DUSP15 p.Val201Met
c.601G>A · rs749993547 · VCV2595973
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0041%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.06 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP 0.95, phastCons 1 |
| Regional constraint | o/e 1.14 | unconstrained · MANE · 8,931 bp · p 0.015 · regional, not allelic |
| Overall | ||
| CADD | 22.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0041%
European (non-Finnish) · 47/1,146,484 alleles
Filtering AF
0.00316%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00283%
Overall
0.00321%
49/1,527,792 alleles · very rare
exomes 41/1,375,562 · genomes 8/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0041% | 24,393 |
| Remaining individualsnot grpmax-eligible | 0.00335% | 29,810 |
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.Val201Met
- Coding
- c.601G>A
- MANE Select
- NM_080611
- dbSNP
- rs749993547
- Type
- single nucleotide variant
- Location
- chr20:31861510 (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-val201met (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown