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AP4B1 adaptor related protein complex 4 subunit beta 1 [ Homo sapiens (human) ]

Gene ID: 10717, updated on 17-Jun-2019

Summary

Official Symbol
AP4B1provided by HGNC
Official Full Name
adaptor related protein complex 4 subunit beta 1provided by HGNC
Primary source
HGNC:HGNC:572
See related
Ensembl:ENSG00000134262 MIM:607245
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
CPSQ5; SPG47; BETA-4
Summary
This gene encodes a subunit of a heterotetrameric adapter-like complex 4 that is involved in targeting proteins from the trans-Golgi network to the endosomal-lysosomal system. Mutations in this gene are associated with cerebral palsy spastic quadriplegic type 5 (CPSQ5) disorder. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Ubiquitous expression in bone marrow (RPKM 6.1), spleen (RPKM 5.4) and 25 other tissues See more
Orthologs

Genomic context

See AP4B1 in Genome Data Viewer
Location:
1p13.2
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (113894194..113905067, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114437370..114447741, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene AP4B1 antisense RNA 1 Neighboring gene protein tyrosine phosphatase non-receptor type 22 Neighboring gene BCL2 like 15 Neighboring gene GATA motif-containing MPRA enhancer 196 Neighboring gene DNA cross-link repair 1B Neighboring gene HIPK1 antisense RNA 1 Neighboring gene homeodomain interacting protein kinase 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from BioSystems

  • Clathrin derived vesicle budding, organism-specific biosystem (from REACTOME)
    Clathrin derived vesicle budding, organism-specific biosystemThere at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the cl...
  • Golgi Associated Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
    Golgi Associated Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
  • Lysosome, organism-specific biosystem (from KEGG)
    Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome, conserved biosystem (from KEGG)
    Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
    Lysosome Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
  • trans-Golgi Network Vesicle Budding, organism-specific biosystem (from REACTOME)
    trans-Golgi Network Vesicle Budding, organism-specific biosystemAfter passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membran...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
clathrin binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
protein localization IC
Inferred by Curator
more info
PubMed 
protein targeting IC
Inferred by Curator
more info
PubMed 
vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
AP-4 adaptor complex IDA
Inferred from Direct Assay
more info
PubMed 
clathrin adaptor complex IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
endosome lumen TAS
Traceable Author Statement
more info
 
extrinsic component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
AP-4 complex subunit beta-1
Names
AP-4 adaptor complex subunit beta
adaptor related protein complex 4 beta 1 subunit
beta 4 subunit of AP-4
beta4-adaptin
spastic paraplegia 47

NCBI Reference Sequences (RefSeq)

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

  1. NG_031901.1 RefSeqGene

    Range
    4996..15926
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001253852.3NP_001240781.1  AP-4 complex subunit beta-1 isoform 1

    See identical proteins and their annotated locations for NP_001240781.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AI431352, AL137856, AW072594, BC014146, DC368382
    Consensus CDS
    CCDS865.1
    UniProtKB/Swiss-Prot
    Q9Y6B7
    UniProtKB/TrEMBL
    A0A024R0D2
    Related
    ENSP00000358582.1, ENST00000369569.6
    Conserved Domains (3) summary
    sd00044
    Location:86113
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:621730
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9525
    Adaptin_N; Adaptin N terminal region
  2. NM_001253853.3NP_001240782.1  AP-4 complex subunit beta-1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate acceptor splice site at an internal exon compared to variant 1. This results in translation initiation from an in-frame downstream start site, and an isoform (2) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI431352, AK300204, AL137856, AW072594, BC014146, HY012945
    UniProtKB/Swiss-Prot
    Q9Y6B7
    UniProtKB/TrEMBL
    B4DTG3
    Conserved Domains (4) summary
    pfam01602
    Location:1426
    Adaptin_N; Adaptin N terminal region
    pfam09066
    Location:522631
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    pfam12717
    Location:2166
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:2250
    HEAT; HEAT repeat [structural motif]
  3. NM_001308312.2NP_001295241.1  AP-4 complex subunit beta-1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks multiple consecutive in-frame exons in the 5' coding region, compared to variant 1. The resulting protein (isoform 3) has the same N- and C-termini, but is shorter than isoform 1.
    Source sequence(s)
    AI431352, AK093740, AL137856, AW072594, BC014146
    Consensus CDS
    CCDS76192.1
    UniProtKB/Swiss-Prot
    Q9Y6B7
    UniProtKB/TrEMBL
    B1ALD0, B3KSJ4
    Related
    ENSP00000358580.1, ENST00000369567.5
    Conserved Domains (2) summary
    pfam01602
    Location:13357
    Adaptin_N; Adaptin N terminal region
    pfam09066
    Location:453562
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
  4. NM_006594.5NP_006585.2  AP-4 complex subunit beta-1 isoform 1

    See identical proteins and their annotated locations for NP_006585.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longer isoform (1). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AI431352, AL137856, AW072594, BC014146, HY012945
    Consensus CDS
    CCDS865.1
    UniProtKB/Swiss-Prot
    Q9Y6B7
    UniProtKB/TrEMBL
    A0A024R0D2
    Related
    ENSP00000256658.4, ENST00000256658.8
    Conserved Domains (3) summary
    sd00044
    Location:86113
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:621730
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9525
    Adaptin_N; Adaptin N terminal region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    113894194..113905067 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000091.2XP_016855580.1  AP-4 complex subunit beta-1 isoform X6

  2. XM_011540525.3XP_011538827.1  AP-4 complex subunit beta-1 isoform X2

    Conserved Domains (2) summary
    pfam09066
    Location:528637
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9432
    Adaptin_N; Adaptin N terminal region
  3. XM_024452423.1XP_024308191.1  AP-4 complex subunit beta-1 isoform X3

    Conserved Domains (3) summary
    sd00044
    Location:86113
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:517626
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9400
    Adaptin_N; Adaptin N terminal region
  4. XM_017000090.1XP_016855579.1  AP-4 complex subunit beta-1 isoform X4

    UniProtKB/TrEMBL
    B1ALD0
    Conserved Domains (2) summary
    pfam01602
    Location:13357
    Adaptin_N; Adaptin N terminal region
    pfam09066
    Location:453562
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
  5. XM_017000092.2XP_016855581.1  AP-4 complex subunit beta-1 isoform X8

    Conserved Domains (1) summary
    pfam09066
    Location:296405
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
  6. XM_024452435.1XP_024308203.1  AP-4 complex subunit beta-1 isoform X5

    Conserved Domains (3) summary
    sd00044
    Location:4674
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:442551
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    pfam12717
    Location:37185
    Cnd1; non-SMC mitotic condensation complex subunit 1
  7. XM_011540523.3XP_011538825.1  AP-4 complex subunit beta-1 isoform X1

    See identical proteins and their annotated locations for XP_011538825.1

    Conserved Domains (4) summary
    pfam01602
    Location:37450
    Adaptin_N; Adaptin N terminal region
    pfam09066
    Location:546655
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    pfam12717
    Location:37190
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:4674
    HEAT; HEAT repeat [structural motif]
  8. XM_024452441.1XP_024308209.1  AP-4 complex subunit beta-1 isoform X7

    Conserved Domains (2) summary
    pfam09066
    Location:349458
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:42232
    Adaptin_N; Adaptin N terminal region
  9. XM_017000089.2XP_016855578.1  AP-4 complex subunit beta-1 isoform X3

    Conserved Domains (3) summary
    sd00044
    Location:86113
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:517626
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9400
    Adaptin_N; Adaptin N terminal region
  10. XM_024452422.1XP_024308190.1  AP-4 complex subunit beta-1 isoform X2

    Conserved Domains (2) summary
    pfam09066
    Location:528637
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9432
    Adaptin_N; Adaptin N terminal region
  11. XM_017000093.2XP_016855582.1  AP-4 complex subunit beta-1 isoform X9

    Conserved Domains (3) summary
    pfam01602
    Location:30401
    Adaptin_N; Adaptin N terminal region
    pfam12717
    Location:98265
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:86113
    HEAT; HEAT repeat [structural motif]

RNA

  1. XR_002958805.1 RNA Sequence

  2. XR_002958806.1 RNA Sequence

  3. XR_001736928.2 RNA Sequence

  4. XR_001736930.2 RNA Sequence

  5. XR_002958807.1 RNA Sequence

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