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Aliases for CLHC1 Gene

Aliases for CLHC1 Gene

  • Clathrin Heavy Chain Linker Domain Containing 1 2 3 5
  • C2orf63 3 4
  • Clathrin Heavy Chain Linker Domain-Containing Protein 1 3
  • Chromosome 2 Open Reading Frame 63 2

External Ids for CLHC1 Gene

Previous HGNC Symbols for CLHC1 Gene

  • C2orf63

Previous GeneCards Identifiers for CLHC1 Gene

  • GC02M055400

Summaries for CLHC1 Gene

GeneCards Summary for CLHC1 Gene

CLHC1 (Clathrin Heavy Chain Linker Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include binding.

Additional gene information for CLHC1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLHC1 Gene

Genomics for CLHC1 Gene

GeneHancer (GH) Regulatory Elements for CLHC1 Gene

Promoters and enhancers for CLHC1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J055231 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 713 -0.4 -422 3.7 PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B CLHC1 RPS27A RTN4 GC02P055233 PRORSD1P
GH02J055222 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 48.8 +8.5 8522 3 HDGF SIN3A ZNF2 YY1 ZNF121 POLR2B GLIS2 ZNF207 ZNF143 ZNF592 LOC100128027 CLHC1 EML6 RTN4 CCDC88A ENSG00000203327
GH02J055150 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 39.3 +77.4 77391 9.9 PKNOX1 TCF12 GATA2 ATF7 ZNF592 NFIL3 ATF4 GMEB1 HMBOX1 KDM1A CLHC1 ENSG00000203327 RTN4 RNU6-433P RPS27A PRORSD1P MTIF2 PPP4R3B GC02M055160 LOC105374674
GH02J055163 Enhancer 1.1 Ensembl ENCODE dbSUPER 52.1 +69.0 68987 2.1 NCOA3 FOXA2 NFIB FEZF1 ZIC2 TEAD3 CTBP1 GATA3 POLR2A PRDM10 CLHC1 RNU6-433P RTN4 ENSG00000203327 RNU7-81P EML6 PRORSD1P GC02M055160 LOC105374674
GH02J055166 Enhancer 1.2 Ensembl ENCODE dbSUPER 44.2 +64.6 64605 2.7 HDAC1 PKNOX1 ATF1 RB1 ARID4B ZSCAN9 RAD21 RFX5 ZNF766 E2F8 CLHC1 RNU6-433P ENSG00000203327 MTIF2 EML6 LOC105374674 GC02M055160
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLHC1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CLHC1 Gene

Genomic Locations for CLHC1 Gene
60,017 bases
Minus strand
60,017 bases
Minus strand

Genomic View for CLHC1 Gene

Genes around CLHC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLHC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLHC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLHC1 Gene

Proteins for CLHC1 Gene

  • Protein details for CLHC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Clathrin heavy chain linker domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • B2RDV1
    • Q53R93
    • Q8N403

    Protein attributes for CLHC1 Gene

    586 amino acids
    Molecular mass:
    67250 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CLHC1 Gene


neXtProt entry for CLHC1 Gene

Post-translational modifications for CLHC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLHC1 Gene

Domains & Families for CLHC1 Gene

Gene Families for CLHC1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CLHC1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CLHC1: view

No data available for Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for CLHC1 Gene

Function for CLHC1 Gene

Phenotypes From GWAS Catalog for CLHC1 Gene

Gene Ontology (GO) - Molecular Function for CLHC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with CLHC1: view
genes like me logo Genes that share phenotypes with CLHC1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLHC1

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLHC1 Gene

Localization for CLHC1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLHC1 gene
Compartment Confidence
mitochondrion 2
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (2)
  • Nucleoli fibrillar center (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for CLHC1 Gene

Pathways & Interactions for CLHC1 Gene

SuperPathways for CLHC1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CLHC1 Gene


No data available for Pathways by source and SIGNOR curated interactions for CLHC1 Gene

Drugs & Compounds for CLHC1 Gene

No Compound Related Data Available

Transcripts for CLHC1 Gene

Unigene Clusters for CLHC1 Gene

Clathrin heavy chain linker domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLHC1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLHC1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c · 9d ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^
SP1: - - - - - - - - - - - - - - - - - -
SP4: -
SP5: - - - - - - - - - - - - - - -
SP8: - - - - -
SP9: - - - - - -
SP10: - - - - - - -
SP11: - - - - - - -
SP12: - - - - - - - -
SP13: - - - - - - - - - - - - - - - - - - - -
SP14: - - - - - -
SP15: - -
SP16: -

ExUns: 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a · 19b · 19c · 19d
SP1: - - - -
SP2: -
SP4: - - - - -
SP6: - - -
SP7: - - - -
SP13: - - - - - -

Relevant External Links for CLHC1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLHC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLHC1 Gene

Protein differential expression in normal tissues from HIPED for CLHC1 Gene

This gene is overexpressed in Liver (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLHC1 Gene

Protein tissue co-expression partners for CLHC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLHC1 Gene:


SOURCE GeneReport for Unigene cluster for CLHC1 Gene:

genes like me logo Genes that share expression patterns with CLHC1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLHC1 Gene

Orthologs for CLHC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLHC1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLHC1 33
  • 99.28 (n)
C2AH2ORF63 34
  • 99 (a)
(Canis familiaris)
Mammalia CLHC1 34 33
  • 88.28 (n)
(Bos Taurus)
Mammalia CLHC1 33
  • 86.69 (n)
MGC139228 34
  • 79 (a)
(Mus musculus)
Mammalia 1700034F02Rik 33
  • 80.57 (n)
Clhc1 16 34
  • 68 (a)
(Rattus norvegicus)
Mammalia Clhc1 33
  • 80 (n)
(Monodelphis domestica)
Mammalia CLHC1 34
  • 60 (a)
(Ornithorhynchus anatinus)
Mammalia CLHC1 34
  • 56 (a)
(Anolis carolinensis)
Reptilia CLHC1 34
  • 46 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clhc1 33
  • 53.74 (n)
Species where no ortholog for CLHC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CLHC1 Gene

Gene Tree for CLHC1 (if available)
Gene Tree for CLHC1 (if available)
Evolutionary constrained regions (ECRs) for CLHC1: view image

Paralogs for CLHC1 Gene

(1) SIMAP similar genes for CLHC1 Gene using alignment to 6 proteins:

  • B5MC48_HUMAN
  • C9J143_HUMAN
  • H7C1D8_HUMAN
genes like me logo Genes that share paralogs with CLHC1: view

No data available for Paralogs for CLHC1 Gene

Variants for CLHC1 Gene

Sequence variations from dbSNP and Humsavar for CLHC1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs144133542 likely-pathogenic, Marked Hypotonia, Waddling gait 55,181,606(-) C/T coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs1000004442 -- 55,225,614(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000042922 -- 55,233,105(-) G/A upstream_transcript_variant
rs1000074323 -- 55,233,227(-) A/T upstream_transcript_variant
rs1000115493 -- 55,196,918(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLHC1 Gene

Variant ID Type Subtype PubMed ID
esv2720078 CNV deletion 23290073
esv3590853 CNV loss 21293372
nsv1010438 CNV loss 25217958
nsv522016 CNV gain 19592680

Variation tolerance for CLHC1 Gene

Residual Variation Intolerance Score: 83% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.12; 95.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLHC1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLHC1 Gene

Disorders for CLHC1 Gene

Additional Disease Information for CLHC1

No disorders were found for CLHC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLHC1 Gene

Publications for CLHC1 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2. (PMID: 24322204) Winham SJ … Biernacka JM (Molecular psychiatry 2014) 3 58
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58
  4. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. (PMID: 22658674) Castello A … Hentze MW (Cell 2012) 3 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 58

Products for CLHC1 Gene

Sources for CLHC1 Gene

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