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    AP1S3 adaptor related protein complex 1 subunit sigma 3 [ Homo sapiens (human) ]

    Gene ID: 130340, updated on 3-Apr-2024

    Summary

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    Official Symbol
    AP1S3provided by HGNC
    Official Full Name
    adaptor related protein complex 1 subunit sigma 3provided by HGNC
    Primary source
    HGNC:HGNC:18971
    See related
    Ensembl:ENSG00000152056 MIM:615781; AllianceGenome:HGNC:18971
    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
    PSORS15; sigma1C
    Summary
    This gene encodes a member of the adaptor-related protein complex 1, sigma subunit genes. The encoded protein is a component of adaptor protein complex 1 (AP-1), one of the AP complexes involved in claathrin-mediated vesicular transport from the Golgi or endosomes. Disruption of the pathway for display of HIV-1 antigens, which prevents recognition of the virus by cytotoxic T cells, has been shown to involve the AP-1 complex (PMID: 15569716). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
    Expression
    Broad expression in thyroid (RPKM 6.9), stomach (RPKM 3.1) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2q36.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (223755326..223837582, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (224238499..224320784, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (224620043..224702299, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12775 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:224482816-224483471 Neighboring gene secretogranin II Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:224561972-224563171 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:224563821-224565020 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:224590012-224591211 Neighboring gene MLX pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 2258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12376 Neighboring gene uncharacterized LOC124907988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:224746345-224746846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:224746847-224747346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17181 Neighboring gene WD repeat and FYVE domain containing 1 Neighboring gene general transcription factor IIIA pseudogene 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
    • 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. Adaptor Protein Complex 1 Sigma 3 Is Highly Expressed in Glioma and Could Enhance Its Progression. Ye T, et al. Comput Math Methods Med, 2021. PMID 34367317, Free PMC Article
    2. AP1S3 Mutations Cause Skin Autoinflammation by Disrupting Keratinocyte Autophagy and Up-Regulating IL-36 Production. Mahil SK, et al. J Invest Dermatol, 2016 Nov. PMID 27388993, Free PMC Article
    3. Replication of Caucasian loci associated with bone mineral density in Koreans. Kim YA, et al. Osteoporos Int, 2013 Oct. PMID 23575750
    4. AP1S3 is required for hepatitis C virus infection by stabilizing E2 protein. Li X, et al. Antiviral Res, 2016 Jul. PMID 27079945
    5. AP1S3 mutations are associated with pustular psoriasis and impaired Toll-like receptor 3 trafficking. Setta-Kaffetzi N, et al. Am J Hum Genet, 2014 May 1. PMID 24791904, Free PMC Article

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Adaptor Protein Complex 1 Sigma 3 Is Highly Expressed in Glioma and Could Enhance Its Progression.
      Title: Adaptor Protein Complex 1 Sigma 3 Is Highly Expressed in Glioma and Could Enhance Its Progression.
    2. study demonstrated that AP1S3 interacts with hepatitis C virus E2 and protects it from proteasome-dependent degradation
      Title: AP1S3 is required for hepatitis C virus infection by stabilizing E2 protein.
    3. AP1S3 silencing disrupted the endosomal translocation of the innate pattern-recognition receptor TLR-3 (Toll-like receptor 3) and resulted in a marked inhibition of downstream signaling.
      Title: AP1S3 mutations are associated with pustular psoriasis and impaired Toll-like receptor 3 trafficking.
    4. 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

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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
    Psoriasis 15, pustular, susceptibility to
    MedGen: C4015235 OMIM: 616106 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env The highly conserved C-terminal dileucine motif (residues 851-856) in the cytosolic domain of HIV-1 gp41 interacts with clathrin-associated AP-1 adaptor complexes PubMed
    env The cytoplasmic domain (residues 707-856) of HIV-1 gp41 interacts with whole clathrin-associated AP-1 and AP-2 adaptor complexes PubMed
    Nef nef Genome-wide shRNA screening identifies AP1S3, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed
    nef Adaptor-related protein complex 1 (AP-1) is necessary for cross-presentation by MHC-I HLA-A and HLA-B molecules containing a cytoplasmic tail tyrosine signal and that HIV-1 Nef inhibits the cross-presentation in antigen-presenting cells PubMed
    nef HIV-1 Nef stabilizes AP-1 complexes on endosomal membranes after ADP-ribosylation factor-1 (ARF1) -dependent attachment PubMed
    nef The dileucine motif (residues 164-165) in HIV-1 Nef is required for binding to AP-1 complexes and stabilizing their association with membranes PubMed
    nef A leucine-based motif near the C-terminus of HIV-1 Nef interacts with AP-1 complexes; residues 164 and 165 in Nef are required for the interaction with AP-1 PubMed

    Go to the HIV-1, Human Interaction Database

    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 adaptor activity 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 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 protein targeting IMP
    Inferred from Mutant Phenotype
    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-1 adaptor complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in clathrin-coated pit IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic vesicle membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    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 lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in trans-Golgi network membrane 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-1 complex subunit sigma-3
    Names
    adapter-related protein complex 1 subunit sigma-1C
    adaptor protein complex AP-1 sigma-1C subunit
    adaptor related protein complex 1 sigma 3 subunit
    adaptor-related protein complex 1 subunit sigma-1C
    clathrin assembly protein complex 1 sigma-1C small chain
    golgi adaptor HA1/AP1 adaptin sigma-1C subunit
    sigma 1C subunit of AP-1 clathrin

    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_034017.1 RefSeqGene

      Range
      5021..87277
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001039569.2 → NP_001034658.1  AP-1 complex subunit sigma-3

      See identical proteins and their annotated locations for NP_001034658.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the functional protein.
      Source sequence(s)
      AC093884, BE856458, BG177582, BG340480
      Consensus CDS
      CCDS42827.1
      UniProtKB/TrEMBL
      Q53R44
      Related
      ENSP00000379891.2, ENST00000396654.7
      Conserved Domains (1) summary
      cd14831
      Location:3 → 143
      AP1_sigma; AP-1 complex subunit sigma

    RNA

    1. NR_110905.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC093884, AK025338, BC009606, BC021898

    2. NR_110906.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC093884, AK025338, BC021898

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      223755326..223837582 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510600.4 → XP_011508902.1  AP-1 complex subunit sigma-3 isoform X1

      UniProtKB/TrEMBL
      A0A8V8TN69
      Related
      ENSP00000401705.1, ENST00000415298.5
      Conserved Domains (1) summary
      cl02092
      Location:1 → 100
      Clat_adaptor_s; Clathrin adaptor complex small chain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      224238499..224320784 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340528.1 → XP_054196503.1  AP-1 complex subunit sigma-3 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_178814.2: Suppressed sequence

      Description
      NM_178814.2: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96PC3.1 GenPept UniProtKB/Swiss-Prot:Q96PC3

    Gene LinkOut

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

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