U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

AP3S1 adaptor related protein complex 3 subunit sigma 1 [ Homo sapiens (human) ]

Gene ID: 1176, updated on 3-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
AP3S1provided by HGNC
Official Full Name
adaptor related protein complex 3 subunit sigma 1provided by HGNC
Primary source
HGNC:HGNC:2013
See related
Ensembl:ENSG00000177879 MIM:601507; AllianceGenome:HGNC:2013
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
CLAPS3; Sigma3A
Summary
This gene encodes a subunit of the AP3 adaptor complex. This complex functions in the formation of subcellular vesicles budded from the Golgi body. Several related pseudogenes of this gene have been found. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in bone marrow (RPKM 9.7), small intestine (RPKM 6.5) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
5q22.3-q23.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (115841935..115914081)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (116354331..116426478)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (115177632..115249778)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14872 Neighboring gene uncharacterized LOC124901049 Neighboring gene cysteine dioxygenase type 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:115176125-115176625 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:115176629-115177530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22939 Neighboring gene autophagy related 12 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:115216191-115216388 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:115265650-115266849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22940 Neighboring gene lincRNA adipogenesis and lipogenesis associated Neighboring gene laeverin Neighboring gene DEAD-box helicase 43 pseudogene 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Cloning, expression pattern and mapping to 12p 13.2 --> p13.1 of CLAPS3, a gene encoding a novel clathrin-adaptor small chain. Watanabe TK, et al. Cytogenet Cell Genet, 1996. PMID 8697810
  2. Downregulation of genes encoding for subunits of adaptor complex-3 in cervical carcinomas. Petrenko AA, et al. Biochemistry (Mosc), 2006 Oct. PMID 17125464
  3. Structural requirements for interactions between leucine-sorting signals and clathrin-associated adaptor protein complex AP3. Rodionov DG, et al. J Biol Chem, 2002 Dec 6. PMID 12370188
  4. RNF13 Dileucine Motif Variants L311S and L312P Interfere with Endosomal Localization and AP-3 Complex Association. Cabana VC, et al. Cells, 2021 Nov 6. PMID 34831286, Free PMC Article
  5. Interaction of insulin receptor substrate-1 with the sigma3A subunit of the adaptor protein complex-3 in cultured adipocytes. VanRenterghem B, et al. J Biol Chem, 1998 Nov 6. PMID 9792713

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KCNQ and AP3S1, but not MAN2A1 or ALDH7A1 have a role in risk of type 2 diabetes in the Chinese Northern Han population
    Title: Variants in KCNQ1, AP3S1, MAN2A1, and ALDH7A1 and the risk of type 2 diabetes in the Chinese Northern Han population: a case-control study and meta-analysis.
  2. Observational study and meta-analysis of gene-disease association. (HuGE Navigator)
    Title: Variants in KCNQ1, AP3S1, MAN2A1, and ALDH7A1 and the risk of type 2 diabetes in the Chinese Northern Han population: a case-control study and meta-analysis.
  3. 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.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
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
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify adaptor-related protein complex 3 sigma 1 subunit (AP3S1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
gag AP3S1 deficiency in HPS2 fibroblasts inhibits HIV-1 Gag assembly and release 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
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

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi to vacuole transport IEA
Inferred from Electronic Annotation
more info
  
involved_in anterograde axonal transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in anterograde synaptic vesicle transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in clathrin-coated vesicle cargo loading, AP-3-mediated NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in insulin receptor signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in melanosome assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in platelet dense granule organization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in synaptic vesicle coating NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in synaptic vesicle recycling NAS
Non-traceable Author Statement
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-3 adaptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of AP-3 adaptor complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of AP-type membrane coat adaptor complex TAS
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
  
located_in cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  
located_in early endosome NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  
located_in transport vesicle TAS
Traceable Author Statement
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
AP-3 complex subunit sigma-1
Names
adapter-related protein complex 3 subunit sigma-1
adaptor related protein complex 3 sigma 1 subunit
clathrin adaptor complex AP3, sigma-3A subunit
clathrin-associated/assembly/adapter protein, small 3
clathrin-associated/assembly/adaptor protein, small 3 (22kD)
sigma-adaptin 3a

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

mRNA and Protein(s)

  1. NM_001002924.3 → NP_001002924.2  AP-3 complex subunit sigma-1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' region, lacks an alternate in-frame exon in the 3' end, and initiates translation at an alternate start codon compared to variant 7. The encoded isoform (2) has a shorter N-terminus and lacks an alternate C-terminal segment compared to isoform 7.
    Source sequence(s)
    BC000804, BC012614, BP368651, BX647735
    UniProtKB/TrEMBL
    B2R4I8
    Related
    ENST00000395548.6
    Conserved Domains (1) summary
    COG5030
    Location:1 → 130
    APS2; Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]

  2. NM_001284.4 → NP_001275.1  AP-3 complex subunit sigma-1 isoform 1

    See identical proteins and their annotated locations for NP_001275.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon in the 3' end compared to variant 7. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 7.
    Source sequence(s)
    BC000804, BP368651, BX647735
    Consensus CDS
    CCDS4123.1
    UniProtKB/Swiss-Prot
    O00647, O00676, O00721, O00727, Q53XL4, Q6ICQ2, Q92572
    UniProtKB/TrEMBL
    B2R4I8
    Related
    ENSP00000325369.7, ENST00000316788.12
    Conserved Domains (1) summary
    cd14834
    Location:1 → 146
    AP3_sigma; AP-3 complex subunit sigma

  3. NM_001318090.2 → NP_001305019.1  AP-3 complex subunit sigma-1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks three alternate in-frame exons compared to variant 7. The encoded isoform (3) is shorter than isoform 7.
    Source sequence(s)
    BC000804, DB483797
    UniProtKB/Swiss-Prot
    Q92572
    Conserved Domains (1) summary
    cl38905
    Location:1 → 78
    longin-like; Longin-like domains

  4. NM_001318091.2 → NP_001305020.1  AP-3 complex subunit sigma-1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 7. The encoded isoform (4) is shorter than isoform 7.
    Source sequence(s)
    BC000804, CN411347
    UniProtKB/TrEMBL
    B2R4I8
    Conserved Domains (1) summary
    cd14834
    Location:1 → 122
    AP3_sigma; AP-3 complex subunit sigma

  5. NM_001318093.2 → NP_001305022.1  AP-3 complex subunit sigma-1 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon and contains another alternate exon, which results in a frameshift, compared to variant 7. The encoded isoform (5) has a shorter, distinct C-terminus compared to isoform 7.
    Source sequence(s)
    AC010282, BC000804, BI757703, BP368651, BX647735
    Consensus CDS
    CCDS83021.1
    UniProtKB/TrEMBL
    B2R4I8, F5H459
    Related
    ENSP00000446179.1, ENST00000506430.2
    Conserved Domains (1) summary
    cd14834
    Location:1 → 146
    AP3_sigma; AP-3 complex subunit sigma

  6. NM_001318094.2 → NP_001305023.1  AP-3 complex subunit sigma-1 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks two alternate in-frame exons compared to variant 7. The encoded isoform (6) is shorter than isoform 7.
    Source sequence(s)
    BC000804, BP368651, BX394598, BX647735
    UniProtKB/TrEMBL
    B2R4I8
    Conserved Domains (1) summary
    cd14834
    Location:1 → 115
    AP3_sigma; AP-3 complex subunit sigma

  7. NM_001364119.1 → NP_001351048.1  AP-3 complex subunit sigma-1 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) encodes the longest isoform (7).
    Source sequence(s)
    AC010282, AC026449
    UniProtKB/TrEMBL
    B2R4I8
    Conserved Domains (1) summary
    cd14834
    Location:1 → 146
    AP3_sigma; AP-3 complex subunit sigma

  8. NM_001364120.1 → NP_001351049.1  AP-3 complex subunit sigma-1 isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains an alternate exon and lacks two other alternate exons compared to variant 7. The resulting isoform (8) has a shorter and distinct C-terminus compared to isoform 7.
    Source sequence(s)
    AC010282, AC026449
    Conserved Domains (1) summary
    cd14834
    Location:1 → 122
    AP3_sigma; AP-3 complex subunit sigma

  9. NM_001364122.1 → NP_001351051.1  AP-3 complex subunit sigma-1 isoform 9

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks three alternate exons compared to variant 7. The resulting isoform (9) is shorter compared to isoform 7.
    Source sequence(s)
    AC010282, AC026449
    Conserved Domains (1) summary
    cl38905
    Location:1 → 91
    longin-like; Longin-like domains

RNA

  1. NR_157084.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC010282, AC026449

  2. NR_157085.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC010282, AC026449

  3. NR_157086.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC010282, AC026449

  4. NR_157087.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC010282, AC026449

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    115841935..115914081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416696.1 → XP_047272652.1  AP-3 complex subunit sigma-1 isoform X2

  2. XM_017009024.3 → XP_016864513.2  AP-3 complex subunit sigma-1 isoform X1

    UniProtKB/TrEMBL
    B2R4I8, F5H459
    Conserved Domains (1) summary
    cd14834
    Location:1 → 146
    AP3_sigma; AP-3 complex subunit sigma

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    116354331..116426478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351566.1 → XP_054207541.1  AP-3 complex subunit sigma-1 isoform X2

  2. XM_054351565.1 → XP_054207540.1  AP-3 complex subunit sigma-1 isoform X1

    UniProtKB/TrEMBL
    F5H459
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92572.1 GenPept UniProtKB/Swiss-Prot:Q92572

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous