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    AP1S2 adaptor related protein complex 1 subunit sigma 2 [ Homo sapiens (human) ]

    Gene ID: 8905, updated on 2-Nov-2024

    Summary

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    Official Symbol
    AP1S2provided by HGNC
    Official Full Name
    adaptor related protein complex 1 subunit sigma 2provided by HGNC
    Primary source
    HGNC:HGNC:560
    See related
    Ensembl:ENSG00000182287 MIM:300629; AllianceGenome:HGNC:560
    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
    PGS; DC22; MRX59; MRXS5; MRXSF; MRXS21; SIGMA1B
    Summary
    Adaptor protein complex 1 is found at the cytoplasmic face of coated vesicles located at the Golgi complex, where it mediates both the recruitment of clathrin to the membrane and the recognition of sorting signals within the cytosolic tails of transmembrane receptors. This complex is a heterotetramer composed of two large, one medium, and one small adaptin subunit. The protein encoded by this gene serves as the small subunit of this complex and is a member of the adaptin protein family. Transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2013]
    Expression
    Ubiquitous expression in heart (RPKM 13.6), endometrium (RPKM 13.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See AP1S2 in Genome Data Viewer
    Location:
    Xp22.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (15825806..15854813, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (15408728..15437727, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (15843929..15872936, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CA5BP1-CA5B readthrough Neighboring gene carbonic anhydrase 5B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:15809593-15810094 Neighboring gene inactivation escape 2 Neighboring gene zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20674 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:15872970-15873574 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:15926789-15927701 Neighboring gene RNA, U5F small nuclear 7, pseudogene Neighboring gene SET pseudogene 15

    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. Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation. Tarpey PS, et al. Am J Hum Genet, 2006 Dec. PMID 17186471, Free PMC Article
    2. A novel AP1S2 variant causing leaky splicing in X-linked intellectual disability: Further delineation and intrafamilial variability. Noojarern S, et al. Am J Med Genet A, 2024 Sep. PMID 38682877
    3. Mutations in the AP1S2 gene encoding the sigma 2 subunit of the adaptor protein 1 complex are associated with syndromic X-linked mental retardation with hydrocephalus and calcifications in basal ganglia. Saillour Y, et al. J Med Genet, 2007 Nov. PMID 17617514, Free PMC Article
    4. AP1S2 is mutated in X-linked Dandy-Walker malformation with intellectual disability, basal ganglia disease and seizures (Pettigrew syndrome). Cacciagli P, et al. Eur J Hum Genet, 2014 Mar. PMID 23756445, Free PMC Article
    5. Next-generation sequencing in X-linked intellectual disability. Tzschach A, et al. Eur J Hum Genet, 2015 Nov. PMID 25649377, Free PMC Article

    See all (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel AP1S2 variant causing leaky splicing in X-linked intellectual disability: Further delineation and intrafamilial variability.
      Title: A novel AP1S2 variant causing leaky splicing in X-linked intellectual disability: Further delineation and intrafamilial variability.
    2. MiR-204-5p-targeted AP1S2 is necessary for papillary thyroid carcinoma.
      Title: MiR-204-5p-targeted AP1S2 is necessary for papillary thyroid carcinoma.
    3. Long noncoding RNA LINC00518 acts as a competing endogenous RNA to promote the metastasis of malignant melanoma via miR-204-5p/AP1S2 axis.
      Title: Long noncoding RNA LINC00518 acts as a competing endogenous RNA to promote the metastasis of malignant melanoma via miR-204-5p/AP1S2 axis.
    4. Four generations in Chinese pedigree with Pettigrew syndrome resulting from a novel splice site mutation in AP1S2. AP1S2 mutations appear to be an important cause of Mental retardation,delayed in walking, abnormal speech, hypotonia, dysmorphic features, abnormal behavior and brain.
      Title: A novel splice site mutation in AP1S2 gene for X-linked mental retardation in a Chinese pedigree and literature review.
    5. sigma1B adaptin regulates adipogenesis by mediating the sorting of sortilin in adipose tissue.
      Title: σ1B adaptin regulates adipogenesis by mediating the sorting of sortilin in adipose tissue.
    6. The AP1S2 c.426+1 G>T mutation segregates with the disease in the Pettigrew syndrome family.
      Title: AP1S2 is mutated in X-linked Dandy-Walker malformation with intellectual disability, basal ganglia disease and seizures (Pettigrew syndrome).
    7. absence of an AP-1 defect in peripheral tissues is due to functional redundancy among AP-1 subunits
      Title: Clinical, cellular, and neuropathological consequences of AP1S2 mutations: further delineation of a recognizable X-linked mental retardation syndrome.
    8. A mutation in the 3d intron causes skipping of exon 3 yielding a protein with 3 new AAs terminating at codon 64. A new nonsense mutation p.Gln66X was found in exon 3. Without AP1S2, defective membrane protein trafficking alters brain neural cell fate.
      Title: Mutations in the AP1S2 gene encoding the sigma 2 subunit of the adaptor protein 1 complex are associated with syndromic X-linked mental retardation with hydrocephalus and calcifications in basal ganglia.
    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
    Pettigrew syndrome
    MedGen: C0796254 OMIM: 304340 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-04-28)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-04-28)

    ClinGen Genome Curation Page

    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 cytoplasmic domain (residues 707-856) of HIV-1 gp41 interacts with whole clathrin-associated AP-1 and AP-2 adaptor complexes PubMed
    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
    Nef 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 Exogenous Nef and TNF-alpha synergistically activate NF-kappaB and AP-1 resulting in enhancing viral replication in both chronically infected promonocytic cells and acutely infected primary macrophages 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 HIV-1 Nef stabilizes AP-1 complexes on endosomal membranes after ADP-ribosylation factor-1 (ARF1) -dependent attachment 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 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 
    part_of AP-type membrane coat adaptor complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    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-2
    Names
    adapter-related protein complex 1 sigma-1B subunit
    adaptor protein complex AP-1 sigma-1B subunit
    adaptor related protein complex 1 sigma 2 subunit
    adaptor-related protein complex 1 subunit sigma-1B
    clathrin adaptor complex AP1 sigma 1B subunit
    clathrin assembly protein complex 1 sigma-1B small chain
    golgi adaptor HA1/AP1 adaptin sigma-1B subunit
    sigma1B-adaptin

    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_009274.2 RefSeqGene

      Range
      5165..34172
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001272071.2 → NP_001259000.1  AP-1 complex subunit sigma-2 isoform 1

      See identical proteins and their annotated locations for NP_001259000.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC004106, AK312594
      Consensus CDS
      CCDS75958.1
      UniProtKB/TrEMBL
      A0A5F9ZHW1, B7Z853
      Related
      ENSP00000500695.1, ENST00000672987.1
      Conserved Domains (1) summary
      cd14831
      Location:2 → 144
      AP1_sigma; AP-1 complex subunit sigma

    2. NM_001368994.1 → NP_001355923.1  AP-1 complex subunit sigma-2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC004106, AK296135
      Consensus CDS
      CCDS94559.1
      UniProtKB/TrEMBL
      B7Z853, H7BZG6
      Related
      ENSP00000389474.2, ENST00000450644.2
      Conserved Domains (1) summary
      cd14831
      Location:2 → 142
      AP1_sigma; AP-1 complex subunit sigma

    3. NM_001369007.1 → NP_001355936.1  AP-1 complex subunit sigma-2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC004106, AF251295, AK299921
      Consensus CDS
      CCDS94560.1
      UniProtKB/TrEMBL
      A6NH01, B7Z853
      Related
      ENSP00000369645.1, ENST00000380291.5
      Conserved Domains (1) summary
      cd14831
      Location:2 → 144
      AP1_sigma; AP-1 complex subunit sigma

    4. NM_001369008.1 → NP_001355937.1  AP-1 complex subunit sigma-2 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC004106, AK130075, AK302908, AK312594
      Consensus CDS
      CCDS94561.1
      UniProtKB/TrEMBL
      A0A5F9ZI43, B7Z853
      Related
      ENSP00000500066.1, ENST00000673591.1
      Conserved Domains (1) summary
      cd14831
      Location:2 → 143
      AP1_sigma; AP-1 complex subunit sigma

    5. NM_003916.5 → NP_003907.3  AP-1 complex subunit sigma-2 isoform 2

      See identical proteins and their annotated locations for NP_003907.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame 3' exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC004106, BC001117, DC401898
      Consensus CDS
      CCDS14173.1
      UniProtKB/Swiss-Prot
      B4DSU4, O95326, P56377, Q9H2N6
      UniProtKB/TrEMBL
      B7Z853, Q549M9
      Related
      ENSP00000328789.2, ENST00000329235.6
      Conserved Domains (1) summary
      cd14831
      Location:2 → 144
      AP1_sigma; AP-1 complex subunit sigma

    RNA

    1. NR_160932.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC004106, AK296135, DC391819

    2. NR_160933.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC004106

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      15825806..15854813 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442606.1 → XP_047298562.1  AP-1 complex subunit sigma-2 isoform X1

    2. XM_047442607.1 → XP_047298563.1  AP-1 complex subunit sigma-2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      15408728..15437727 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328047.1 → XP_054184022.1  AP-1 complex subunit sigma-2 isoform X1

    2. XM_054328048.1 → XP_054184023.1  AP-1 complex subunit sigma-2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P56377.1 GenPept UniProtKB/Swiss-Prot:P56377

    Gene LinkOut

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

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