USP19 p.Pro487=
c.1461G>A · rs144914640 · VCV715569
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.67%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.035 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.7 | GERP -4.8 |
| Overall | ||
| CADD | 1.359 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.67%
African / African-American · 1,969/73,616 alleles
Filtering AF
2.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.54%
Overall
0.141%
2,255/1,597,820 alleles · low-frequency
exomes 1,101/1,445,480 · genomes 1,154/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.67% | 37 |
| Remaining individualsnot grpmax-eligible | 0.193% | 519 |
| Admixed American | 0.171% | 586 |
| Middle Eastern | 0.117% | 856 |
| South Asian | 0.0123% | 8,109 |
| European (non-Finnish) | 0.00485% | 20,627 |
| Finnishnot grpmax-eligible | 0.00157% | 63,624 |
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
- USP19
- Protein
- p.Pro487=
- Coding
- c.1461G>A
- MANE Select
- NM_001199161
- dbSNP
- rs144914640
- Type
- single nucleotide variant
- Location
- chr3:49116057 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.32 · 5 PDB
Similar variants
- USP19 p.Pro487Leu Uncertain significance ★ ⚠ same residue
- USP19 c.2292+7T>C Benign ★★ same type
- USP19 c.4039-440G>A Uncertain significance ★ ⚠ same type
- USP19 c.4039-477G>A Uncertain significance ★ ⚠ same type
- USP19 c.4039-482C>G Uncertain significance ★ ⚠ same type
- USP19 c.4039-518G>A Uncertain significance ★ ⚠ same type
- USP19 c.4039-519C>T Uncertain significance ★ ⚠ same type
- USP19 c.4039-543A>T 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/usp19-p-pro487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown