DUSP2 p.Thr309=
c.927C>T · rs781733980 · VCV2651140
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.12%, 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 -0.71 | GERP -3.8 |
| Overall | ||
| CADD | 5.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.12%
Middle Eastern · 7/5,844 alleles
Filtering AF
0.0561%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0398%
Overall
0.00397%
64/1,613,158 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.12% | 835 |
| South Asian | 0.022% | 4,553 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,245 |
| European (non-Finnish) | 0.00229% | 43,705 |
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
- DUSP2
- Protein
- p.Thr309=
- Coding
- c.927C>T
- MANE Select
- NM_004418
- dbSNP
- rs781733980
- Type
- single nucleotide variant
- Location
- chr2:96143841 (GRCh38)
- Gene constraint
- LOEUF 1.442 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.59 · 1 PDB
- Residue 309
- an α-helix; the tyrosine-protein phosphatase domain
Similar variants
- DUSP2 p.Ala107Val Uncertain significance ★ ⚠ same type
- DUSP2 p.Ala265Pro Uncertain significance ★ same type
- DUSP2 p.Ala265Val Uncertain significance ★ ⚠ same type
- DUSP2 p.Ala45Val Uncertain significance ★ ⚠ same type
- DUSP2 p.Ala65Gly Uncertain significance ★ ⚠ same type
- DUSP2 p.Arg263Cys Uncertain significance ★ ⚠ same type
- DUSP2 p.Arg26His Uncertain significance ★ ⚠ same type
- DUSP2 p.Arg26Ser 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/dusp2-p-thr309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown