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

Gene ID: 130162, updated on 17-Sep-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
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55172547..55232563, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55169784..55229793, complement)
RS_2024_09 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 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 (15) 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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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_2024_08

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

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