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    CLHC1 clathrin heavy chain linker domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 130162, updated on 17-Jun-2024

    Summary

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    Official Symbol
    CLHC1provided by HGNC
    Official Full Name
    clathrin heavy chain linker domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:26453
    See related
    Ensembl:ENSG00000162994 AllianceGenome:HGNC:26453
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C2orf63
    Expression
    Broad expression in testis (RPKM 1.3), thyroid (RPKM 0.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Try the new Transcript table

    Genomic context

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    See CLHC1 in Genome Data Viewer
    Location:
    2p16.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55172547..55232563, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55169784..55229793, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (55399683..55459699, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene reticulon 4 Neighboring gene RNA, U6 small nuclear 433, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15772 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55276593-55277405 Neighboring gene uncharacterized LOC105374662 Neighboring gene Sharpr-MPRA regulatory region 4359 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:55360796-55361708 Neighboring gene CRISPRi-validated cis-regulatory element chr2.2087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15778 Neighboring gene CDPF1 pseudogene 1 Neighboring gene ribosomal protein S27a Neighboring gene mitochondrial translational initiation factor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55496405-55497228 Neighboring gene Sharpr-MPRA regulatory regions 8685 and 822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55508487-55509380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55509381-55510272 Neighboring gene prolyl-tRNA synthetase associated domain containing 1, 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. Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2. Winham SJ, et al. Mol Psychiatry, 2014 Sep. PMID 24322204
    2. BRCA2 mediates centrosome cohesion via an interaction with cytoplasmic dynein. Malik S, et al. Cell Cycle, 2016 Aug 17. PMID 27433848, Free PMC Article
    3. A Cross-Species Study of PI3K Protein-Protein Interactions Reveals the Direct Interaction of P85 and SHP2. Breitkopf SB, et al. Sci Rep, 2016 Feb 3. PMID 26839216, Free PMC Article
    4. Gsk3β and Tomm20 are substrates of the SCFFbxo7/PARK15 ubiquitin ligase associated with Parkinson's disease. Teixeira FR, et al. Biochem J, 2016 Oct 15. PMID 27503909, Free PMC Article
    5. A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Zhou Y, et al. Nat Biotechnol, 2023 Jan. PMID 36217030, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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

    EBI GWAS Catalog

    Description
    Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: RTN4

    Homology

    Clone Names

    • FLJ31438

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    clathrin heavy chain linker domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_033063.1 RefSeqGene

      Range
      5271..65017
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135598.2 → NP_001129070.1  clathrin heavy chain linker domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001129070.1

      Status: VALIDATED

      Source sequence(s)
      AC093165, BC029502, BC036908, BM046729, BM968338
      Consensus CDS
      CCDS46287.1
      UniProtKB/Swiss-Prot
      Q8NHS4
      Related
      ENSP00000385512.1, ENST00000406076.5
      Conserved Domains (1) summary
      pfam13838
      Location:175 → 232
      Clathrin_H_link; Clathrin-H-link

    2. NM_001353779.2 → NP_001340708.1  clathrin heavy chain linker domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Conserved Domains (1) summary
      pfam13838
      Location:113 → 166
      Clathrin_H_link; Clathrin-H-link

    3. NM_001353780.2 → NP_001340709.1  clathrin heavy chain linker domain-containing protein 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Conserved Domains (2) summary
      pfam13838
      Location:235 → 288
      Clathrin_H_link; Clathrin-H-link
      pfam15739
      Location:30 → 136
      TSNAXIP1_N; Translin-associated factor X-interacting N-terminus

    4. NM_001353781.2 → NP_001340710.1  clathrin heavy chain linker domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Consensus CDS
      CCDS46287.1
      Conserved Domains (1) summary
      pfam13838
      Location:175 → 232
      Clathrin_H_link; Clathrin-H-link

    5. NM_001353782.2 → NP_001340711.1  clathrin heavy chain linker domain-containing protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Conserved Domains (1) summary
      pfam13838
      Location:157 → 214
      Clathrin_H_link; Clathrin-H-link

    6. NM_001353783.2 → NP_001340712.1  clathrin heavy chain linker domain-containing protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Conserved Domains (1) summary
      pfam13838
      Location:157 → 214
      Clathrin_H_link; Clathrin-H-link

    7. NM_001353784.2 → NP_001340713.1  clathrin heavy chain linker domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Consensus CDS
      CCDS46287.1
      Conserved Domains (1) summary
      pfam13838
      Location:175 → 232
      Clathrin_H_link; Clathrin-H-link

    8. NM_001353785.2 → NP_001340714.1  clathrin heavy chain linker domain-containing protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Conserved Domains (1) summary
      pfam13838
      Location:95 → 148
      Clathrin_H_link; Clathrin-H-link

    9. NM_001353786.2 → NP_001340715.1  clathrin heavy chain linker domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Conserved Domains (1) summary
      pfam13838
      Location:113 → 166
      Clathrin_H_link; Clathrin-H-link

    10. NM_001353787.2 → NP_001340716.1  clathrin heavy chain linker domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165
      Conserved Domains (1) summary
      pfam13838
      Location:113 → 166
      Clathrin_H_link; Clathrin-H-link

    11. NM_152385.4 → NP_689598.2  clathrin heavy chain linker domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_689598.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC093165, AK315683, BC029502, BM046729, BM968338, DA249479, DA713663, DB055534
      Consensus CDS
      CCDS33201.1
      UniProtKB/Swiss-Prot
      B2RDV1, Q53R93, Q8N403, Q8NHS4
      Related
      ENSP00000384869.1, ENST00000401408.6
      Conserved Domains (2) summary
      pfam13838
      Location:297 → 354
      Clathrin_H_link; Clathrin-H-link
      pfam15739
      Location:30 → 136
      TSNAXIP1_N; Translin-associated factor X-interacting N-terminus

    RNA

    1. NR_148538.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165

    2. NR_148539.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165

    3. NR_148540.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165

    4. NR_148541.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165

    5. NR_148542.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165

    6. NR_148543.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC012358, AC093165

    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
      55172547..55232563 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      55169784..55229793 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NHS4.3 GenPept UniProtKB/Swiss-Prot:Q8NHS4

    Gene LinkOut

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

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