DUSP22 p.Ala56=
c.168G>A · rs372273804 · VCV3054593
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, mid)
Conditions
1
DUSP22-related disorder
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 -2.9 | GERP -3.6 |
| Overall | ||
| CADD | 11.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,080 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00716%
Overall
0.007%
113/1,613,498 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,027 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0473% | 2,112 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,939 |
| African / African-American | 0.0133% | 7,495 |
| Admixed American | 0.0117% | 8,572 |
| European (non-Finnish) | 0.00576% | 17,346 |
| South Asian | 0.0022% | 45,530 |
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
- DUSP22
- Protein
- p.Ala56=
- Coding
- c.168G>A
- MANE Select
- NM_001286555
- dbSNP
- rs372273804
- Type
- single nucleotide variant
- Location
- chr6:335143 (GRCh38)
- Gene constraint
- LOEUF 1.407 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.64 · 8 PDB
- Residue 56
- the tyrosine-protein phosphatase domain
Disease context
DUSP22-related disorder
Similar variants
- DUSP22 c.189-4C>T Likely benign same condition
- DUSP22 c.-5C>T Likely benign same condition
- DUSP22 c.*1871C>G Likely benign same condition
- DUSP22 c.*1878G>A Benign same condition
- DUSP22 c.*2G>A Likely benign same condition
- DUSP22 c.*8G>A Likely benign same condition
- DUSP22 p.Ala23= Likely benign same condition
- DUSP22 p.His75= Likely benign same condition
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/dusp22-p-ala56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown