USP18 p.Ile339=
c.1017T>A · rs745758063 · VCV742098
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00242%, nfe)
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 0.29 | phastCons 1 |
| Overall | ||
| CADD | 4.273 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00242%
European (non-Finnish) · 28/1,158,180 alleles
Filtering AF
0.00168%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00144%
Overall
0.00179%
28/1,566,826 alleles · very rare
exomes 28/1,414,758 · genomes 0/152,068 · joint denominator
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
- USP18
- Protein
- p.Ile339=
- Coding
- c.1017T>A
- MANE Select
- NM_017414
- dbSNP
- rs745758063
- Type
- single nucleotide variant
- Location
- chr22:18173275 (GRCh38)
- Gene constraint
- LOEUF 0.459 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.60 · 2 PDB
- Residue 339
- the usp domain; a UniProt-annotated variant site (in ptorch2); the 'mediates interaction with ifnar2' region
Similar variants
- USP18 p.Ser2Asn Uncertain significance ★★ ⚠ same type
- USP18 p.Thr80Ile Uncertain significance ★★ ⚠ same type
- USP18 c.158-5T>G Benign/Likely benign ★★ same type
- USP18 p.Arg289Gln Likely benign ★★ same type
- USP18 p.Asn325Ser Benign/Likely benign ★★ same type
- USP18 p.Asp211= Benign/Likely benign ★★ same type
- USP18 p.Asp33Asn Likely benign ★★ same type
- USP18 p.Ile323Val Benign ★★ 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/usp18-p-ile339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown