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    C9orf72 chromosome 9 open reading frame 72 [ Homo sapiens (human) ]

    Gene ID: 203228, updated on 30-Jun-2015
    Official Symbol
    C9orf72provided by HGNC
    Official Full Name
    chromosome 9 open reading frame 72provided by HGNC
    Primary source
    HGNC:HGNC:28337
    See related
    Ensembl:ENSG00000147894; HPRD:12975; MIM:614260; Vega:OTTHUMG00000019716
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALSFTD; FTDALS
    Summary
    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]
    Orthologs
    See C9orf72 in Epigenomics, MapViewer
    Location:
    9p21.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 9 NC_000009.12 (27546546..27573866, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (27546543..27573864, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MOB kinase activator 3B Neighboring gene uncharacterized LOC105376001 Neighboring gene interferon, kappa Neighboring gene CTAGE family, member 12, pseudogene Neighboring gene uncharacterized LOC105376002

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
    NHGRI GWA Catalog
    Chromosome 9p21 in amyotrophic lateral sclerosis in Finland: a genome-wide association study.
    NHGRI GWA Catalog
    Chromosome 9p21 in sporadic amyotrophic lateral sclerosis in the UK and seven other countries: a genome-wide association study.
    NHGRI GWA Catalog
    Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis.
    NHGRI GWA Catalog
    Genome-wide association study identifies genetic determinants of urine PCA3 levels in men.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC23980

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    Rab GTPase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    autophagosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
     
    cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intercellular bridge IDA
    Inferred from Direct Assay
    more info
     
    lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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_031977.1 RefSeqGene

      Range
      5001..32322
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256054.2NP_001242983.1  protein C9orf72 isoform a

      See identical proteins and their annotated locations for NP_001242983.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longer isoform (a). Hexanucleotide expansions that can occur in a repeat region between the first and second exon of this variant have been associated with frontotemporal dementia and amyotrophic lateral sclerosis (FTD-ALS;PMID: 21944778, PMID: 21944779 ). Variants 2 and 3 encode the same protein.
      Source sequence(s)
      AL832229, BQ068108, JN681271
      Consensus CDS
      CCDS6522.1
      UniProtKB/Swiss-Prot
      Q96LT7
      Related
      ENSP00000482753, ENST00000619707
      Conserved Domains (1) summary
      pfam15019
      Location:60325
      C9orf72-like; C9orf72-like protein family
    2. NM_018325.4NP_060795.1  protein C9orf72 isoform a

      See identical proteins and their annotated locations for NP_060795.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 3. Both variants 2 and 3 encode the same protein.
      Source sequence(s)
      AK291425, AL832229, BC020851, BC039112, BC068445, BG718065, BQ777139
      Consensus CDS
      CCDS6522.1
      UniProtKB/Swiss-Prot
      Q96LT7
      Related
      ENSP00000369339, OTTHUMP00000021170, ENST00000380003, OTTHUMT00000051969
      Conserved Domains (1) summary
      pfam15019
      Location:60325
      C9orf72-like; C9orf72-like protein family
    3. NM_145005.6NP_659442.2  protein C9orf72 isoform b

      See identical proteins and their annotated locations for NP_659442.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks multiple exons in the central and 3' coding regions, and its 3' terminal exon extends beyond a splice site that is used in variant 3 . This results in a novel 3' UTR, compared to variant 3. It encodes isoform b which is significantly shorter, and its C-terminal amino acid is distinct, compared to isoform a.
      Source sequence(s)
      AI141996, AK057806, BC020851, BQ068108, DA802421
      Consensus CDS
      CCDS6523.1
      UniProtKB/Swiss-Prot
      Q96LT7
      Related
      ENSP00000369333, OTTHUMP00000021171, ENST00000379997, OTTHUMT00000051971
      Conserved Domains (1) summary
      pfam15019
      Location:60207
      C9orf72-like; C9orf72-like protein family

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p2 Primary Assembly

      Range
      27546546..27573866
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      27546337..27573669
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)