DUSP4 p.Ala282=
c.846G>A · rs141546461 · VCV2658511
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
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 -7.2 | GERP -3.8 |
| Overall | ||
| CADD | 5.671 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,998 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00236%
38/1,610,404 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,571 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,578 |
| European (non-Finnish) | 0.00237% | 42,140 |
| East Asian | 0.00223% | 44,876 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,450 |
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
- DUSP4
- Protein
- p.Ala282=
- Coding
- c.846G>A
- MANE Select
- NM_001394
- dbSNP
- rs141546461
- Type
- single nucleotide variant
- Location
- chr8:29337365 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 78.78 · 1 PDB
- Residue 282
- a β-strand; the tyrosine-protein phosphatase domain
Similar variants
- DUSP4 p.Ala163Gly Uncertain significance ★ ⚠ same type
- DUSP4 p.Ala166Thr Uncertain significance ★ ⚠ same type
- DUSP4 p.Ala212Ser Uncertain significance ★ ⚠ same type
- DUSP4 p.Ala341Ser Uncertain significance ★ ⚠ same type
- DUSP4 p.Arg213Gln Uncertain significance ★ ⚠ same type
- DUSP4 p.Arg213Trp Uncertain significance ★ ⚠ same type
- DUSP4 p.Arg273His Uncertain significance ★ ⚠ same type
- DUSP4 p.Arg313His 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/dusp4-p-ala282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown