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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

Related articles in PubMed

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

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)