DUSP16 p.Val360=
c.1080G>A · rs2111269 · VCV2642738
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0887%, 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 -0.44 | GERP -0.38 |
| Overall | ||
| CADD | 0.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0887%
East Asian · 22/24,810 alleles
Filtering AF
0.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0506%
Overall
0.00229%
35/1,525,148 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0887% | 1,128 |
| Middle Eastern | 0.0171% | 5,844 |
| South Asian | 0.00876% | 11,417 |
| Remaining individualsnot grpmax-eligible | 0.00518% | 19,305 |
| Admixed American | 0.00215% | 46,486 |
| African / African-American | 0.00144% | 69,608 |
| European (non-Finnish) | 8.6e-05% | 1,162,430 |
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
- DUSP16
- Protein
- p.Val360=
- Coding
- c.1080G>A
- MANE Select
- NM_030640
- dbSNP
- rs2111269
- Type
- single nucleotide variant
- Location
- chr12:12477751 (GRCh38)
- Gene constraint
- LOEUF 0.502 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81 · 3 PDB
- Residue 360
- the 'disordered' region
Similar variants
- DUSP16 p.Ala2Thr Uncertain significance ★ ⚠ same type
- DUSP16 p.Ala358Thr Uncertain significance ★ ⚠ same type
- DUSP16 p.Ala73Val Uncertain significance ★ ⚠ same type
- DUSP16 p.Arg130His Uncertain significance ★ ⚠ same type
- DUSP16 p.Arg14Lys Uncertain significance ★ ⚠ same type
- DUSP16 p.Arg208His Uncertain significance ★ ⚠ same type
- DUSP16 p.Arg483Gln Uncertain significance ★ ⚠ same type
- DUSP16 p.Arg598Cys 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/dusp16-p-val360 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown