USB1 p.Ile171=
c.513T>C · VCV3813881
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
Conditions
1
Inborn genetic diseases
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 -3.3 | GERP 0.53 |
| Overall | ||
| CADD | 6.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,878 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000205%
3/1,461,826 alleles · very rare
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
- USB1
- Protein
- p.Ile171=
- Coding
- c.513T>C
- MANE Select
- NM_024598
- Type
- single nucleotide variant
- Location
- chr16:58017343 (GRCh38)
- Gene constraint
- LOEUF 1.016 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.91 · 5 PDB
- Residue 171
- a β-strand
Similar variants
- USB1 p.Ile171Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
- USB1 p.Ala106Ser Uncertain significance ★★ ⚠ same condition
- USB1 p.Ala218Thr Uncertain significance ★★ ⚠ same condition
- USB1 p.Ala218Val Uncertain significance ★★ ⚠ same condition
- USB1 p.Arg112Gln Uncertain significance ★★ ⚠ same condition
- USB1 p.Arg112Trp Uncertain significance ★★ ⚠ same condition
- USB1 p.Arg130Cys Uncertain significance ★★ ⚠ same condition
- USB1 p.Arg130His Uncertain significance ★★ ⚠ same condition
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/usb1-p-ile171 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown