Human Gene AP4B1 (ENST00000369569.6) from GENCODE V44
  Description: Homo sapiens adaptor related protein complex 4 subunit beta 1 (AP4B1), transcript variant 2, mRNA. (from RefSeq NM_001253852)
RefSeq Summary (NM_001253852): 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].
Gencode Transcript: ENST00000369569.6
Gencode Gene: ENSG00000134262.13
Transcript (Including UTRs)
   Position: hg38 chr1:113,894,194-113,904,799 Size: 10,606 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chr1:113,895,065-113,904,717 Size: 9,653 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:113,894,194-113,904,799)mRNA (may differ from genome)Protein (739 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: AP4B1_HUMAN
DESCRIPTION: RecName: Full=AP-4 complex subunit beta-1; AltName: Full=AP-4 adapter complex subunit beta; AltName: Full=Adapter-related protein complex 4 subunit beta-1; AltName: Full=Beta subunit of AP-4; AltName: Full=Beta4-adaptin;
FUNCTION: Subunit of novel type of clathrin- or non-clathrin- associated protein coat involved in targeting proteins from the trans-Golgi network (TGN) to the endosomal-lysosomal system.
SUBUNIT: Adapter-like complex 4 (AP-4) is a heterotetramer composed of two large adaptins (epsilon-type subunit AP4E1 and beta-type subunit AP4B1), a medium adaptin (mu-type subunit AP4M1) and a small adaptin (sigma-type AP4S1). Interacts with C17orf56/tepsin; this interaction requires the presence of a functional AP-4 complex.
SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network. Note=Associated with the trans-Golgi network. Found in soma and dendritic shafts of neuronal cells.
TISSUE SPECIFICITY: Widely expressed.
DISEASE: Defects in AP4B1 are the cause of cerebral palsy spastic quadriplegic type 5 (CPSQ5) [MIM:614066]. CPSQ5 is a neurodevelopmental disorder characterized by neonatal hypotonia that progresses to hypertonia and spasticity, and severe mental retardation with poor or absent speech development.
SIMILARITY: Belongs to the adaptor complexes large subunit family.
SEQUENCE CAUTION: Sequence=BAD93054.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: AP4B1
Diseases sorted by gene-association score: spastic paraplegia 47, autosomal recessive* (927), severe intellectual disability and progressive spastic paraplegia* (175), spastic paraplegia 47* (129), hypertonia (13), hereditary spastic paraplegia 51 (12), spastic paraplegia 52, autosomal recessive (12), cerebral palsy (9), spastic paraplegia 50, autosomal recessive (8), spastic paraplegia 28, autosomal recessive (7), spastic paraplegia 56, autosomal recessive (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.86 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 287.76 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.0082-0.378 Picture PostScript Text
3' UTR -185.50871-0.213 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR026739 - AP_beta
IPR016342 - AP_complex_bsu_1_2_4
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR015151 - B-adaptin_app_sub_C
IPR012295 - Beta2_adaptin/TBP_C_dom
IPR002553 - Clathrin/coatomer_adapt-like_N

Pfam Domains:
PF01602 - Adaptin N terminal region
PF09066 - Beta2-adaptin appendage, C-terminal sub-domain

ModBase Predicted Comparative 3D Structure on Q9Y6B7
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0030276 clathrin binding

Biological Process:
GO:0006605 protein targeting
GO:0006886 intracellular protein transport
GO:0008104 protein localization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport

Cellular Component:
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0016020 membrane
GO:0019898 extrinsic component of membrane
GO:0030117 membrane coat
GO:0030124 AP-4 adaptor complex
GO:0030131 clathrin adaptor complex
GO:0031904 endosome lumen
GO:0032588 trans-Golgi network membrane


-  Descriptions from all associated GenBank mRNAs
  BC014146 - Homo sapiens adaptor-related protein complex 4, beta 1 subunit, mRNA (cDNA clone MGC:20704 IMAGE:2906087), complete cds.
AB209817 - Homo sapiens mRNA for adaptor-related protein complex 4, beta 1 subunit variant protein.
AF092094 - Homo sapiens AP-4 adaptor complex beta4 subunit mRNA, complete cds.
AK300204 - Homo sapiens cDNA FLJ53653 complete cds, highly similar to Adapter-relatedprotein complex 4 beta 1 subunit.
AK093740 - Homo sapiens cDNA FLJ36421 fis, clone THYMU2011259, highly similar to Adapter-related protein complex 4 beta 1 subunit.
AX748284 - Sequence 1809 from Patent EP1308459.
AK314641 - Homo sapiens cDNA, FLJ95484, highly similar to Homo sapiens adaptor-related protein complex 4, beta 1 subunit (AP4B1), mRNA.
JF432293 - Synthetic construct Homo sapiens clone IMAGE:100073471 adaptor-related protein complex 4, beta 1 subunit (AP4B1) gene, encodes complete protein.
KJ893119 - Synthetic construct Homo sapiens clone ccsbBroadEn_02513 AP4B1 gene, encodes complete protein.
AB385090 - Synthetic construct DNA, clone: pF1KB5378, Homo sapiens AP4B1 gene for AP-4 complex subunit beta-1, complete cds, without stop codon, in Flexi system.
AK298037 - Homo sapiens cDNA FLJ54036 complete cds, highly similar to Adapter-relatedprotein complex 4 beta 1 subunit.
AK001045 - Homo sapiens cDNA FLJ10183 fis, clone HEMBA1004276, highly similar to Homo sapiens AP-4 adaptor complex beta4 subunit mRNA.
AK057567 - Homo sapiens cDNA FLJ33005 fis, clone THYMU1000291, highly similar to Homo sapiens AP-4 adaptor complex beta4 subunit mRNA.
CU680806 - Synthetic construct Homo sapiens gateway clone IMAGE:100020050 5' read AP4B1 mRNA.
JD338761 - Sequence 319785 from Patent EP1572962.
JD467370 - Sequence 448394 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein Q9Y6B7 (Reactome details) participates in the following event(s):

R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-421833 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture
R-HSA-5229132 AP4 binds APP
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-5229111 AP4 transports APP from trans-Golgi network to endosome lumen
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: AP4B1_HUMAN, ENST00000369569.1, ENST00000369569.2, ENST00000369569.3, ENST00000369569.4, ENST00000369569.5, NM_001253852, Q59EJ4, Q96CL6, Q9Y6B7, uc001eeb.1, uc001eeb.2, uc001eeb.3, uc001eeb.4, uc001eeb.5
UCSC ID: ENST00000369569.6
RefSeq Accession: NM_001253852
Protein: Q9Y6B7 (aka AP4B1_HUMAN or A4B1_HUMAN)
CCDS: CCDS865.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene AP4B1:
ap4-def (AP-4-Associated Hereditary Spastic Paraplegia)
hsp (Hereditary Spastic Paraplegia Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.