DUSP22 p.Thr105=
c.315C>T · rs200444409 · VCV3039993
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.158%, eas)
Conditions
1
DUSP22-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.184 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -3.9 |
| Overall | ||
| CADD | 3.997 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.158%
East Asian · 71/44,850 alleles
Filtering AF
0.129%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.118%
Overall
0.0107%
172/1,614,216 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.158% | 632 |
| African / African-American | 0.0306% | 3,264 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Admixed American | 0.00833% | 12,008 |
| South Asian | 0.00659% | 15,182 |
| European (non-Finnish) | 0.005% | 20,000 |
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.Thr105=
- Coding
- c.315C>T
- MANE Select
- NM_001286555
- dbSNP
- rs200444409
- Type
- single nucleotide variant
- Location
- chr6:348154 (GRCh38)
- Gene constraint
- LOEUF 1.407 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.64 · 8 PDB
- Residue 105
- the tyrosine-protein phosphatase domain; an α-helix
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.Ala56= 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-thr105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown