DUSP6 p.Gln42=
c.126G>A · rs1592768047 · VCV752065
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 1.1 | GERP 0.004, phastCons 1 |
| Overall | ||
| CADD | 16.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,880 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000205%
3/1,460,556 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,880 |
| European (non-Finnish) | 0.000169% | 589,977 |
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.Gln42=
- Coding
- c.126G>A
- MANE Select
- NM_001946
- dbSNP
- rs1592768047
- Type
- single nucleotide variant
- Location
- chr12:89351914 (GRCh38)
- Gene constraint
- LOEUF 0.45 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 76.13 · 2 PDB
- Residue 42
- the rhodanese domain
Similar variants
- 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
- DUSP6 c.401-113T>A 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-gln42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown