USP20 p.Ala362=
c.1086G>A · rs200928022 · VCV722847
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.456%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -2.5 |
| Overall | ||
| CADD | 0.282 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.456%
African / African-American · 342/74,998 alleles
Filtering AF
0.416%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.401%
Overall
0.0303%
489/1,612,410 alleles · rare
exomes 272/1,460,214 · genomes 217/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.456% | 219 |
| Admixed American | 0.0617% | 1,622 |
| South Asian | 0.0516% | 1,938 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,462 |
| Middle Eastern | 0.0165% | 6,058 |
| East Asian | 0.00669% | 14,953 |
| European (non-Finnish) | 0.00373% | 26,809 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,578 |
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
- USP20
- Protein
- p.Ala362=
- Coding
- c.1086G>A
- MANE Select
- NM_001110303
- dbSNP
- rs200928022
- Type
- single nucleotide variant
- Location
- chr9:129868400 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.11 · 1 PDB
- Residue 362
- the usp domain; the 'disordered' region
Similar variants
- USP20 p.Ala362Thr Likely benign ★ same residue
- USP20 p.Ala362Val Likely benign ★ same residue
- USP20 p.Arg330Gly Uncertain significance ★★ ⚠ same type
- USP20 p.Ile907= Benign ★★ same type
- USP20 p.Pro367= Benign ★★ same type
- USP20 p.Ser103Tyr Benign ★★ same type
- USP20 p.Ser288= Benign ★★ same type
- USP20 p.Ala260Ser 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/usp20-p-ala362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown