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Aliases for C9orf72 Gene

Aliases for C9orf72 Gene

  • Chromosome 9 Open Reading Frame 72 2 3
  • ALSFTD 3 6
  • FTDALS 3 6
  • Protein C9orf72 3

External Ids for C9orf72 Gene

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 hexanucleotide repeat in non-coding 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, Feb 2015]

GeneCards Summary for C9orf72 Gene

C9orf72 (Chromosome 9 Open Reading Frame 72) is a Protein Coding gene. Diseases associated with C9orf72 include huntington disease-like syndrome due to c9orf72 expansions and amyotrophic lateral sclerosis and/or frontotemporal dementia.

UniProtKB/Swiss-Prot for C9orf72 Gene

  • May play a role in endosomal trafficking and autophagy.

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

Genomics for C9orf72 Gene

Genomic Location for C9orf72 Gene

Start:
27,546,545 bp from pter
End:
27,573,866 bp from pter
Size:
27,322 bases
Orientation:
Minus strand

Genomic View for C9orf72 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for C9orf72 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C9orf72 Gene

Regulatory Elements for C9orf72 Gene

Proteins for C9orf72 Gene

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

    Protein Symbol:
    Q96LT7-CI072_HUMAN
    Recommended name:
    Protein C9orf72
    Protein Accession:
    Q96LT7
    Secondary Accessions:
    • A8K5W0
    • D3DRK6
    • G8I0B6
    • Q6NUS9

    Protein attributes for C9orf72 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for C9orf72 Gene

Proteomics data for C9orf72 Gene at MOPED

Post-translational modifications for C9orf72 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys388

Other Protein References for C9orf72 Gene

No data available for DME Specific Peptides for C9orf72 Gene

Domains for C9orf72 Gene

Protein Domains for C9orf72 Gene

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

No data available for Gene Families 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 24549040
GO:0017137 Rab GTPase binding IDA 24549040
genes like me logo Genes that share ontologies with C9orf72: view

Phenotypes for C9orf72 Gene

MGI mutant phenotypes for C9orf72:
inferred from 1 alleles
genes like me logo Genes that share phenotypes with C9orf72: view

miRNA for C9orf72 Gene

miRTarBase miRNAs that target C9orf72

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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

COMPARTMENTS
Jensen Localization Image for C9orf72 Gene COMPARTMENTS Subcellular localization image for C9orf72 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for C9orf72 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 24549040
GO:0005634 nucleus IDA 24549040
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IDA --
GO:0005764 lysosome IDA 24549040
genes like me logo Genes that share ontologies with C9orf72: view

Pathways for C9orf72 Gene

SuperPathways for C9orf72 Gene

No Data Available

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:0008219 cell death --
genes like me logo Genes that share ontologies with C9orf72: view

No data available for Pathways by source for C9orf72 Gene

Compounds for C9orf72 Gene

(1) PharmGKB related drug/compound annotations for C9orf72 Gene

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:

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: - -
SP7:

Relevant External Links for C9orf72 Gene

GeneLoc Exon Structure for
C9orf72
ECgene alternative splicing isoforms for
C9orf72

Expression for C9orf72 Gene

mRNA expression in normal human tissues for C9orf72 Gene

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

This gene is overexpressed in Whole Blood (5.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for C9orf72 Gene

SOURCE GeneReport for Unigene cluster for C9orf72 Gene Hs.493639

mRNA Expression by UniProt/SwissProt for C9orf72 Gene

Q96LT7-CI072_HUMAN
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).
genes like me logo Genes that share expressions with C9orf72: view

Orthologs for C9orf72 Gene

This gene was present in the common ancestor of animals.

Orthologs for C9orf72 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C9H9orf72 36
  • 99.58 (n)
  • 99.58 (a)
C9orf72 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia C8H9orf72 36
  • 91.89 (n)
  • 98.75 (a)
C9orf72 37
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia C11H9orf72 36
  • 93.76 (n)
  • 98.54 (a)
C9orf72 37
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 3110043O21Rik 36
  • 90.44 (n)
  • 98.13 (a)
3110043O21Rik 16
3110043O21Rik 37
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia C9orf72 37
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia C9orf72 37
  • 95 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia RGD1359108 36
  • 89.4 (n)
  • 97.71 (a)
chicken
(Gallus gallus)
Aves C9ORF72 36
  • 83.3 (n)
  • 93.56 (a)
C9orf72 37
  • 94 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C9orf72 37
  • 93 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii C13H9orf72 37
  • 76 (a)
OneToOne
zgc:100846 36
  • 68.55 (n)
  • 76.14 (a)
worm
(Caenorhabditis elegans)
Secernentea alfa-1 37
  • 15 (a)
OneToOne
Species with no ortholog for C9orf72:
  • 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

ENSEMBL:
Gene Tree for C9orf72 (if available)
TreeFam:
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 MAF
rs9103 -- 27,546,830(-) AGATG(A/C/T)GGACA utr-variant-3-prime
rs13691 -- 27,546,892(-) CACAA(C/T)AAAAT utr-variant-3-prime
rs15540 -- 27,547,361(+) AAGAA(A/G)AAAAC utr-variant-3-prime
rs700824 -- 27,570,350(+) TATTG(C/T)AAACA intron-variant
rs700825 -- 27,570,156(+) GCACT(A/G)GATAT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv892870 CNV Gain 21882294
nsv892871 CNV Gain 21882294
nsv892872 CNV Gain 21882294
nsv831532 CNV Gain 17160897

Relevant External Links for C9orf72 Gene

HapMap Linkage Disequilibrium report
C9orf72
Human Gene Mutation Database (HGMD)
C9orf72

Disorders for C9orf72 Gene

(1) OMIM Diseases for C9orf72 Gene (614260)

UniProtKB/Swiss-Prot

CI072_HUMAN
  • 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}.

(3) University of Copenhagen DISEASES for C9orf72 Gene

Relevant External Links for C9orf72

Genetic Association Database (GAD)
C9orf72
Human Genome Epidemiology (HuGE) Navigator
C9orf72
genes like me logo Genes that share disorders with C9orf72: view

Publications for C9orf72 Gene

  1. 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
  2. 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
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray S.J. … Dunham I. (Nature 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4

Products for C9orf72 Gene

Sources for C9orf72 Gene

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