AP3B1 adaptor related protein complex 3 subunit beta 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: AP3B1provided by HGNC
Official Full Name: adaptor related protein complex 3 subunit beta 1provided by HGNC
Primary source: HGNC:HGNC:566
See related: Ensembl:ENSG00000132842 MIM:603401; AllianceGenome:HGNC:566
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PE; HPS; HPS2; ADTB3; ADTB3A
Summary: This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. The encoded protein is part of the heterotetrameric AP-3 protein complex which interacts with the scaffolding protein clathrin. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2012]
Expression: Ubiquitous expression in thyroid (RPKM 10.7), colon (RPKM 8.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q14.1

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (78000522..78294698, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (78482312..78776325, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (77296346..77590522, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HDL cholesterol concentrations and risk of atherosclerotic cardiovascular disease - Insights from randomized clinical trials and human genetics.
Title: HDL cholesterol concentrations and risk of atherosclerotic cardiovascular disease - Insights from randomized clinical trials and human genetics.
Germline variants in UNC13D and AP3B1 are enriched in COVID-19 patients experiencing severe cytokine storms.
Title: Germline variants in UNC13D and AP3B1 are enriched in COVID-19 patients experiencing severe cytokine storms.
data show that defects in adaptor protein complex 3-dependent maturation of Weibel-Palade bodies impairs exocytosis by affecting the recruitment of VAMP8.
Title: Defective AP-3-dependent VAMP8 trafficking impairs Weibel-Palade body exocytosis in Hermansky-Pudlak Syndrome type 2 blood outgrowth endothelial cells.
point mutation c.2702C>G in exon 23 of the AP3B1 gene caused deletion of 112 bp in the mRNA in two siblings. This mutation activates a cryptic donor splice site that overrules the wild-type donor splice site of this exon. Three other novel mutations in AP3B1 were identified, that is, a nonsense mutation c.716G>A (p.Trp239Ter), a 1-bp and a 4-bp deletion c.177delA and c.1839_1842delTAGA, respectively
Title: Hermansky-Pudlak syndrome type 2: Aberrant pre-mRNA splicing and mislocalization of granule proteins in neutrophils.
Synergistic defects of UNC13D and AP3B1 leading to adult hemophagocytic lymphohistiocytosis.
Title: Synergistic defects of UNC13D and AP3B1 leading to adult hemophagocytic lymphohistiocytosis.
Using a co-affinity purification strategy, authors have identified the beta subunit of the AP-3 adapter protein complex, AP3B1, as a binding partner for the M proteins of the zoonotic paramyxoviruses Nipah virus and Hendra virus.
Title: Matrix proteins of Nipah and Hendra viruses interact with beta subunits of AP-3 complexes.
Data indicate that RUN and FYVE domain protein Rabip4'(RUFY1) interacts specifically and directly with adaptor protein complex AP-3.
Title: AP-3 and Rabip4' coordinately regulate spatial distribution of lysosomes.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
The study provides a description of two unrelated individuals with Hermansky Pudlak syndrome type 2 associated with novel mutations in AP3B1.
Title: Two patients with Hermansky Pudlak syndrome type 2 and novel mutations in AP3B1.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hermansky-Pudlak syndrome 2 MedGen: C1842362 OMIM: 608233 GeneReviews: Hermansky-Pudlak Syndrome	Compare labs

EBI GWAS Catalog

Description
Genome-wide detection of allele specific copy number variation associated with insulin resistance in African Americans from the HyperGEN study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp160, precursor	env	In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding	PubMed
Pr55(Gag)	gag	AP3B1 deficiency in HPS2 fibroblasts inhibits HIV-1 Gag assembly and release. Expression of the AP3B1 reverses the inhibited assembly and release of HIV-1 in HPS2 fibroblasts	PubMed
	gag	In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding	PubMed
	gag	Changes of IP7 intracellular levels affect HIV-1 Gag release through modulation of AP3B1 and Kif3A interaction	PubMed
matrix	gag	In the absence of Vpu, Env accumulates extensively within clathrin-coated endosomal structures, including the viral proteins Gag and MA; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-81837 (e-PCR)
- UniSTS:103970

L31442 (e-PCR)
- UniSTS:6958

A002S29 (e-PCR)
- UniSTS:44135

SHGC-83541 (e-PCR)
- UniSTS:101749

RH16414 (e-PCR)
- UniSTS:25482

G63314 (e-PCR)
- UniSTS:140427

SHGC-79370 (e-PCR)
- UniSTS:184227

1842 (e-PCR)
- UniSTS:2020

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTP-dependent protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein phosphatase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in anterograde axonal transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in anterograde synaptic vesicle transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterograde synaptic vesicle transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib	IEA Inferred from Electronic Annotation more info
involved_in blood coagulation	IEA Inferred from Electronic Annotation more info
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in clathrin-coated vesicle cargo loading, AP-3-mediated	NAS Non-traceable Author Statement more info	PubMed
involved_in establishment of protein localization to mitochondrial membrane involved in mitochondrial fission	IEA Inferred from Electronic Annotation more info
involved_in granulocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in hematopoietic progenitor cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in homeostasis of number of cells	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in intracellular protein transport	TAS Traceable Author Statement more info	PubMed
involved_in intracellular transport	NAS Non-traceable Author Statement more info	PubMed
involved_in intracellular zinc ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in lung morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in lysosome organization	IEA Inferred from Electronic Annotation more info
involved_in mRNA transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in melanosome assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in melanosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in platelet dense granule organization	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of NK T cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein modification process	IEA Inferred from Electronic Annotation more info
involved_in protein targeting to lysosome	IEA Inferred from Electronic Annotation more info
involved_in respiratory system process	IEA Inferred from Electronic Annotation more info
involved_in single fertilization	IEA Inferred from Electronic Annotation more info
involved_in skin epidermis development	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in toll-like receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle-mediated transport	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of AP-3 adaptor complex	NAS Non-traceable Author Statement more info	PubMed
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in axon cytoplasm	IEA Inferred from Electronic Annotation more info
part_of clathrin adaptor complex	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in early endosome	NAS Non-traceable Author Statement more info	PubMed
located_in lysosomal membrane	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in microvesicle	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: AP-3 complex subunit beta-1

Names: AP-3 complex beta-3A subunit; adaptor protein complex AP-3 subunit beta-1; adaptor related protein complex 3 beta 1 subunit; beta-3A; beta-3A-adaptin; clathrin assembly protein complex 3 beta-1 large chain

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007268.1 RefSeqGene

Range

4950..297379

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_170

mRNA and Protein(s)

NM_001271769.2 → NP_001258698.1 AP-3 complex subunit beta-1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice junction at the 3' end of the first exon compared to variant 1. This transcript initiates translation at an alternate start codon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AC024578, BC038444, BX538041, DA889915, KU178426

Consensus CDS

CCDS64186.1

UniProtKB/TrEMBL

A0A8Q3WKK0

Related

ENSP00000430597.1, ENST00000519295.6

Conserved Domains (5) summary

pfam01602
Location:1 → 532

Adaptin_N; Adaptin N terminal region

pfam12717
Location:79 → 202

Cnd1; non-SMC mitotic condensation complex subunit 1

pfam14796
Location:765 → 909

AP3B1_C; Clathrin-adaptor complex-3 beta-1 subunit C-terminal

pfam14797
Location:680 → 715

SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex

sd00044
Location:67 → 95

HEAT; HEAT repeat [structural motif]
NM_001410752.1 → NP_001397681.1 AP-3 complex subunit beta-1 isoform 3

Status: REVIEWED

Source sequence(s)

AC024568, AC104108, AC112197

Consensus CDS

CCDS93737.1

UniProtKB/TrEMBL

A0A8Q3SIM7

Related

ENSP00000511880.1, ENST00000519888.6
NM_003664.5 → NP_003655.3 AP-3 complex subunit beta-1 isoform 1

See identical proteins and their annotated locations for NP_003655.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

BC038444, DA889915, KU178426

Consensus CDS

CCDS4041.1

UniProtKB/Swiss-Prot

E5RJ68, O00203, O00580, Q7Z393, Q9HD66

UniProtKB/TrEMBL

A0A0S2Z5J4, A8K586

Related

ENSP00000255194.7, ENST00000255194.11

Conserved Domains (5) summary

pfam01602
Location:46 → 581

Adaptin_N; Adaptin N terminal region

pfam12717
Location:128 → 251

Cnd1; non-SMC mitotic condensation complex subunit 1

pfam14796
Location:814 → 958

AP3B1_C; Clathrin-adaptor complex-3 beta-1 subunit C-terminal

pfam14797
Location:729 → 764

SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex

sd00044
Location:116 → 144

HEAT; HEAT repeat [structural motif]