AP3B1 p.Pro840fs
c.2514_2515del · VCV3897901
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Hermansky-Pudlak syndrome 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 22 of 27 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.9 | GERP 1.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- AP3B1
- Protein
- p.Pro840fs
- Coding
- c.2514_2515del
- MANE Select
- NM_003664
- Type
- Deletion
- Location
- chr5:78089455 (GRCh38)
- Gene constraint
- LOEUF 0.59 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.85 · 5 PDB
Disease context
Hermansky-Pudlak syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Familial hemophagocytic lymphohistiocytosis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Infancy
- Prevalence
- 1-9 / 100 000 (Sweden)
Similar variants
- AP3B1 p.Gly881fs Pathogenic/Likely pathogenic ★★ same condition
- AP3B1 p.Lys59fs Pathogenic ★★ same condition
- AP3B1 p.Lys923fs Pathogenic/Likely pathogenic ★★ same condition
- AP3B1 c.1168-12_1168-8del Likely benign ★★ same condition
- AP3B1 c.1650+12del Benign/Likely benign ★★ same condition
- AP3B1 c.536+20del Likely benign ★★ same condition
- AP3B1 p.Lys804del Benign/Likely benign ★★ same condition
- AP3B1 c.2072_2077+2del Likely pathogenic ★ 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/ap3b1-p-pro840fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown