Is USP24 p.Ser533Arg (c.1599C>A) pathogenic?

USP24 p.Ser533Arg (c.1599C>A) is classified Uncertain significance in USP24 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-21). AlphaMissense: likely pathogenic (0.939); Ultra-rare (popmax 0.0314%, afr).

How common is USP24 p.Ser533Arg (c.1599C>A) in the general population?

USP24 p.Ser533Arg (c.1599C>A) is ultra-rare (popmax 0.0314%, afr) (gnomAD).

What do computational predictors say about USP24 p.Ser533Arg (c.1599C>A)?

AlphaMissense predicts likely pathogenic (score 0.939) — an in-silico prediction, not a clinical call.

USP24 p.Ser533Arg

c.1599C>A · VCV3331395

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.939 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0314%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.939	likely pathogenic
REVEL	0.595	indeterminate
SaProt	LLR -6.83	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP -0.69, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 28 kb · p 1.7e-13 · regional, not allelic
Overall
CADD	20.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0314% African / African-American · 23/73,136 alleles

Filtering AF 0.0215% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0182%

Overall 0.00155% 24/1,551,440 alleles · ultra-rare exomes 11/1,399,200 · genomes 13/152,240 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0314%	3,180
Remaining individualsnot grpmax-eligible	0.00166%	60,096

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.Ser533Arg
Coding: c.1599C>A
MANE Select: NM_015306
Type: single nucleotide variant
Location: chr1:55154422 (GRCh38)
Gene constraint: LOEUF 0.361 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.15

Full USP24 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

USP24 p.Ala1561= Benign ★★ same type
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

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-ser533arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown