DUSP15 p.Arg199Leu
c.596G>T · rs766056551 · VCV2224110
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0215%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.025 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.4 | GERP 0.92, phastCons 1 |
| Regional constraint | o/e 1.14 | unconstrained · MANE · 8,931 bp · p 0.015 · regional, not allelic |
| Overall | ||
| CADD | 22.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0215%
European (non-Finnish) · 246/1,145,842 alleles
Filtering AF
0.0192%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0184%
Overall
0.0168%
256/1,526,420 alleles · ultra-rare
exomes 241/1,374,230 · genomes 15/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0215% | 4,658 |
| Remaining individualsnot grpmax-eligible | 0.0084% | 11,908 |
| Finnishnot grpmax-eligible | 0.00447% | 22,395 |
| African / African-American | 0.00283% | 35,360 |
| Admixed American | 0.00201% | 49,868 |
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.Arg199Leu
- Coding
- c.596G>T
- MANE Select
- NM_080611
- dbSNP
- rs766056551
- Type
- single nucleotide variant
- Location
- chr20:31861515 (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-arg199leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown