AP3B2 p.Gln899=
c.2697A>G · rs765658666 · VCV1623580
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00407%, nfe)
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 -0.54 | GERP -3.8, phastCons 0.025 |
| Overall | ||
| CADD | 5.224 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00407%
European (non-Finnish) · 48/1,179,778 alleles
Filtering AF
0.00315%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00279%
Overall
0.00297%
48/1,613,554 alleles · very rare
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.Gln899=
- Coding
- c.2697A>G
- MANE Select
- NM_001278512
- dbSNP
- rs765658666
- Type
- single nucleotide variant
- Location
- chr15:82662830 (GRCh38)
- Gene constraint
- LOEUF 0.52 · pLI 0.22 (gnomAD)
- Structure
- AlphaFold pLDDT 75.73
Similar variants
- AP3B2 c.114-1G>A Likely pathogenic ★★ same type
- AP3B2 p.Arg977Ter Pathogenic ★★ same type
- AP3B2 p.Gln839Ter Pathogenic/Likely pathogenic ★★ same type
- AP3B2 c.1110+3G>C Uncertain significance ★★ same type
- AP3B2 c.1853-5C>A Uncertain significance ★★ same type
- AP3B2 c.2834-3C>A Uncertain significance ★★ same type
- AP3B2 p.Ala1076Pro Uncertain significance ★★ ⚠ same type
- AP3B2 p.Ala1098Asp 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/ap3b2-p-gln899 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown