281
- dbSNP
- rs199943928
- Type
- single nucleotide variant
- Location
- chrX:86148833 (GRCh38)
- Structure
- AlphaFold pLDDT 62.69
- Residue 71
- the 'dachbox-n' region
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-val71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown