DUSP9 p.Gly377=
c.1131C>T · rs375976650 · VCV723101
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0326%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.065 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -3.8 |
| Overall | ||
| CADD | 0.389 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0326%
European (non-Finnish) · 289/886,888 alleles
Filtering AF
0.0295%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0283%
Overall
0.0258%
309/1,195,607 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0326% | 3,069 |
| Admixed American | 0.011% | 9,071 |
| Remaining individualsnot grpmax-eligible | 0.0106% | 9,398 |
| Finnishnot grpmax-eligible | 0.00663% | 15,085 |
| South Asian | 0.0055% | 18,175 |
| African / African-American | 0.00524% | 19,076 |
| East Asian | 0.00298% | 33,566 |
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.Gly377=
- Coding
- c.1131C>T
- MANE Select
- NM_001318503
- dbSNP
- rs375976650
- Type
- single nucleotide variant
- Location
- chrX:153650281 (GRCh38)
- Structure
- AlphaFold pLDDT 77.23 · 2 PDB
- Residue 377
- the 'disordered' region
Similar variants
- DUSP9 p.Ala151Val Benign ★★ same type
- DUSP9 p.Ala174= Benign ★★ same type
- DUSP9 p.Pro158= Benign ★★ same type
- DUSP9 p.Ala174Val Uncertain significance ★ ⚠ 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
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-gly377 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown