USP5 p.Val18=
c.54C>T · rs143249320 · VCV783654
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.27%, afr)
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 0.75 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 10.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.27%
African / African-American · 2,454/75,040 alleles
Filtering AF
3.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.12%
Overall
0.181%
2,927/1,613,370 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.27% | 31 |
| Middle Eastern | 0.363% | 275 |
| Remaining individualsnot grpmax-eligible | 0.237% | 422 |
| Admixed American | 0.164% | 612 |
| European (non-Finnish) | 0.0166% | 6,019 |
| South Asian | 0.00992% | 10,083 |
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
- USP5
- Protein
- p.Val18=
- Coding
- c.54C>T
- MANE Select
- NM_001098536
- dbSNP
- rs143249320
- Type
- single nucleotide variant
- Location
- chr12:6852233 (GRCh38)
- Gene constraint
- LOEUF 0.329 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 12 PDB
Similar variants
- USP5 p.Leu380= Benign ★★ same type
- USP5 p.Leu489= Benign ★★ same type
- USP5 p.Pro609= Benign ★★ same type
- USP5 p.Ala495Thr Uncertain significance ★ ⚠ same type
- USP5 p.Ala549Val Uncertain significance ★ ⚠ same type
- USP5 p.Ala718Thr Uncertain significance ★ ⚠ same type
- USP5 p.Ala780Ser Uncertain significance ★ ⚠ same type
- USP5 p.Arg133Trp 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/usp5-p-val18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown