PSMB3 p.Pro160=
c.480G>A · rs138004688 · VCV2647707
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, 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 -1.9 | GERP -4.2 |
| Overall | ||
| CADD | 12.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,080 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.0013%
21/1,613,878 alleles · very rare
exomes 16/1,461,716 · genomes 5/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,770 |
| African / African-American | 0.00267% | 37,461 |
| European (non-Finnish) | 0.00127% | 78,660 |
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
- PSMB3
- Protein
- p.Pro160=
- Coding
- c.480G>A
- MANE Select
- NM_002795
- dbSNP
- rs138004688
- Type
- single nucleotide variant
- Location
- chr17:38762416 (GRCh38)
- Gene constraint
- LOEUF 0.452 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 97.31 · 155 PDB
- Residue 160
- an α-helix
Similar variants
- PSMB3 p.Arg26Ser Uncertain significance ★ ⚠ same type
- PSMB3 p.Arg66His Uncertain significance ★ ⚠ same type
- PSMB3 p.Arg66Ser Uncertain significance ★ ⚠ same type
- PSMB3 p.Asn7Ser Uncertain significance ★ same type
- PSMB3 p.Asp135Tyr Uncertain significance ★ ⚠ same type
- PSMB3 p.Gln31His Uncertain significance ★ ⚠ same type
- PSMB3 p.Glu144Lys Uncertain significance ★ ⚠ same type
- PSMB3 p.Glu191Lys 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/psmb3-p-pro160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown