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    AP4S1 adaptor related protein complex 4 subunit sigma 1 [ Homo sapiens (human) ]

    Gene ID: 11154, updated on 5-Mar-2024

    Summary

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    Official Symbol
    AP4S1provided by HGNC
    Official Full Name
    adaptor related protein complex 4 subunit sigma 1provided by HGNC
    Primary source
    HGNC:HGNC:575
    See related
    Ensembl:ENSG00000100478 MIM:607243; AllianceGenome:HGNC:575
    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
    AP47B; CLA20; CPSQ6; SPG52; CLAPS4
    Summary
    This gene encodes a member of the adaptor complexes small subunit protein family. These proteins are components of the heterotetrameric adaptor protein complexes, which play important roles in the secretory and endocytic pathways by mediating vesicle formation and sorting of integral membrane proteins. The encoded protein is the small subunit of adaptor protein complex-4, which is associated with both clathrin- and nonclathrin-coated vesicles. Mutations in this gene are associated with spastic quadriplegic cerebral palsy-6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 6. [provided by RefSeq, Dec 2011]
    Expression
    Ubiquitous expression in brain (RPKM 1.8), testis (RPKM 1.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    14q12
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (31025106..31096450)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (25222939..25294259)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (31494312..31565656)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene striatin 3 Neighboring gene intraflagellar transport 20 homolog (Chlamydomonas) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8228 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:31494803-31494984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8229 Neighboring gene microRNA 624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:31516497-31517022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5652 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:31591905-31592742 Neighboring gene HECT domain E3 ubiquitin protein ligase 1 Neighboring gene ribosomal protein L21 pseudogene 5 Neighboring gene RNA, U6 small nuclear 541, pseudogene

    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. Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia. McCullough CG, et al. Hum Mutat, 2020 Feb. PMID 31660686
    2. Identification of mutations in AP4S1/SPG52 through next generation sequencing in three families. Tessa A, et al. Eur J Neurol, 2016 Oct. PMID 27444738
    3. Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly. Hardies K, et al. Hum Mol Genet, 2015 Apr 15. PMID 25552650, Free PMC Article
    4. AP-4-Associated Hereditary Spastic Paraplegia. Adam MP, et al. , 1993. PMID 30543385
    5. Adaptor protein complex 4 deficiency causes severe autosomal-recessive intellectual disability, progressive spastic paraplegia, shy character, and short stature. Abou Jamra R, et al. Am J Hum Genet, 2011 Jun 10. PMID 21620353, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia.
      Title: Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia.
    2. Loss of ap4s1 in zebrafish leads to neurodevelopmental defects resembling spastic paraplegia 52.
      Title: Loss of ap4s1 in zebrafish leads to neurodevelopmental defects resembling spastic paraplegia 52.
    3. Identification of mutations in AP4S1/SPG52 in hereditary spastic paraplegia.
      Title: Identification of mutations in AP4S1/SPG52 through next generation sequencing in three families.
    4. Premature stop mutations in AP4S1 result in loss of AP-4 complex assembly and cause fever-sensitive seizures, developmental delay and spastic paraplegia.
      Title: Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly.
    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

    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

    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

    Clone Names

    • FLJ32366, FLJ41011

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in protein localization IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in protein targeting IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 
    located_in endosome lumen TAS
    Traceable Author Statement
    more info
    		  
    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 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 sigma-1
    Names
    AP-4 adapter complex subunit sigma-1
    AP-4 adaptor complex subunit sigma-1
    adaptor related protein complex 4 sigma 1 subunit
    clathrin-associated/assembly/adaptor protein, sigma 4
    sigma-4-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_031913.1 RefSeqGene

      Range
      5544..76345
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001128126.3 → NP_001121598.1  AP-4 complex subunit sigma-1 isoform 2

      See identical proteins and their annotated locations for NP_001121598.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region and has an alternate terminal exon, compared to variant 1. Variants 2, 5 and 6 encode the same isoform (2), which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI570549, AK304115, AL121808, R46468
      Consensus CDS
      CCDS45093.1
      UniProtKB/Swiss-Prot
      G3V2N8, Q6IAQ4, Q86U36, Q9BVE7, Q9Y587
      UniProtKB/TrEMBL
      B7ZB52
      Related
      ENSP00000438170.2, ENST00000542754.7
      Conserved Domains (1) summary
      cd14832
      Location:3 → 140
      AP4_sigma; AP-4 complex subunit sigma

    2. NM_001254726.2 → NP_001241655.1  AP-4 complex subunit sigma-1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AL121808, BC001259, BG702035, BX388185
      Consensus CDS
      CCDS58310.1
      UniProtKB/Swiss-Prot
      Q9Y587
      Related
      ENSP00000452383.2, ENST00000554609.6
      Conserved Domains (1) summary
      cl02092
      Location:1 → 102
      Clat_adaptor_s; Clathrin adaptor complex small chain

    3. NM_001254727.2 → NP_001241656.1  AP-4 complex subunit sigma-1 isoform 4

      See identical proteins and their annotated locations for NP_001241656.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate internal exon, which results in a frameshift, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL121808, BC001259, BG702035, BX247969
      Consensus CDS
      CCDS58309.1
      UniProtKB/TrEMBL
      A0A5F9ZH42
      Related
      ENSP00000334484.4, ENST00000334725.8
      Conserved Domains (2) summary
      cl02092
      Location:1 → 105
      Clat_adaptor_s; Clathrin adaptor complex small chain
      pfam13900
      Location:128 → 149
      GVQW; Putative domain of unknown function

    4. NM_001254728.2 → NP_001241657.1  AP-4 complex subunit sigma-1 isoform 2

      See identical proteins and their annotated locations for NP_001241657.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, uses an alternate splice site in the 3' coding region and has an alternate terminal exon, compared to variant 1. Variants 2, 5 and 6 encode the same isoform (2), which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI570549, AL121808, BC035622, R46468
      Consensus CDS
      CCDS45093.1
      UniProtKB/Swiss-Prot
      G3V2N8, Q6IAQ4, Q86U36, Q9BVE7, Q9Y587
      UniProtKB/TrEMBL
      B7ZB52
      Related
      ENSP00000451609.2, ENST00000555417.6
      Conserved Domains (1) summary
      cd14832
      Location:3 → 140
      AP4_sigma; AP-4 complex subunit sigma

    5. NM_001254729.2 → NP_001241658.1  AP-4 complex subunit sigma-1 isoform 2

      See identical proteins and their annotated locations for NP_001241658.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, uses an alternate splice site in the 3' coding region and has an alternate terminal exon, compared to variant 1. Variants 2, 5 and 6 encode the same isoform (2), which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI570549, AK304115, AL049830, AL121808, BF671561, R46468
      Consensus CDS
      CCDS45093.1
      UniProtKB/Swiss-Prot
      G3V2N8, Q6IAQ4, Q86U36, Q9BVE7, Q9Y587
      UniProtKB/TrEMBL
      B7ZB52
      Related
      ENSP00000451479.2, ENST00000557346.6
      Conserved Domains (1) summary
      cd14832
      Location:3 → 140
      AP4_sigma; AP-4 complex subunit sigma

    6. NM_007077.5 → NP_009008.2  AP-4 complex subunit sigma-1 isoform 1

      See identical proteins and their annotated locations for NP_009008.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL121808, BC001259, BG702035
      Consensus CDS
      CCDS9642.1
      UniProtKB/Swiss-Prot
      Q9Y587
      Related
      ENSP00000450768.2, ENST00000554345.6
      Conserved Domains (1) summary
      cl02092
      Location:1 → 105
      Clat_adaptor_s; Clathrin adaptor complex small chain

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      31025106..31096450
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536371.4 → XP_011534673.1  AP-4 complex subunit sigma-1 isoform X1

      See identical proteins and their annotated locations for XP_011534673.1

      UniProtKB/Swiss-Prot
      Q9Y587
      Conserved Domains (1) summary
      cl02092
      Location:1 → 105
      Clat_adaptor_s; Clathrin adaptor complex small chain

    2. XM_005267293.6 → XP_005267350.1  AP-4 complex subunit sigma-1 isoform X1

      See identical proteins and their annotated locations for XP_005267350.1

      UniProtKB/Swiss-Prot
      Q9Y587
      Conserved Domains (1) summary
      cl02092
      Location:1 → 105
      Clat_adaptor_s; Clathrin adaptor complex small chain

    3. XM_011536372.4 → XP_011534674.1  AP-4 complex subunit sigma-1 isoform X1

      See identical proteins and their annotated locations for XP_011534674.1

      UniProtKB/Swiss-Prot
      Q9Y587
      Conserved Domains (1) summary
      cl02092
      Location:1 → 105
      Clat_adaptor_s; Clathrin adaptor complex small chain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      25222939..25294259
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375291.1 → XP_054231266.1  AP-4 complex subunit sigma-1 isoform X1

    2. XM_054375292.1 → XP_054231267.1  AP-4 complex subunit sigma-1 isoform X1

    3. XM_054375293.1 → XP_054231268.1  AP-4 complex subunit sigma-1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y587.1 GenPept UniProtKB/Swiss-Prot:Q9Y587

    Gene LinkOut

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

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