Aliases for C9orf50 Gene

Aliases for C9orf50 Gene

  • Chromosome 9 Open Reading Frame 50 2 3 5
  • Uncharacterized Protein C9orf50 3 4
  • FLJ35803 2
  • C9orf50 5

External Ids for C9orf50 Gene

Previous GeneCards Identifiers for C9orf50 Gene

  • GC09M129455
  • GC09M131414
  • GC09M132374
  • GC09M101973

Summaries for C9orf50 Gene

GeneCards Summary for C9orf50 Gene

C9orf50 (Chromosome 9 Open Reading Frame 50) is a Protein Coding gene. Diseases associated with C9orf50 include Spastic Paraplegia 20, Autosomal Recessive.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for C9orf50 Gene

Genomics for C9orf50 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for C9orf50 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J129619 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 256.7 +2.0 1974 1.4 ZNF600 ZNF592 ZIC2 NONO ZFP64 ELF1 KLF9 SIN3B SP2 CTCF C9orf50 NUP188 NTMT1 piR-56037-114 RF00017-7387
GH09J129621 Promoter/Enhancer 0.5 EPDnew Ensembl 250.7 +0.4 374 0.2 C9orf50 piR-56037-114 NTMT1 RF00017-7387
GH09J129618 Promoter 0.3 EPDnew 250.7 +4.2 4201 0.1 C9orf50 piR-56037-114 NTMT1 RF00017-7387
GH09J129605 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 16.1 +13.4 13392 5.8 BCLAF1 ZNF654 ZNF207 MYC NCOR1 IKZF1 SSRP1 ZNF580 ZNF592 ZMYM3 NTMT1 lnc-NTMT1-6 NUP188 ENSG00000267834 PKN3 SPOUT1 C9orf50 MIGA2 USP20 GPR107
GH09J129025 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.2 +594.9 594865 3.2 SP1 MYC ZNF600 ZNF580 ZNF592 ZMYM3 ZSCAN16 BRCA1 ZIC2 CHD4 SH3GLB2 lnc-DOLK-2 ENSG00000267834 C9orf50 SPTAN1 ENSG00000272696 piR-61945-518 RF00017-7373 NUP188
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C9orf50 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for C9orf50

Top Transcription factor binding sites by QIAGEN in the C9orf50 gene promoter:
  • C/EBPalpha
  • E47
  • Egr-3
  • GATA-1
  • Pax-5
  • POU2F1
  • POU2F1a
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for C9orf50 Gene

Latest Assembly
10,051 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
8,552 bases
Minus strand

(GRCh37/hg19 by Ensembl)
8,552 bases
Minus strand

Genomic View for C9orf50 Gene

Genes around C9orf50 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C9orf50 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C9orf50 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C9orf50 Gene

Proteins for C9orf50 Gene

  • Protein details for C9orf50 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Uncharacterized protein C9orf50
    Protein Accession:
    Secondary Accessions:
    • Q2M1I2
    • Q8NA65

    Protein attributes for C9orf50 Gene

    431 amino acids
    Molecular mass:
    47639 Da
    Quaternary structure:
    No Data Available
    • Sequence=AK093122; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};

neXtProt entry for C9orf50 Gene

Post-translational modifications for C9orf50 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for C9orf50 Gene

Domains & Families for C9orf50 Gene

Gene Families for C9orf50 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for C9orf50 Gene

genes like me logo Genes that share domains with C9orf50: view

No data available for Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for C9orf50 Gene

Function for C9orf50 Gene

Phenotypes From GWAS Catalog for C9orf50 Gene

genes like me logo Genes that share phenotypes with C9orf50: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for C9orf50

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for C9orf50 Gene

Localization for C9orf50 Gene

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 C9orf50 gene
Compartment Confidence
nucleus 3
mitochondrion 0
cytosol 0

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for C9orf50 Gene

Pathways & Interactions for C9orf50 Gene

PathCards logo

SuperPathways for C9orf50 Gene

No Data Available

Interacting Proteins for C9orf50 Gene

Selected Interacting proteins: Q5SZB4-CI050_HUMAN for C9orf50 Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for C9orf50 Gene


No data available for Pathways by source and SIGNOR curated interactions for C9orf50 Gene

Drugs & Compounds for C9orf50 Gene

No Compound Related Data Available

Transcripts for C9orf50 Gene

mRNA/cDNA for C9orf50 Gene

7 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for C9orf50

Alternative Splicing Database (ASD) splice patterns (SP) for C9orf50 Gene

No ASD Table

Relevant External Links for C9orf50 Gene

GeneLoc Exon Structure for

Expression for C9orf50 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for C9orf50 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for C9orf50 Gene

This gene is overexpressed in Testis (x17.8).

Protein differential expression in normal tissues from HIPED for C9orf50 Gene

This gene is overexpressed in Serum (62.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for C9orf50 Gene

Protein tissue co-expression partners for C9orf50 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for C9orf50

SOURCE GeneReport for Unigene cluster for C9orf50 Gene:

genes like me logo Genes that share expression patterns with C9orf50: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for C9orf50 Gene

Orthologs for C9orf50 Gene

This gene was present in the common ancestor of mammals.

Orthologs for C9orf50 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C9orf50 30
  • 98 (a)
(Canis familiaris)
Mammalia C9H9orf50 29
  • 74.17 (n)
-- 30
  • 51 (a)
-- 30
  • 42 (a)
(Bos Taurus)
Mammalia C11H9orf50 29
  • 72.56 (n)
C9orf50 30
  • 53 (a)
(Rattus norvegicus)
Mammalia RGD1311084 29
  • 70.68 (n)
(Mus musculus)
Mammalia 1700001O22Rik 29 16 30
  • 65.21 (n)
Species where no ortholog for C9orf50 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for C9orf50 Gene

Gene Tree for C9orf50 (if available)
Gene Tree for C9orf50 (if available)
Alliance of Genome Resources:
Additional Orthologs for C9orf50

Paralogs for C9orf50 Gene

No data available for Paralogs for C9orf50 Gene

Variants for C9orf50 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for C9orf50 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs2302779 -- p.Arg381Gln
rs3087721 -- p.Lys415Arg
rs3213763 -- p.Arg312Gln
rs918165 -- p.Arg248Lys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for C9orf50 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for C9orf50 Gene

Variant ID Type Subtype PubMed ID
esv2669087 CNV deletion 23128226
esv3621837 CNV loss 21293372
nsv1046477 CNV gain 25217958
nsv469901 CNV loss 18288195
nsv831731 CNV gain+loss 17160897
nsv951783 CNV deletion 24416366

Variation tolerance for C9orf50 Gene

Residual Variation Intolerance Score: 90.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.80; 73.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C9orf50 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C9orf50 Gene

Disorders for C9orf50 Gene

MalaCards: The human disease database

(1) MalaCards diseases for C9orf50 Gene - From: COP

Disorder Aliases PubMed IDs
spastic paraplegia 20, autosomal recessive
  • spg20
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for C9orf50

genes like me logo Genes that share disorders with C9orf50: view

No data available for UniProtKB/Swiss-Prot and Genatlas for C9orf50 Gene

Publications for C9orf50 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  2. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. (PMID: 32694731) Aregger M … Moffat J (Nature metabolism 2020) 3
  3. Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study. (PMID: 23934736) Yu B … Boerwinkle E (Genetic epidemiology 2013) 3
  4. Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D. (PMID: 22041458) Clark SL … van den Oord EJ (Psychological medicine 2012) 3
  5. Identification of the human testis protein phosphatase 1 interactome. (PMID: 21382349) Fardilha M … da Cruz e Silva EF (Biochemical pharmacology 2011) 3

Products for C9orf50 Gene

Sources for C9orf50 Gene