Aliases for C9orf78 Gene

Aliases for C9orf78 Gene

  • Chromosome 9 Open Reading Frame 78 2 3 5
  • Hepatocellular Carcinoma-Associated Antigen 59 2 3 4
  • HCA59 2 3 4
  • Telomere Length And Silencing Protein 1 Homolog 3 4
  • HSPC220 2 3
  • CSU2 2 3
  • Uncharacterized Protein C9orf78 3
  • BA409K20.3 3
  • C9orf78 5

External Ids for C9orf78 Gene

Previous GeneCards Identifiers for C9orf78 Gene

  • GC09M127965
  • GC09M127946
  • GC09M129669
  • GC09M131629
  • GC09M132590
  • GC09M102188

Summaries for C9orf78 Gene

GeneCards Summary for C9orf78 Gene

C9orf78 (Chromosome 9 Open Reading Frame 78) is a Protein Coding gene. Diseases associated with C9orf78 include Emery-Dreifuss Muscular Dystrophy 4, Autosomal Dominant.

UniProtKB/Swiss-Prot Summary for C9orf78 Gene

  • Involved in the regulation of telomeric heterochromatin assembly and control of telomere length.

Gene Wiki entry for C9orf78 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for C9orf78 Gene

Genomics for C9orf78 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for C9orf78 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
GH09J129834 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 289.8 +0.5 490 3.5 BCLAF1 SP1 NCOR1 MYC SIX5 POLR2A BRCA1 ZIC2 YY1 MXD4 C9orf78 USP20 lnc-TOR1A-1 EXOSC2 NUP188 TOR1A TOR1B IER5L
GH09J129822 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 39.7 +12.2 12247 2.4 SP1 ZNF207 NCOR1 MYC IKZF1 ZNF600 SIX5 ZNF580 ZNF592 POLR2A TOR1A lnc-C9orf78-1 C9orf78 TOR1B
GH09J129802 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 39 +32.4 32362 2.2 BCLAF1 SP1 ZNF207 MYC ZNF600 NCOR1 SIX5 ZNF580 KLF9 POLR2A TOR1B C9orf78 EXOSC2 SPOUT1 NUP188 TOR1A USP20 piR-43106-213
GH09J129882 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 27.1 -54.3 -54306 14.6 BCLAF1 SP1 ZNF207 ZNF654 IKZF1 MYC ZNF600 POLR2A CEBPA ZNF10 USP20 C9orf78 FNBP1 TOR1A TOR1B FUBP3 EXOSC2 ABL1 ASB6 ENSG00000230684
GH09J129789 Enhancer 1.2 Ensembl ENCODE 46.5 +45.6 45626 1.7 BCLAF1 ZNF654 NCOR1 MYC IKZF1 MXD4 CTCF REST KLF11 TRIM22 UBE2V1P4 lnc-TOR1B-1 C9orf78 NUP188 ASB6 USP20 TOR1A EXOSC2 PRRX2-AS1 ENSG00000234789
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C9orf78 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for C9orf78

Top Transcription factor binding sites by QIAGEN in the C9orf78 gene promoter:
  • aMEF-2
  • AP-2gamma
  • AREB6
  • Arnt
  • ATF6
  • E47
  • Lmo2
  • MEF-2A
  • p53
  • Roaz

Genomic Locations for C9orf78 Gene

Latest Assembly
8,574 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
7,986 bases
Minus strand

(GRCh37/hg19 by Ensembl)
8,574 bases
Minus strand

Genomic View for C9orf78 Gene

Genes around C9orf78 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C9orf78 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C9orf78 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C9orf78 Gene

Proteins for C9orf78 Gene

  • Protein details for C9orf78 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Telomere length and silencing protein 1 homolog
    Protein Accession:
    Secondary Accessions:
    • B3KPX8
    • Q8WVU6
    • Q9NT39

    Protein attributes for C9orf78 Gene

    289 amino acids
    Molecular mass:
    33688 Da
    Quaternary structure:
    No Data Available

neXtProt entry for C9orf78 Gene

Post-translational modifications for C9orf78 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for C9orf78 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for C9orf78 Gene

Domains & Families for C9orf78 Gene

Gene Families for C9orf78 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for C9orf78 Gene


Suggested Antigen Peptide Sequences for C9orf78 Gene

GenScript: Design optimal peptide antigens:
  • Hepatocellular carcinoma-associated antigen 59 (CI078_HUMAN)
  • Hepatocellular carcinoma-associated antigen 59 (Q6GVN4_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TLS1 family.
  • Belongs to the TLS1 family.
genes like me logo Genes that share domains with C9orf78: view

Function for C9orf78 Gene

Molecular function for C9orf78 Gene

UniProtKB/Swiss-Prot Function:
Involved in the regulation of telomeric heterochromatin assembly and control of telomere length.

Phenotypes From GWAS Catalog for C9orf78 Gene

Gene Ontology (GO) - Molecular Function for C9orf78 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21044950
genes like me logo Genes that share ontologies with C9orf78: view
genes like me logo Genes that share phenotypes with C9orf78: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for C9orf78

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for C9orf78 Gene

Localization for C9orf78 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 C9orf78 gene
Compartment Confidence
nucleus 5
cytosol 4

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for C9orf78 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005681 spliceosomal complex IBA 21873635
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with C9orf78: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for C9orf78 Gene

Pathways & Interactions for C9orf78 Gene

PathCards logo

SuperPathways for C9orf78 Gene

No Data Available

Gene Ontology (GO) - Biological Process for C9orf78 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0048024 regulation of mRNA splicing, via spliceosome IBA 21873635
genes like me logo Genes that share ontologies with C9orf78: view

No data available for Pathways by source and SIGNOR curated interactions for C9orf78 Gene

Drugs & Compounds for C9orf78 Gene

No Compound Related Data Available

Transcripts for C9orf78 Gene

mRNA/cDNA for C9orf78 Gene

12 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for C9orf78

Alternative Splicing Database (ASD) splice patterns (SP) for C9orf78 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c
SP1: -
SP2: - - - - -
SP3: - -
SP4: -

Relevant External Links for C9orf78 Gene

GeneLoc Exon Structure for

Expression for C9orf78 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for C9orf78 Gene

Protein differential expression in normal tissues from HIPED for C9orf78 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (32.3) and CD8 Tcells (10.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for C9orf78 Gene

Protein tissue co-expression partners for C9orf78 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for C9orf78

SOURCE GeneReport for Unigene cluster for C9orf78 Gene:


Evidence on tissue expression from TISSUES for C9orf78 Gene

  • Blood(4.5)
  • Liver(4.4)
  • Bone marrow(4.4)
  • Muscle(4.4)
  • Nervous system(3.2)
genes like me logo Genes that share expression patterns with C9orf78: view

Primer products for research

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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for C9orf78 Gene

Orthologs for C9orf78 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for C9orf78 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C9orf78 30
  • 100 (a)
C9H9orf78 29
  • 99.65 (n)
(Canis familiaris)
Mammalia -- 30
  • 98 (a)
-- 30
  • 96 (a)
C9H9orf78 29
  • 92.96 (n)
(Bos Taurus)
Mammalia C11H9ORF78 30
  • 98 (a)
C11H9orf78 29
  • 90.82 (n)
(Mus musculus)
Mammalia BC005624 29 16 30
  • 87.31 (n)
(Monodelphis domestica)
Mammalia C9orf78 30
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia C9orf78 30
  • 71 (a)
(Gallus gallus)
Aves C9orf78 30
  • 86 (a)
C17H9ORF78 29
  • 79.47 (n)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia c9orf78 29
  • 74.42 (n)
(Danio rerio)
Actinopterygii C5H9orf78 30
  • 77 (a)
zgc:103692 29
  • 71.24 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG7974 29 30
  • 59.57 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006620 29
  • 58.88 (n)
(Caenorhabditis elegans)
Secernentea T23G11.4 30
  • 29 (a)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT1G02330 29
  • 43.16 (n)
(Oryza sativa)
Liliopsida Os03g0374100 29
  • 44.73 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.8931 30
  • 52 (a)
Species where no ortholog for C9orf78 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for C9orf78 Gene

Gene Tree for C9orf78 (if available)
Gene Tree for C9orf78 (if available)
Alliance of Genome Resources:
Additional Orthologs for C9orf78

Paralogs for C9orf78 Gene Pseudogenes for C9orf78 Gene

genes like me logo Genes that share paralogs with C9orf78: view

No data available for Paralogs for C9orf78 Gene

Variants for C9orf78 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for C9orf78 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs1237745 -- p.Gln70His

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for C9orf78 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for C9orf78 Gene

Variant ID Type Subtype PubMed ID
dgv1511e214 CNV gain 21293372
esv3621839 CNV loss 21293372
nsv1046477 CNV gain 25217958
nsv1161909 CNV duplication 26073780

Variation tolerance for C9orf78 Gene

Residual Variation Intolerance Score: 20.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.49; 10.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C9orf78 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C9orf78 Gene

Disorders for C9orf78 Gene

MalaCards: The human disease database

(1) MalaCards diseases for C9orf78 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for C9orf78

genes like me logo Genes that share disorders with C9orf78: view

No data available for UniProtKB/Swiss-Prot and Genatlas for C9orf78 Gene

Publications for C9orf78 Gene

  1. Large scale identification of human hepatocellular carcinoma-associated antigens by autoantibodies. (PMID: 12097419) Wang Y … Chen WF (Journal of immunology (Baltimore, Md. : 1950) 2002) 2 3 4
  2. Tls1 regulates splicing of shelterin components to control telomeric heterochromatin assembly and telomere length. (PMID: 25245948) Wang J … Jia S (Nucleic acids research 2014) 2 3
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  4. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J … Comb MJ (Nature biotechnology 2005) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for C9orf78 Gene

Sources for C9orf78 Gene