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Aliases for C9orf72 Gene

Aliases for C9orf72 Gene

  • Chromosome 9 Open Reading Frame 72 2 3 5
  • Guanine Nucleotide Exchange C9orf72 3
  • Protein C9orf72 3
  • DENNL72 3
  • FTDALS1 3
  • ALSFTD 3
  • FTDALS 3

External Ids for C9orf72 Gene

Previous GeneCards Identifiers for C9orf72 Gene

  • GC09M027550
  • GC09M027538

Summaries for C9orf72 Gene

Entrez Gene Summary for C9orf72 Gene

  • The protein encoded by this gene plays an important role in the regulation of endosomal trafficking, and has been shown to interact with Rab proteins that are involved in autophagy and endocytic transport. Expansion of a GGGGCC repeat from 2-22 copies to 700-1600 copies in the intronic sequence between alternate 5' exons in transcripts from this gene is associated with 9p-linked ALS (amyotrophic lateral sclerosis) and FTD (frontotemporal dementia) (PMID: 21944778, 21944779). Studies suggest that hexanucleotide expansions could result in the selective stabilization of repeat-containing pre-mRNA, and the accumulation of insoluble dipeptide repeat protein aggregates that could be pathogenic in FTD-ALS patients (PMID: 23393093). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2016]

GeneCards Summary for C9orf72 Gene

C9orf72 (Chromosome 9 Open Reading Frame 72) is a Protein Coding gene. Diseases associated with C9orf72 include Frontotemporal Dementia And/Or Amyotrophic Lateral Sclerosis 1 and Huntington Disease-Like Syndrome Due To C9orf72 Expansions. Among its related pathways are Mesodermal Commitment Pathway. GO annotations related to this gene include Rab GTPase binding.

UniProtKB/Swiss-Prot for C9orf72 Gene

  • May play a role in endosomal trafficking and autophagy.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C9orf72 Gene

Genomics for C9orf72 Gene

Regulatory Elements for C9orf72 Gene

Enhancers for C9orf72 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09G027563 1.7 FANTOM5 Ensembl ENCODE dbSUPER 36.5 +8.7 8651 3.2 ELF3 FOXA2 RAD21 YY1 RARA CREM MIXL1 THAP11 CEBPB PPARG C9orf72 MOB3B
GH09G027598 1.3 FANTOM5 Ensembl ENCODE dbSUPER 30 -25.9 -25868 1.9 CREB1 ATF2 C9orf72 CTAGE12P
GH09G027458 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.8 +111.5 111459 7.3 HDAC1 PKNOX1 FOXA2 TAL1 JUN FOSL1 TCF12 FOXM1 FOXK2 NCOR1 C9orf72 MOB3B ENSG00000237734 IFNK EQTN LOC105376001
GH09G027586 1.2 FANTOM5 Ensembl ENCODE dbSUPER 24.2 -12.6 -12635 1.0 FOXM1 C9orf72 CTAGE12P
GH09G027571 1.3 ENCODE dbSUPER 16.2 +0.8 796 3.4 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 CBX5 ZNF143 ZNF207 C9orf72 MOB3B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around C9orf72 on UCSC Golden Path with GeneCards custom track

Promoters for C9orf72 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000234210 366 2201 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 CBX5 ZNF143 ZNF207

Genomic Location for C9orf72 Gene

27,546,545 bp from pter
27,573,866 bp from pter
27,322 bases
Minus strand

Genomic View for C9orf72 Gene

Genes around C9orf72 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C9orf72 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C9orf72 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C9orf72 Gene

Proteins for C9orf72 Gene

  • Protein details for C9orf72 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein C9orf72
    Protein Accession:
    Secondary Accessions:
    • A8K5W0
    • D3DRK6
    • G8I0B6
    • Q6NUS9

    Protein attributes for C9orf72 Gene

    481 amino acids
    Molecular mass:
    54328 Da
    Quaternary structure:
    • Interacts with HNRNPA1, HNRNPA2B1 and UBQLN2. Interacts with small Rab GTPases including RAB1A and RAB7A.

    Alternative splice isoforms for C9orf72 Gene


neXtProt entry for C9orf72 Gene

Post-translational modifications for C9orf72 Gene

  • Ubiquitination at posLast=388388
  • Modification sites at PhosphoSitePlus

Other Protein References for C9orf72 Gene

No data available for DME Specific Peptides for C9orf72 Gene

Domains & Families for C9orf72 Gene

Gene Families for C9orf72 Gene

Protein Domains for C9orf72 Gene


Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with C9orf72: view

No data available for Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for C9orf72 Gene

Function for C9orf72 Gene

Molecular function for C9orf72 Gene

UniProtKB/Swiss-Prot Function:
May play a role in endosomal trafficking and autophagy.

Gene Ontology (GO) - Molecular Function for C9orf72 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21516116
GO:0017112 contributes_to Rab guanyl-nucleotide exchange factor activity IDA 27103069
GO:0017137 Rab GTPase binding IDA 24549040
genes like me logo Genes that share ontologies with C9orf72: view
genes like me logo Genes that share phenotypes with C9orf72: view

Human Phenotype Ontology for C9orf72 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for C9orf72 Gene

MGI Knock Outs for C9orf72:

Animal Model Products

CRISPR Products

miRNA for C9orf72 Gene

miRTarBase miRNAs that target C9orf72

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for C9orf72 Gene

Localization for C9orf72 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C9orf72 Gene

Nucleus. Cytoplasm. Endosome. Lysosome. Cytoplasmic vesicle, autophagosome. Secreted. Note=Detected in the cytoplasm of neurons from post mortem brain tissue (PubMed:21944778). Detected in the nucleus in fibroblasts (PubMed:21944779). {ECO:0000269 PubMed:21944778, ECO:0000269 PubMed:21944779}.

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 C9orf72 gene
Compartment Confidence
extracellular 5
nucleus 5
lysosome 5
endosome 5
cytoskeleton 3
cytosol 3
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for C9orf72 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IDA 24549040
GO:0005634 nucleus IEA,IDA 24549040
GO:0005737 cytoplasm IEA,IDA 27193190
GO:0005764 lysosome IDA,IEA 24549040
genes like me logo Genes that share ontologies with C9orf72: view

Pathways & Interactions for C9orf72 Gene

SuperPathways for C9orf72 Gene

SuperPathway Contained pathways
1 Mesodermal Commitment Pathway
genes like me logo Genes that share pathways with C9orf72: view

Pathways by source for C9orf72 Gene

1 BioSystems pathway for C9orf72 Gene

Gene Ontology (GO) - Biological Process for C9orf72 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis IMP 24549040
GO:0006914 autophagy IMP 24549040
GO:0010506 regulation of autophagy IMP 27103069
GO:0016239 positive regulation of macroautophagy IMP 27103069
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with C9orf72: view

No data available for SIGNOR curated interactions for C9orf72 Gene

Drugs & Compounds for C9orf72 Gene

(1) Drugs for C9orf72 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Tumor necrosis factor alpha (TNF-alpha) inhibitors Pharma 0
genes like me logo Genes that share compounds with C9orf72: view

Transcripts for C9orf72 Gene

Unigene Clusters for C9orf72 Gene

Chromosome 9 open reading frame 72:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for C9orf72 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b
SP1: - -
SP2: -
SP3: - - -
SP4: -
SP5: -
SP6: - -

Relevant External Links for C9orf72 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for C9orf72 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for C9orf72 Gene

mRNA differential expression in normal tissues according to GTEx for C9orf72 Gene

This gene is overexpressed in Whole Blood (x5.1).

Protein differential expression in normal tissues from HIPED for C9orf72 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (27.8), Testis (12.0), Ovary (10.4), Frontal cortex (9.4), and Placenta (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for C9orf72 Gene

Protein tissue co-expression partners for C9orf72 Gene

NURSA nuclear receptor signaling pathways regulating expression of C9orf72 Gene:


SOURCE GeneReport for Unigene cluster for C9orf72 Gene:


mRNA Expression by UniProt/SwissProt for C9orf72 Gene:

Tissue specificity: Both isoforms are widely expressed, including kidney, lung, liver, heart, testis and several brain regions, such as cerebellum. Also expressed in the frontal cortex and in lymphoblasts (at protein level).

Evidence on tissue expression from TISSUES for C9orf72 Gene

  • Nervous system(4.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for C9orf72 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • epiglottis
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • tongue
  • vocal cord
  • bronchus
  • clavicle
  • esophagus
  • heart
  • lung
  • scapula
  • trachea
  • biliary tract
  • liver
  • stomach
  • prostate
  • urinary bladder
  • arm
  • digit
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • shin
  • shoulder
  • thigh
  • toe
  • upper limb
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with C9orf72: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for C9orf72 Gene

Orthologs for C9orf72 Gene

This gene was present in the common ancestor of animals.

Orthologs for C9orf72 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C9orf72 35
  • 100 (a)
C9H9orf72 34
  • 99.58 (n)
(Bos Taurus)
Mammalia C9orf72 35
  • 99 (a)
C8H9orf72 34
  • 91.89 (n)
(Canis familiaris)
Mammalia C9orf72 35
  • 99 (a)
C11H9orf72 34
  • 93.76 (n)
(Monodelphis domestica)
Mammalia C9orf72 35
  • 97 (a)
(Ornithorhynchus anatinus)
Mammalia C9orf72 35
  • 95 (a)
(Mus musculus)
Mammalia 3110043O21Rik 34 16 35
  • 90.44 (n)
(Rattus norvegicus)
Mammalia RGD1359108 34
  • 89.4 (n)
(Gallus gallus)
Aves C9orf72 35
  • 94 (a)
C9ORF72 34
  • 83.3 (n)
(Anolis carolinensis)
Reptilia C9orf72 35
  • 93 (a)
(Danio rerio)
Actinopterygii C13H9orf72 35
  • 76 (a)
zgc:100846 34
  • 68.55 (n)
(Caenorhabditis elegans)
Secernentea alfa-1 35
  • 15 (a)
Species where no ortholog for C9orf72 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for C9orf72 Gene

Gene Tree for C9orf72 (if available)
Gene Tree for C9orf72 (if available)

Paralogs for C9orf72 Gene

No data available for Paralogs for C9orf72 Gene

Variants for C9orf72 Gene

Sequence variations from dbSNP and Humsavar for C9orf72 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs10757668 Likely benign 27,567,147(+) TTATC(C/T)AAATG utr-variant-5-prime
rs139352974 Likely benign 27,550,641(+) AGTTC(A/G)ACATT intron-variant
rs141012074 Likely benign 27,546,767(-) TTTTA(A/C/T)ATGAC utr-variant-3-prime
rs141063383 Likely benign 27,548,278(+) GTGTA(A/G)AAAGG reference, synonymous-codon
rs147752518 Likely benign 27,566,833(+) ATTAA(C/G/T)GAAAC reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for C9orf72 Gene

Variant ID Type Subtype PubMed ID
nsv1015259 CNV gain 25217958
nsv831532 CNV gain 17160897

Variation tolerance for C9orf72 Gene

Residual Variation Intolerance Score: 17.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.02; 60.36% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for C9orf72 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C9orf72 Gene

Disorders for C9orf72 Gene

MalaCards: The human disease database

(26) MalaCards diseases for C9orf72 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Frontotemporal dementia and/or amyotrophic lateral sclerosis 1 (FTDALS1) [MIM:105550]: An autosomal dominant neurodegenerative disorder characterized by adult onset of frontotemporal dementia and/or amyotrophic lateral sclerosis in an affected individual. There is high intrafamilial variation. Frontotemporal dementia is characterized by frontal and temporal lobe atrophy associated with neuronal loss, gliosis, and dementia. Patients exhibit progressive changes in social, behavioral, and/or language function. Amyotrophic lateral sclerosis is characterized by the death of motor neurons in the brain, brainstem, and spinal cord, resulting in fatal paralysis. {ECO:0000269 PubMed:21944778, ECO:0000269 PubMed:21944779, ECO:0000269 PubMed:22936364}. Note=The disease is caused by mutations affecting the gene represented in this entry. In the first intron of the gene, the expansion of a GGGGCC hexanucleotide that can vary from 10 to thousands of repeats, represents the most common genetic cause of both familial and sporadic FTDALS. The hexanucleotide repeat expansion (HRE) is structurally polymorphic and during transcription, is responsible for the formation of RNA and DNA G-quadruplexes resulting in the production of aborted transcripts at the expense of functional transcripts. The accumulation of those aborted transcripts may cause nucleolar stress and indirectly cell death (PubMed:24598541). {ECO:0000269 PubMed:24598541}.

Relevant External Links for C9orf72

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with C9orf72: view

No data available for Genatlas for C9orf72 Gene

Publications for C9orf72 Gene

  1. C9ORF72, implicated in amytrophic lateral sclerosis and frontotemporal dementia, regulates endosomal trafficking. (PMID: 24549040) Farg M.A. … Atkin J.D. (Hum. Mol. Genet. 2014) 2 3 4 64
  2. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9orf72 causes chromosome 9p-linked FTD and ALS. (PMID: 21944778) Dejesus-Hernandez M. … Rademakers R. (Neuron 2011) 2 3 4 64
  3. C9orf72 nucleotide repeat structures initiate molecular cascades of disease. (PMID: 24598541) Haeusler A.R. … Wang J. (Nature 2014) 3 4 64
  4. Analysis of the C9orf72 gene in patients with amyotrophic lateral sclerosis in Spain and different populations worldwide. (PMID: 22936364) Garcia-Redondo A. … Lleo A. (Hum. Mutat. 2013) 3 4 64
  5. A hexanucleotide repeat expansion in C9orf72 is the cause of chromosome 9p21-linked ALS-FTD. (PMID: 21944779) Renton A.E. … Traynor B.J. (Neuron 2011) 3 4 64

Products for C9orf72 Gene

Sources for C9orf72 Gene

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