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

Gene ID: 203228, updated on 31-Aug-2014
Official Symbol
C9orf72provided by HGNC
Official Full Name
chromosome 9 open reading frame 72provided by HGNC
Primary source
HGNC:28337
See related
Ensembl:ENSG00000147894; HPRD:12975; MIM:614260; Vega:OTTHUMG00000019716
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ALSFTD; FTDALS
Summary
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). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
See C9orf72 in Epigenomics, MapViewer
Location:
9p21.2
Exon count:
12
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 9 NC_000009.12 (27546545..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 LOC102724192 Neighboring gene CTAGE family, member 12, pseudogene Neighboring gene interferon, kappa Neighboring gene leucine rich repeat and Ig domain containing 2 Neighboring gene UPF0607 protein ENSP00000381418-like pseudogene

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
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
 
protein binding IPI
Inferred from Physical Interaction
more info
 
Process Evidence Code Pubs
autophagy IMP
Inferred from Mutant Phenotype
more info
 
cell death IEA
Inferred from Electronic Annotation
more info
 
endocytosis IMP
Inferred from Mutant Phenotype
more info
 
Component Evidence Code Pubs
autophagic vacuole IDA
Inferred from Direct Assay
more info
 
cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
 
endosome IDA
Inferred from Direct Assay
more info
 
extracellular space IDA
Inferred from Direct Assay
more info
 
lysosome IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
Preferred Names
protein C9orf72
Names
protein C9orf72

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 

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

mRNA and Protein(s)

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

    See proteins identical to NP_001242983.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and 3' coding region and UTR compared to variant 1. The resulting protein (isoform a) is longer compared to isoform 1. Variants 2 and 3 encode the same protein.
    Source sequence(s)
    AL451123, JN681271
    Consensus CDS
    CCDS6522.1
    UniProtKB/Swiss-Prot
    Q96LT7
    Related
    ENSP00000482753, ENST00000619707
    Conserved Domains (1) summary
    pfam15019
    Location:60325
    Blast Score: 635
    C9orf72-like; C9orf72-like protein family
  2. NM_018325.3NP_060795.1  protein C9orf72 isoform a

    See proteins identical to NP_060795.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 3' coding region and UTR compared to variant 1. The resulting protein (isoform a) is longer compared to isoform 1. Variants 2 and 3 encode the same protein.
    Source sequence(s)
    AK001971, AK291425, AL451123, BC020851, BC039112, BC068445
    Consensus CDS
    CCDS6522.1
    UniProtKB/Swiss-Prot
    Q96LT7
    UniProtKB/TrEMBL
    Q9NUW0
    Related
    ENSP00000369339, OTTHUMP00000021170, ENST00000380003, OTTHUMT00000051969
    Conserved Domains (1) summary
    pfam15019
    Location:60325
    Blast Score: 635
    C9orf72-like; C9orf72-like protein family
  3. NM_145005.5NP_659442.2  protein C9orf72 isoform b

    See proteins identical to NP_659442.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript and encodes the shorter protein (isoform b).
    Source sequence(s)
    AK057806, AL451123, BC020851
    Consensus CDS
    CCDS6523.1
    UniProtKB/Swiss-Prot
    Q96LT7
    Related
    ENSP00000369333, OTTHUMP00000021171, ENST00000379997, OTTHUMT00000051971
    Conserved Domains (1) summary
    pfam15019
    Location:60207
    Blast Score: 322
    C9orf72-like; C9orf72-like protein family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000009.12 

    Range
    27546545..27573866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006716739.1XP_006716802.1  

    Conserved Domains (1) summary
    pfam15019
    Location:60325
    Blast Score: 637
    C9orf72-like; C9orf72-like protein family

Alternate HuRef

Genomic

  1. AC_000141.1 

    Range
    27499333..27526665
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018920.2 

    Range
    27546336..27573669
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)