USP53 p.Ser796=
c.2388A>G · rs745899292 · VCV2866724
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.316%, amr)
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 -0.93 | GERP -3.9 |
| Overall | ||
| CADD | 0.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.316%
Admixed American · 186/58,932 alleles
Filtering AF
0.278%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.264%
Overall
0.0137%
221/1,609,658 alleles · rare
exomes 161/1,457,490 · genomes 60/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.316% | 317 |
| Remaining individualsnot grpmax-eligible | 0.0241% | 4,152 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0239% | 4,185 |
| African / African-American | 0.00268% | 37,258 |
| European (non-Finnish) | 0.000933% | 107,157 |
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
- USP53
- Protein
- p.Ser796=
- Coding
- c.2388A>G
- MANE Select
- NM_001371395
- dbSNP
- rs745899292
- Type
- single nucleotide variant
- Location
- chr4:119292377 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.34
- Residue 796
- 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-ser796 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown