USP53 p.Pro922=
c.2766C>A · rs765257155 · VCV2720144
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.76 | GERP -3.6, phastCons 0.009 |
| Overall | ||
| CADD | 5.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- USP53
- Protein
- p.Pro922=
- Coding
- c.2766C>A
- MANE Select
- NM_001371395
- dbSNP
- rs765257155
- Type
- single nucleotide variant
- Location
- chr4:119292755 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.34
- Residue 922
- a UniProt-annotated variant site (in pfic7)
Similar variants
- USP53 p.Arg111Ter Likely pathogenic ★★ same type
- USP53 p.Arg338Ter Pathogenic ★★ same type
- USP53 p.Arg476Ter Pathogenic/Likely pathogenic ★★ same type
- USP53 p.Arg520Ter Pathogenic ★★ same type
- USP53 p.Arg582Ter Pathogenic/Likely pathogenic ★★ same type
- USP53 p.Arg58Gln Uncertain significance ★★ ⚠ same type
- USP53 p.Asn97Asp Uncertain significance ★★ ⚠ same type
- USP53 p.Asn97Ser 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/usp53-p-pro922 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown