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Aliases for C21orf2 Gene

Aliases for C21orf2 Gene

  • Chromosome 21 Open Reading Frame 2 2 3 5
  • Leucine-Rich Repeat-Containing Protein 76 3 4
  • Leucine Rich Repeat Containing 76 2 3
  • C21orf-HUMF09G8.5 3 4
  • LRRC76 3 4
  • YF5/A2 3 4
  • Nuclear Encoded Mitochondrial Protein C21orf2 3
  • Nuclear Encoded Mitochondrial Protein 2
  • Protein C21orf2 3

External Ids for C21orf2 Gene

Previous GeneCards Identifiers for C21orf2 Gene

  • GC21M042258
  • GC21M042341
  • GC21M044605
  • GC21M044573
  • GC21M045749
  • GC21M031119

Summaries for C21orf2 Gene

Entrez Gene Summary for C21orf2 Gene

  • Four alternatively spliced transcript variants encoding four different isoforms have been found for this nuclear gene. All isoforms contain leucine-rich repeats. Three of these isoforms are mitochondrial proteins and one of them lacks the target peptide, so is not located in mitochondrion. This gene is down-regulated in Down syndrome (DS) brain, which may represent mitochondrial dysfunction in DS patients. [provided by RefSeq, Sep 2012]

GeneCards Summary for C21orf2 Gene

C21orf2 (Chromosome 21 Open Reading Frame 2) is a Protein Coding gene. Diseases associated with C21orf2 include St. Louis Encephalitis and Spondylometaphyseal Dysplasia, Axial.

UniProtKB/Swiss-Prot for C21orf2 Gene

  • May play a role in cilia formation and/or maintenance (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization (PubMed:21834987).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C21orf2 Gene

Genomics for C21orf2 Gene

Regulatory Elements for C21orf2 Gene

Enhancers for C21orf2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21G044337 1.4 ENCODE dbSUPER 62.2 +0.1 59 3.1 HDGF HNRNPUL1 PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 C21orf2 TRPM2 ENSG00000184441 ENSG00000232969
GH21G044328 0.9 dbSUPER 16 +10.1 10139 2.1 PKNOX1 AGO1 KLF17 SIN3A GLI4 ZNF366 SCRT2 FOS ZNF263 USF2 C21orf2 TRPM2 ENSG00000184441 ENSG00000241728 PIR46789
GH21G044297 1.6 Ensembl ENCODE dbSUPER 6.9 +37.9 37917 8.5 HDGF FOXA2 MLX CREB3L1 AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 ENSG00000184441 PFKL ENSG00000215447 C21orf2 PIR46789
GH21G044239 1.8 FANTOM5 ENCODE dbSUPER 4.9 +96.1 96104 6.9 HDGF PKNOX1 FOXA2 MLX WRNIP1 ARID4B SIN3A DMAP1 ZBTB7B SLC30A9 ICOSLG HSF2BP PWP2 ENSG00000184441 C21orf2 TRAPPC10 ENSG00000278158 ENSG00000275799
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around C21orf2 on UCSC Golden Path with GeneCards custom track

Promoters for C21orf2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for C21orf2 Gene

44,328,944 bp from pter
44,339,402 bp from pter
10,459 bases
Minus strand

Genomic View for C21orf2 Gene

Genes around C21orf2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C21orf2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C21orf2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C21orf2 Gene

Proteins for C21orf2 Gene

  • Protein details for C21orf2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein C21orf2
    Protein Accession:
    Secondary Accessions:
    • A8MPS9
    • O14993
    • Q8N5X6
    • Q99837
    • Q99838

    Protein attributes for C21orf2 Gene

    256 amino acids
    Molecular mass:
    28340 Da
    Quaternary structure:
    • Found in a complex with C21orf2, NEK1 and SPATA7 (PubMed:26167768). Interacts with NEK1 (PubMed:26167768).

    Alternative splice isoforms for C21orf2 Gene


neXtProt entry for C21orf2 Gene

Post-translational modifications for C21orf2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for C21orf2 Gene

Domains & Families for C21orf2 Gene

Suggested Antigen Peptide Sequences for C21orf2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with C21orf2: view

No data available for Gene Families and UniProtKB/Swiss-Prot for C21orf2 Gene

Function for C21orf2 Gene

Molecular function for C21orf2 Gene

GENATLAS Biochemistry:
chromosome 21 open reading frame 2,mitochondrial protein,25kDa,with two alternatively spliced transcripts,widely expressed,encoded by a nuclear gene in the DFNB8/DFNB10 region
UniProtKB/Swiss-Prot Function:
May play a role in cilia formation and/or maintenance (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization (PubMed:21834987).

Gene Ontology (GO) - Molecular Function for C21orf2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with C21orf2: view
genes like me logo Genes that share phenotypes with C21orf2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for C21orf2 Gene

Localization for C21orf2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C21orf2 Gene

Mitochondrion. Cytoplasm, cytoskeleton, cilium basal body. Note=Colocalizes with NEK1 and SPATA7 at the basal body. {ECO:0000269 PubMed:26167768}.

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 C21orf2 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
mitochondrion 5
nucleus 4
cytosol 3
peroxisome 1

Gene Ontology (GO) - Cellular Components for C21orf2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA,IEA 21834987
GO:0005739 mitochondrion IEA,IDA 9325172
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane IDA 21834987
GO:0032391 photoreceptor connecting cilium ISS --
genes like me logo Genes that share ontologies with C21orf2: view

Pathways & Interactions for C21orf2 Gene

SuperPathways for C21orf2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for C21orf2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007010 cytoskeleton organization IMP 21834987
GO:0007224 smoothened signaling pathway IEA --
GO:0008360 regulation of cell shape IMP 21834987
GO:0030030 cell projection organization IEA --
GO:0060271 cilium assembly IEA --
genes like me logo Genes that share ontologies with C21orf2: view

No data available for Pathways by source and SIGNOR curated interactions for C21orf2 Gene

Drugs & Compounds for C21orf2 Gene

No Compound Related Data Available

Transcripts for C21orf2 Gene

Unigene Clusters for C21orf2 Gene

Chromosome 21 open reading frame 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for C21orf2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c · 10d ^ 11 ^ 12
SP1: - - - -
SP2: - - -
SP3: - - -
SP4: - -
SP5: -
SP6: -
SP7: - -

Relevant External Links for C21orf2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for C21orf2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for C21orf2 Gene

Protein differential expression in normal tissues from HIPED for C21orf2 Gene

This gene is overexpressed in Testis (17.3), Adrenal (17.1), Heart (12.5), and Pancreas (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for C21orf2 Gene

Protein tissue co-expression partners for C21orf2 Gene

NURSA nuclear receptor signaling pathways regulating expression of C21orf2 Gene:


SOURCE GeneReport for Unigene cluster for C21orf2 Gene:


mRNA Expression by UniProt/SwissProt for C21orf2 Gene:

Tissue specificity: Widely expressed (PubMed:26974433, PubMed:9325172).

Evidence on tissue expression from TISSUES for C21orf2 Gene

  • Lung(4.2)
  • Intestine(4.1)
  • Pancreas(4.1)
  • Nervous system(2.6)
genes like me logo Genes that share expression patterns with C21orf2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for C21orf2 Gene

Orthologs for C21orf2 Gene

This gene was present in the common ancestor of animals.

Orthologs for C21orf2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C21H21orf2 34
  • 99.35 (n)
C21orf2 35
  • 98 (a)
(Canis familiaris)
Mammalia C31H21orf2 34
  • 82.87 (n)
C21orf2 35
  • 55 (a)
(Bos Taurus)
Mammalia C1H21orf2 34
  • 80.39 (n)
C1H21ORF2 35
  • 74 (a)
(Mus musculus)
Mammalia 1810043G02Rik 34 16 35
  • 79.38 (n)
(Rattus norvegicus)
Mammalia RGD1309594 34
  • 78.31 (n)
(Ornithorhynchus anatinus)
Mammalia C21orf2 35
  • 65 (a)
(Gallus gallus)
Aves C9H21ORF2 34 35
  • 68.94 (n)
(Anolis carolinensis)
Reptilia C21orf2 35
  • 50 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia c21orf2 34
  • 54.65 (n)
(Danio rerio)
Actinopterygii LOC100537391 34
  • 62.87 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG14995 35
  • 24 (a)
CG15208 35
  • 23 (a)
(Caenorhabditis elegans)
Secernentea F09G8.5 35
  • 19 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9543 35
  • 31 (a)
Species where no ortholog for C21orf2 was found in the sources mined by GeneCards:
  • 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • 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 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)
  • wheat (Triticum aestivum)

Evolution for C21orf2 Gene

Gene Tree for C21orf2 (if available)
Gene Tree for C21orf2 (if available)

Paralogs for C21orf2 Gene

No data available for Paralogs for C21orf2 Gene

Variants for C21orf2 Gene

Sequence variations from dbSNP and Humsavar for C21orf2 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs1057518441 Uncertain significance 44,333,224(-) CCGGT(A/G)CCAGC nc-transcript-variant, reference, missense, utr-variant-5-prime
rs11552066 Benign 44,330,262(+) TCTGC(C/T)GCACG nc-transcript-variant, reference, missense
rs11552068 Benign 44,330,285(+) TCTGC(A/G)TCCAG nc-transcript-variant, reference, synonymous-codon
rs11870 Benign 44,339,162(-) ACCCG(A/G)GCCAA nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon, missense, utr-variant-5-prime
rs2277809 Benign 44,331,939(+) GGCCT(A/G)TGCCC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for C21orf2 Gene

Variant ID Type Subtype PubMed ID
esv1005686 CNV deletion 20482838
esv1476049 CNV deletion 17803354
esv2723638 CNV deletion 23290073
esv2723642 CNV deletion 23290073
esv2723643 CNV deletion 23290073
esv33817 CNV loss 17666407
esv3647130 CNV gain 21293372
nsv1058359 CNV gain 25217958
nsv1130786 CNV deletion 24896259
nsv509800 CNV insertion 20534489
nsv587740 CNV loss 21841781
nsv587779 CNV loss 21841781
nsv587780 CNV loss 21841781
nsv828907 CNV gain 20364138
nsv828909 CNV gain 20364138
nsv953646 CNV deletion 24416366

Variation tolerance for C21orf2 Gene

Residual Variation Intolerance Score: 95.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.69; 66.05% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for C21orf2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C21orf2 Gene

Disorders for C21orf2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for C21orf2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
st. louis encephalitis
  • neuroinvasive st. louis encephalitis virus infection
spondylometaphyseal dysplasia, axial
  • axial spondylometaphyseal dysplasia
autosomal recessive nonsyndromic deafness 8
  • autosomal recessive deafness 10
- elite association - COSMIC cancer census association via MalaCards


  • Note=Defects in C21orf2 may be the cause of a autosomal recessive spondylometaphyseal dysplasia axial. Spondylometaphyseal dysplasia axial is a clinical subtype of spondylometaphyseal dysplasia, in which mainly axial skeleton and retina are affected. Affected individuals show postnatal growth deficiency, mild short stature, rhizomelic shortening of the limbs without bowing of the long bones of the legs, axial metaphyseal abnormalities with progressive mild platyspondyly, progressive femoral metaphyseal changes, decreased anteroposterior diameter of the thorax with markedly flared anterior ends of the ribs, normal tubular bones, and early onset and progressive visual impairment, with cone-rod dystrophy and/or optic atrophy. {ECO:0000305 PubMed:26974433}.
  • Note=Defects in C21orf2 may play a role in Jeune syndrome. Jeune syndrome is a form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a trident appearance of the acetabular roof. Additional features include polydactyly, kidney cysts and renal failure, retinal degeneration and liver disease are variably present. {ECO:0000305 PubMed:26167768}.

Relevant External Links for C21orf2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with C21orf2: view

No data available for Genatlas for C21orf2 Gene

Publications for C21orf2 Gene

  1. Axial Spondylometaphyseal Dysplasia Is Caused by C21orf2 Mutations. (PMID: 26974433) Wang Z. … Ikegawa S. (PLoS ONE 2016) 2 3 4 64
  2. Characterization of a novel gene, C21orf2, on human chromosome 21q22.3 and its exclusion as the APECED gene by mutation analysis. (PMID: 9465297) Scott H.S. … Antonarakis S.E. (Genomics 1998) 2 3 4 64
  3. The NEK1 interactor, C21ORF2, is required for efficient DNA damage repair. (PMID: 26290490) Fang X. … Zhang P. (Acta Biochim. Biophys. Sin. (Shanghai) 2015) 2 3 64
  4. An siRNA-based functional genomics screen for theA identification of regulators of ciliogenesis and ciliopathyA genes. (PMID: 26167768) Wheway G. … Johnson C.A. (Nat. Cell Biol. 2015) 3 4 64
  5. Identification and characterization of a set of conserved and new regulators of cytoskeletal organisation, cell morphology and migration. (PMID: 21834987) Bai S.W. … Ridley A.J. (BMC Biol. 2011) 3 4 64

Products for C21orf2 Gene

Sources for C21orf2 Gene

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