DUSP6 p.Asp84=
c.252C>T · rs753109290 · VCV726479
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, 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 3.5 | GERP -0.78, phastCons 1 |
| Overall | ||
| CADD | 16.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
Admixed American · 8/59,638 alleles
Filtering AF
0.00665%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00485%
Overall
0.00106%
17/1,610,130 alleles · ultra-rare
exomes 17/1,457,790 · genomes 0/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0134% | 7,455 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,332 |
| European (non-Finnish) | 0.000679% | 147,368 |
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
- DUSP6
- Protein
- p.Asp84=
- Coding
- c.252C>T
- MANE Select
- NM_001946
- dbSNP
- rs753109290
- Type
- single nucleotide variant
- Location
- chr12:89351788 (GRCh38)
- Gene constraint
- LOEUF 0.45 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 76.13 · 2 PDB
- Residue 84
- the rhodanese domain; an α-helix
Similar variants
- DUSP6 p.Asp84Glu Uncertain significance ★ ⚠ same residue
- DUSP6 p.Ala141Asp Uncertain significance ★★ ⚠ same type
- DUSP6 p.Ala57Thr Uncertain significance ★★ ⚠ same type
- DUSP6 p.Asp93Glu Uncertain significance ★★ ⚠ same type
- DUSP6 p.Glu32Lys Uncertain significance ★★ ⚠ same type
- DUSP6 p.Gly30Cys Uncertain significance ★★ ⚠ same type
- DUSP6 p.Phe77Ile Uncertain significance ★★ ⚠ same type
- DUSP6 c.400+231T>C Benign ★★ 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/dusp6-p-asp84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown