Is AP3B2 p.Arg576= (c.1728C>T) pathogenic?

AP3B2 p.Arg576= (c.1728C>T) is classified Likely benign in AP3B2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-11-12). Rare (popmax 0.121%, afr).

How common is AP3B2 p.Arg576= (c.1728C>T) in the general population?

AP3B2 p.Arg576= (c.1728C>T) is rare (popmax 0.121%, afr) (gnomAD).

AP3B2 p.Arg576=

c.1728C>T · rs34585442 · VCV1546961

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.121%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -3.8
Overall
CADD	0.209	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.121% African / African-American · 91/75,032 alleles

Filtering AF 0.101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0936%

Overall 0.00923% 149/1,613,992 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.121%	825
Admixed American	0.01%	10,004
Remaining individualsnot grpmax-eligible	0.0096%	10,415
East Asian	0.00446%	22,438
European (non-Finnish)	0.00347%	28,778
South Asian	0.00329%	30,359

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: AP3B2
Protein: p.Arg576=
Coding: c.1728C>T
dbSNP: rs34585442
Type: single nucleotide variant
Location: chr15:82666871 (GRCh38)

Full AP3B2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/ap3b2-p-arg576 (accessed [today's date]).

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