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

Gene ID: 10717, updated on 3-Nov-2024

Summary

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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; AllianceGenome:HGNC:572
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
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Genomic context

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See AP4B1 in Genome Data Viewer
Location:
1p13.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113894194..113905028, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113905856..113916690, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114436816..114447650, 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 ATAC-STARR-seq lymphoblastoid active region 1537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1538 Neighboring gene BCL2 like 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1541 Neighboring gene GATA motif-containing MPRA enhancer 196 Neighboring gene DNA cross-link repair 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1217 Neighboring gene HIPK1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114480377-114480904 Neighboring gene homeodomain interacting protein kinase 1 Neighboring gene MPRA-validated peak375 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:114519457-114520034 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:114521340-114522173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114523841-114524673 Neighboring gene olfactomedin like 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Mutation in the AP4B1 gene cause hereditary spastic paraplegia type 47 (SPG47) . Bauer P, et al. Neurogenetics, 2012 Feb. PMID 22290197
  2. A novel homozygous AP4B1 mutation in two brothers with AP-4 deficiency syndrome and ocular anomalies. Accogli A, et al. Am J Med Genet A, 2018 Apr. PMID 29430868
  3. Clinical and genetic characterization of AP4B1-associated SPG47. Ebrahimi-Fakhari D, et al. Am J Med Genet A, 2018 Feb. PMID 29193663
  4. AP4B1-associated hereditary spastic paraplegia: expansion of phenotypic spectrum related to homozygous p.Thr387fs variant. Szczałuba K, et al. J Appl Genet, 2020 May. PMID 32166732, Free PMC Article
  5. An AP4B1 frameshift mutation in siblings with intellectual disability and spastic tetraplegia further delineates the AP-4 deficiency syndrome. Abdollahpour H, et al. Eur J Hum Genet, 2015 Feb. PMID 24781758, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. AP4B1-associated hereditary spastic paraplegia: Expansion of clinico-genetic phenotype and geographic range.
    Title: AP4B1-associated hereditary spastic paraplegia: Expansion of clinico-genetic phenotype and geographic range.
  2. AP4B1-associated hereditary spastic paraplegia: expansion of phenotypic spectrum related to homozygous p.Thr387fs variant.
    Title: AP4B1-associated hereditary spastic paraplegia: expansion of phenotypic spectrum related to homozygous p.Thr387fs variant.
  3. AP4B1 mutation is associated with hereditary spastic paraplegia.
    Title: Locus and allelic heterogeneity in five families with hereditary spastic paraplegia.
  4. AP4B1-associated HSP and other AP-4-deficiency syndromes should be suspected in infants and children with hypotonia progressing to spastic paraplegia, delayed motor and speech development, and suggestive findings on brain imaging particularly thinning of the posterior aspect of the corpus callosum.
    Title: Clinical and genetic characterization of AP4B1-associated SPG47.
  5. we report a novel AP4B1 homozygous mutation in two siblings and review the phenotype of AP-4 deficiency, speculating on a possible role of AP-4 complex in eye development.
    Title: A novel homozygous AP4B1 mutation in two brothers with AP-4 deficiency syndrome and ocular anomalies.
  6. Novel homozygous 2-bp deletion in AP4B1 was found in siblings with intellectual disability and spastic tetraplegia.
    Title: An AP4B1 frameshift mutation in siblings with intellectual disability and spastic tetraplegia further delineates the AP-4 deficiency syndrome.
  7. Data suggest that AP4B1 mutations cause spastic paraplegia type 47 and should be considered in early onset spastic paraplegia with intellectual disability.
    Title: Mutation in the AP4B1 gene cause hereditary spastic paraplegia type 47 (SPG47) .
Submit: New GeneRIF Correction

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
Hereditary spastic paraplegia 47
MedGen: C3279738 OMIM: 614066 GeneReviews: AP-4-Associated Hereditary Spastic Paraplegia
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EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables clathrin binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization IC
Inferred by Curator
more info
 PubMed 
involved_in protein localization to somatodendritic compartment IEA
Inferred from Electronic Annotation
more info
  
involved_in protein targeting IC
Inferred by Curator
more info
 PubMed 
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-4 adaptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of AP-4 adaptor complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of clathrin adaptor complex IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic side of trans-Golgi network transport vesicle membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome lumen TAS
Traceable Author Statement
more info
  
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 
located_in trans-Golgi network NAS
Non-traceable Author Statement
more info
 PubMed 
located_in trans-Golgi network membrane TAS
Traceable Author Statement
more info
  

General protein information

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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)

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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

  1. NG_031901.1 RefSeqGene

    Range
    5321..15926
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001253852.3 → NP_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
    B7Z4X3, Q59EJ4, Q96CL6, Q9Y6B7
    UniProtKB/TrEMBL
    B2RBF6
    Related
    ENSP00000358582.1, ENST00000369569.6
    Conserved Domains (3) summary
    sd00044
    Location:86 → 113
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:621 → 730
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9 → 525
    Adaptin_N; Adaptin N terminal region

  2. NM_001253853.3 → NP_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/TrEMBL
    B4DTG3
    Conserved Domains (4) summary
    pfam01602
    Location:1 → 426
    Adaptin_N; Adaptin N terminal region
    pfam09066
    Location:522 → 631
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    pfam12717
    Location:2 → 166
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:22 → 50
    HEAT; HEAT repeat [structural motif]

  3. NM_001308312.2 → NP_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/TrEMBL
    B1ALD0, B1ALD3, B3KSJ4
    Related
    ENSP00000358580.1, ENST00000369567.6
    Conserved Domains (2) summary
    pfam01602
    Location:13 → 357
    Adaptin_N; Adaptin N terminal region
    pfam09066
    Location:453 → 562
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain

  4. NM_006594.5 → NP_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
    B7Z4X3, Q59EJ4, Q96CL6, Q9Y6B7
    UniProtKB/TrEMBL
    B2RBF6
    Related
    ENSP00000256658.4, ENST00000256658.8
    Conserved Domains (3) summary
    sd00044
    Location:86 → 113
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:621 → 730
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9 → 525
    Adaptin_N; Adaptin N terminal region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    113894194..113905028 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000090.2 → XP_016855579.1  AP-4 complex subunit beta-1 isoform X5

    UniProtKB/TrEMBL
    B1ALD0, B1ALD3, B3KSJ4
    Related
    ENSP00000393622.2, ENST00000432415.6
    Conserved Domains (2) summary
    pfam01602
    Location:13 → 357
    Adaptin_N; Adaptin N terminal region
    pfam09066
    Location:453 → 562
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain

  2. XM_024452435.2 → XP_024308203.1  AP-4 complex subunit beta-1 isoform X6

    UniProtKB/TrEMBL
    B4DTG3
    Conserved Domains (3) summary
    sd00044
    Location:46 → 74
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:442 → 551
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    pfam12717
    Location:37 → 185
    Cnd1; non-SMC mitotic condensation complex subunit 1

  3. XM_011540523.4 → XP_011538825.1  AP-4 complex subunit beta-1 isoform X2

    See identical proteins and their annotated locations for XP_011538825.1

    UniProtKB/TrEMBL
    B1ALD1, B4DTG3
    Related
    ENSP00000358577.2, ENST00000369564.6
    Conserved Domains (3) summary
    smart01020
    Location:545 → 657
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    PTZ00429
    Location:37 → 458
    PTZ00429; beta-adaptin; Provisional
    sd00044
    Location:46 → 74
    HEAT; HEAT repeat [structural motif]

  4. XM_017000091.3 → XP_016855580.1  AP-4 complex subunit beta-1 isoform X7

    UniProtKB/TrEMBL
    B3KSJ4

  5. XM_011540525.4 → XP_011538827.1  AP-4 complex subunit beta-1 isoform X3

    UniProtKB/TrEMBL
    B3KSJ4
    Conserved Domains (2) summary
    pfam09066
    Location:528 → 637
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9 → 432
    Adaptin_N; Adaptin N terminal region

  6. XM_024452423.2 → XP_024308191.1  AP-4 complex subunit beta-1 isoform X4

    UniProtKB/TrEMBL
    B2RBF6
    Conserved Domains (3) summary
    sd00044
    Location:86 → 113
    HEAT; HEAT repeat [structural motif]
    pfam09066
    Location:517 → 626
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:9 → 400
    Adaptin_N; Adaptin N terminal region

  7. XM_047438847.1 → XP_047294803.1  AP-4 complex subunit beta-1 isoform X1

    UniProtKB/Swiss-Prot
    B7Z4X3, Q59EJ4, Q96CL6, Q9Y6B7
    Related
    ENSP00000358584.3, ENST00000369571.3

  8. XM_024452441.2 → XP_024308209.1  AP-4 complex subunit beta-1 isoform X9

    UniProtKB/TrEMBL
    B3KSJ4
    Conserved Domains (2) summary
    pfam09066
    Location:349 → 458
    B2-adapt-app_C; Beta2-adaptin appendage, C-terminal sub-domain
    cl26317
    Location:42 → 232
    Adaptin_N; Adaptin N terminal region

  9. XM_047439008.1 → XP_047294964.1  AP-4 complex subunit beta-1 isoform X8

  10. XM_047439078.1 → XP_047295034.1  AP-4 complex subunit beta-1 isoform X11

  11. XM_047439052.1 → XP_047295008.1  AP-4 complex subunit beta-1 isoform X10

    Related
    ENSP00000518951.1, ENST00000713649.1

  12. XM_017000093.3 → XP_016855582.1  AP-4 complex subunit beta-1 isoform X12

    UniProtKB/TrEMBL
    A0AAQ5BGI8, A0AAQ5BGL5
    Related
    ENSP00000518949.1, ENST00000713647.1
    Conserved Domains (3) summary
    pfam01602
    Location:30 → 401
    Adaptin_N; Adaptin N terminal region
    pfam12717
    Location:98 → 265
    Cnd1; non-SMC mitotic condensation complex subunit 1
    sd00044
    Location:86 → 113
    HEAT; HEAT repeat [structural motif]

RNA

  1. XR_007066904.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    113905856..113916690 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333913.1 → XP_054189888.1  AP-4 complex subunit beta-1 isoform X5

    UniProtKB/TrEMBL
    B1ALD0, B1ALD3

  2. XM_054333914.1 → XP_054189889.1  AP-4 complex subunit beta-1 isoform X6

  3. XM_054333910.1 → XP_054189885.1  AP-4 complex subunit beta-1 isoform X2

    UniProtKB/TrEMBL
    B1ALD1

  4. XM_054333915.1 → XP_054189890.1  AP-4 complex subunit beta-1 isoform X7

  5. XM_054333911.1 → XP_054189886.1  AP-4 complex subunit beta-1 isoform X3

  6. XM_054333912.1 → XP_054189887.1  AP-4 complex subunit beta-1 isoform X4

  7. XM_054333909.1 → XP_054189884.1  AP-4 complex subunit beta-1 isoform X1

    UniProtKB/Swiss-Prot
    B7Z4X3, Q59EJ4, Q96CL6, Q9Y6B7

  8. XM_054333917.1 → XP_054189892.1  AP-4 complex subunit beta-1 isoform X9

  9. XM_054333916.1 → XP_054189891.1  AP-4 complex subunit beta-1 isoform X8

  10. XM_054333919.1 → XP_054189894.1  AP-4 complex subunit beta-1 isoform X11

  11. XM_054333918.1 → XP_054189893.1  AP-4 complex subunit beta-1 isoform X10

  12. XM_054333920.1 → XP_054189895.1  AP-4 complex subunit beta-1 isoform X12

    UniProtKB/TrEMBL
    A0AAQ5BGI8

RNA

  1. XR_008485876.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y6B7.2 GenPept UniProtKB/Swiss-Prot:Q9Y6B7

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