USP24 p.Ala1561=
c.4683G>A · rs61760214 · VCV770846
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.818%, 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 -8.1 | GERP -4.6 |
| Overall | ||
| CADD | 4.566 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.818%
Admixed American · 491/60,002 alleles
Filtering AF
0.758%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.735%
Overall
0.428%
6,905/1,613,882 alleles · rare
exomes 6,312/1,461,658 · genomes 593/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.818% | 122 |
| Ashkenazi Jewishnot grpmax-eligible | 0.791% | 126 |
| European (non-Finnish) | 0.461% | 217 |
| Middle Eastern | 0.445% | 225 |
| Remaining individualsnot grpmax-eligible | 0.419% | 238 |
| South Asian | 0.288% | 348 |
| Finnishnot grpmax-eligible | 0.192% | 520 |
| African / African-American | 0.0893% | 1,120 |
| East Asian | 0.00669% | 14,952 |
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
- USP24
- Protein
- p.Ala1561=
- Coding
- c.4683G>A
- MANE Select
- NM_015306
- dbSNP
- rs61760214
- Type
- single nucleotide variant
- Location
- chr1:55107318 (GRCh38)
- Gene constraint
- LOEUF 0.361 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.15
Similar variants
- USP24 p.His2523= Benign ★★ same type
- USP24 p.Leu726= Benign ★★ same type
- USP24 p.Lys653= Benign ★★ same type
- USP24 p.Thr158Ala Benign ★★ same type
- USP24 c.6554+1G>A Uncertain significance ★ same type
- USP24 p.Ala1077Val Uncertain significance ★ ⚠ same type
- USP24 p.Ala1267Thr Uncertain significance ★ ⚠ same type
- USP24 p.Ala1332Val 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/usp24-p-ala1561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown