DUSP15 p.Ser179Phe
c.536C>T · VCV4245503
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00125%, sas)
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 11 | GERP 2.1, phastCons 1 |
| Regional constraint | o/e 1.14 | unconstrained · MANE · 8,931 bp · p 0.015 · regional, not allelic |
| Overall | ||
| CADD | 23.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00125%
South Asian · 1/80,098 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.0002%
3/1,497,994 alleles · very rare
exomes 2/1,345,832 · genomes 1/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00125% | 80,098 |
| European (non-Finnish) | 0.000177% | 565,976 |
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.Ser179Phe
- Coding
- c.536C>T
- MANE Select
- NM_080611
- Type
- single nucleotide variant
- Location
- chr20:31861575 (GRCh38)
- Gene constraint
- LOEUF 1.5 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.61 · 1 PDB
Similar variants
- DUSP15 p.Ser179Ala Uncertain significance ★ same residue
- 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
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-ser179phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown