AP3B2 p.Ala265Pro
c.793G>C · VCV4581980
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely benign
0.0616 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
0/3 damaging
AlphaMissense, REVEL, SaProt
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0616 | likely benign |
|---|---|---|
| REVEL | 0.015 | strongly benign-leaning |
| SaProt | LLR -6.29 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP -0.61, phastCons 1 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 301 bp · p 0.87 · regional, not allelic |
| Overall | ||
| CADD | 16.58 | 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
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AP3B2
- Protein
- p.Ala265Pro
- Coding
- c.793G>C
- MANE Select
- NM_001278512
- Type
- single nucleotide variant
- Location
- chr15:82680734 (GRCh38)
- Gene constraint
- LOEUF 0.52 · pLI 0.22 (gnomAD)
- Structure
- AlphaFold pLDDT 75.73
Similar variants
- AP3B2 p.Ala265Gly Uncertain significance ★ ⚠ same residue
- AP3B2 c.2834-3C>A Uncertain significance ★★ same condition
- AP3B2 p.Ala1076Pro Uncertain significance ★★ same condition
- AP3B2 p.Ala1098Asp Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Ala4Val Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Ala633Val Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Ala710Thr Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Ala71Thr Uncertain significance ★★ ⚠ same condition
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-ala265pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown