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    CLINT1 clathrin interactor 1 [ Homo sapiens (human) ]

    Gene ID: 9685, updated on 3-Nov-2024

    Summary

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    Official Symbol
    CLINT1provided by HGNC
    Official Full Name
    clathrin interactor 1provided by HGNC
    Primary source
    HGNC:HGNC:23186
    See related
    Ensembl:ENSG00000113282 MIM:607265; AllianceGenome:HGNC:23186
    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
    ENTH; EPN4; EPNR; CLINT
    Summary
    This gene encodes a protein with similarity to the epsin family of endocytic adapter proteins. The encoded protein interacts with clathrin, the adapter protein AP-1 and phosphoinositides. This protein may be involved in the formation of clathrin coated vesicles and trafficking between the trans-Golgi network and endosomes. Mutations in this gene are associated with a susceptibility to schizophrenia and psychotic disorders. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2010]
    Expression
    Ubiquitous expression in bone marrow (RPKM 39.0), gall bladder (RPKM 37.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLINT1 in Genome Data Viewer
    Location:
    5q33.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (157785747..157859145, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (158307922..158381316, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (157212755..157286153, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:157171083-157171583 Neighboring gene tRNA-histidine guanylyltransferase 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16564 Neighboring gene LSM11, U7 small nuclear RNA associated Neighboring gene RNA, U6 small nuclear 260, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:157285783-157286364 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:157308515-157309160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16565 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:157346675-157346817 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:157353623-157354424 Neighboring gene uncharacterized LOC124901193 Neighboring gene ribosomal protein lateral stalk subunit P2 pseudogene 2

    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. The epsin 4 gene is associated with psychotic disorders in families of Latin American origin. Escamilla M, et al. Schizophr Res, 2008 Dec. PMID 18929466
    2. Failure to confirm an association between Epsin 4 and schizophrenia in a Japanese population. Richards M, et al. J Neural Transm (Vienna), 2008 Sep. PMID 18696005
    3. The Epsin 4 gene on chromosome 5q, which encodes the clathrin-associated protein enthoprotin, is involved in the genetic susceptibility to schizophrenia. Pimm J, et al. Am J Hum Genet, 2005 May. PMID 15793701, Free PMC Article
    4. Clathrin adaptor epsinR is required for retrograde sorting on early endosomal membranes. Saint-Pol A, et al. Dev Cell, 2004 Apr. PMID 15068792
    5. Family-based association study of Epsin 4 and Schizophrenia. Tang RQ, et al. Mol Psychiatry, 2006 Apr. PMID 16402136

    See all (144) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection.
      Title: The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection.
    2. Although epsinR has been shown to be a cargo adaptor, the present study indicates that it is an order of magnitude more abundant in CCVs than its known cargo protein, vti1b, suggesting that it may have other functions as well.
      Title: Contributions of epsinR and gadkin to clathrin-mediated intracellular trafficking.
    3. These results do not support a significant role of GRIA1 or CLINT1 in the development of schizophrenia in the German population.
      Title: Association study of the GRIA1 and CLINT1 (Epsin 4) genes in a German schizophrenia sample.
    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.
    5. Variation in the Epsin 4 gene is significantly associated with psychotic disorder in this Latino population
      Title: The epsin 4 gene is associated with psychotic disorders in families of Latin American origin.
    6. Our results suggest that the examined region of Epsin 4 does not have a major influence on susceptibility to schizophrenia in Japanese.
      Title: Failure to confirm an association between Epsin 4 and schizophrenia in a Japanese population.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients.
    8. characterization of the molecular details governing the sorting of a SNARE into clathrin-coated vesicles, namely the direct recognition of the three-helical bundle H(abc) domain of the mouse SNARE Vti1b by the human clathrin adaptor epsinR
      Title: A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles.
    9. might participate in the formation of clathrin-coated vesicles at the level of the trans-Golgi network and remains associated with the vesicles longer than clathrin and adaptors
      Title: Clint: a novel clathrin-binding ENTH-domain protein at the Golgi.
    10. epsinR is an adaptor for vesicle-associated soluble NSF attachment protein receptor
      Title: EpsinR is an adaptor for the SNARE protein Vti1b.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies CLINT1, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ46753, KIAA0171

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cadherin binding HDA PubMed 
    enables clathrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables clathrin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables phospholipid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in clathrin coat assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of clathrin vesicle coat IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    clathrin interactor 1
    Names
    clathrin interacting protein localized in the trans-Golgi region
    enthoprotin
    epsin 4
    epsin-related protein
    epsinR

    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_027820.2 RefSeqGene

      Range
      5031..78429
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001195555.2 → NP_001182484.1  clathrin interactor 1 isoform 1

      See identical proteins and their annotated locations for NP_001182484.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK300257, BC013091, BP246338, D79993
      Consensus CDS
      CCDS56389.1
      UniProtKB/TrEMBL
      A0A0S2Z5H3
      Related
      ENSP00000429824.1, ENST00000523908.5
      Conserved Domains (2) summary
      cd16989
      Location:24 → 149
      ENTH_EpsinR; Epsin N-Terminal Homology (ENTH) domain of Epsin-related protein
      pfam13634
      Location:329 → 407
      Nucleoporin_FG; Nucleoporin FG repeat region

    2. NM_001195556.2 → NP_001182485.1  clathrin interactor 1 isoform 3

      See identical proteins and their annotated locations for NP_001182485.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC026407, AK092765, BC013091, D79993
      Consensus CDS
      CCDS56388.1
      UniProtKB/Swiss-Prot
      Q14677
      Related
      ENSP00000429345.1, ENST00000523094.5
      Conserved Domains (1) summary
      cd03571
      Location:5 → 128
      ENTH_epsin; ENTH domain, Epsin family; The epsin (Eps15 interactor) N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated ...

    3. NM_014666.4 → NP_055481.1  clathrin interactor 1 isoform 2

      See identical proteins and their annotated locations for NP_055481.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      BC013091, BK000414, BP246338
      Consensus CDS
      CCDS47330.1
      UniProtKB/Swiss-Prot
      B7Z6F8, D3DQJ6, Q14677, Q8NAF1, Q96E05
      UniProtKB/TrEMBL
      A0A0S2Z4Y4
      Related
      ENSP00000388340.2, ENST00000411809.7
      Conserved Domains (2) summary
      cd16989
      Location:24 → 149
      ENTH_EpsinR; Epsin N-Terminal Homology (ENTH) domain of Epsin-related protein
      pfam13634
      Location:329 → 407
      Nucleoporin_FG; Nucleoporin FG repeat 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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      157785747..157859145 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017010087.2 → XP_016865576.1  clathrin interactor 1 isoform X2

    2. XM_011534701.4 → XP_011533003.1  clathrin interactor 1 isoform X1

      Conserved Domains (2) summary
      cd03571
      Location:23 → 146
      ENTH_epsin; ENTH domain, Epsin family; The epsin (Eps15 interactor) N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated ...
      pfam13634
      Location:302 → 400
      Nucleoporin_FG; Nucleoporin FG repeat region

    3. XM_017010088.3 → XP_016865577.1  clathrin interactor 1 isoform X3

      Conserved Domains (1) summary
      cd16989
      Location:24 → 149
      ENTH_EpsinR; Epsin N-Terminal Homology (ENTH) domain of Epsin-related protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      158307922..158381316 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353900.1 → XP_054209875.1  clathrin interactor 1 isoform X2

    2. XM_054353899.1 → XP_054209874.1  clathrin interactor 1 isoform X1

    3. XM_054353901.1 → XP_054209876.1  clathrin interactor 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14677.1 GenPept UniProtKB/Swiss-Prot:Q14677

    Gene LinkOut

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

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