DUSP9 p.Ala174=
c.522G>A · rs151054957 · VCV714973
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.5%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.176 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.4 |
| Overall | ||
| CADD | 0.211 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.5%
African / African-American · 2,580/57,325 alleles
Filtering AF
4.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.3%
Overall
0.248%
3,003/1,209,709 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.5% | 22 |
| Remaining individualsnot grpmax-eligible | 0.376% | 266 |
| Admixed American | 0.3% | 333 |
| Middle Eastern | 0.232% | 431 |
| South Asian | 0.0193% | 5,169 |
| European (non-Finnish) | 0.00938% | 10,658 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00454% | 22,032 |
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
- DUSP9
- Protein
- p.Ala174=
- Coding
- c.522G>A
- MANE Select
- NM_001318503
- dbSNP
- rs151054957
- Type
- single nucleotide variant
- Location
- chrX:153649380 (GRCh38)
- Structure
- AlphaFold pLDDT 77.23 · 2 PDB
Similar variants
- DUSP9 p.Ala174Val Uncertain significance ★ ⚠ same residue
- DUSP9 p.Ala151Val Benign ★★ same type
- DUSP9 p.Pro158= Benign ★★ same type
- DUSP9 p.Ala226Ser Uncertain significance ★ ⚠ same type
- DUSP9 p.Ala362Val Uncertain significance ★ ⚠ same type
- DUSP9 p.Ala45Thr Uncertain significance ★ ⚠ same type
- DUSP9 p.Ala48Thr Uncertain significance ★ ⚠ same type
- DUSP9 p.Arg145His 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/dusp9-p-ala174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown