USP20 p.Pro367=
c.1101G>A · rs377337518 · VCV790844
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.79%, sas)
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 -9.5 | GERP -2.5 |
| Overall | ||
| CADD | 0.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.79%
South Asian · 4,363/91,044 alleles
Filtering AF
4.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.63%
Overall
0.391%
6,307/1,612,016 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 4.79% | 21 |
| Ashkenazi Jewishnot grpmax-eligible | 0.7% | 143 |
| Remaining individualsnot grpmax-eligible | 0.448% | 223 |
| Admixed American | 0.253% | 395 |
| Middle Eastern | 0.198% | 505 |
| East Asian | 0.174% | 575 |
| European (non-Finnish) | 0.0997% | 1,003 |
| African / African-American | 0.0467% | 2,142 |
| Finnishnot grpmax-eligible | 0.00637% | 15,701 |
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.Pro367=
- Coding
- c.1101G>A
- MANE Select
- NM_001110303
- dbSNP
- rs377337518
- Type
- single nucleotide variant
- Location
- chr9:129868415 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.11 · 1 PDB
- Residue 367
- the usp domain; the 'disordered' region
Similar variants
- USP20 p.Pro367Leu Uncertain significance ★ ⚠ same residue
- USP20 p.Arg330Gly Uncertain significance ★★ ⚠ same type
- USP20 p.Ile907= Benign ★★ same type
- USP20 p.Ser103Tyr Benign ★★ same type
- USP20 p.Ser288= Benign ★★ same type
- USP20 p.Ala260Ser Uncertain significance ★ ⚠ same type
- USP20 p.Ala317Thr Uncertain significance ★ ⚠ same type
- USP20 p.Ala355Thr 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-pro367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown