DUSP15 p.Arg203Ser
c.607C>A · VCV4662526
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.064 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.6 | GERP 0.95, phastCons 1 |
| Regional constraint | o/e 1.14 | unconstrained · MANE · 8,931 bp · p 0.015 · regional, not allelic |
| Overall | ||
| CADD | 24.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
Middle Eastern · 1/5,342 alleles
Filtering AF
0.000401%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00015%
Overall
0.000436%
6/1,376,596 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0187% | 5,342 |
| South Asian | 0.00241% | 41,414 |
| European (non-Finnish) | 0.000262% | 382,291 |
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
- DUSP15
- Protein
- p.Arg203Ser
- Coding
- c.607C>A
- MANE Select
- NM_080611
- Type
- single nucleotide variant
- Location
- chr20:31861504 (GRCh38)
- Gene constraint
- LOEUF 1.5 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.61 · 1 PDB
Similar variants
- DUSP15 p.Ala191Pro Uncertain significance ★ same type
- DUSP15 p.Ala192Pro Uncertain significance ★ same type
- DUSP15 p.Arg148Gln Uncertain significance ★ same type
- DUSP15 p.Arg166Ser Uncertain significance ★ same type
- DUSP15 p.Arg174Cys Uncertain significance ★ same type
- DUSP15 p.Arg174His Uncertain significance ★ same type
- DUSP15 p.Arg176Pro Uncertain significance ★ same type
- DUSP15 p.Arg176Trp 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/dusp15-p-arg203ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown