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Aliases for CNTLN Gene

Aliases for CNTLN Gene

  • Centlein 2 3 3 5
  • Centlein, Centrosomal Protein 2 3
  • Centrosomal Protein 3 4
  • C9orf101 3 4
  • C9orf39 3 4
  • Chromosome 9 Open Reading Frame 101 2
  • Chromosome 9 Open Reading Frame 39 2
  • BA340N12.1 3

External Ids for CNTLN Gene

Previous HGNC Symbols for CNTLN Gene

  • C9orf101
  • C9orf39

Summaries for CNTLN Gene

GeneCards Summary for CNTLN Gene

CNTLN (Centlein) is a Protein Coding gene. Diseases associated with CNTLN include Microcephalic Osteodysplastic Primordial Dwarfism, Type Ii and Bardet-Biedl Syndrome 2. Gene Ontology (GO) annotations related to this gene include protein kinase binding and protein binding, bridging.

UniProtKB/Swiss-Prot for CNTLN Gene

  • Required for centrosome cohesion and recruitment of CEP68 to centrosomes.

Additional gene information for CNTLN Gene

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

Genomics for CNTLN Gene

GeneHancer (GH) Regulatory Elements for CNTLN Gene

Promoters and enhancers for CNTLN 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
GH09J017134 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 659.1 +0.3 324 2.2 ARID4B SIN3A DMAP1 ZNF2 YY1 GLIS2 KLF7 ZNF202 SP3 YY2 CNTLN PIR42398
GH09J017322 Enhancer 0.9 VISTA UCNEbase 46.5 +188.3 188306 2.2 RCOR1 CNTLN GC09M017401 GC09P017217
GH09J017342 Enhancer 0.6 UCNEbase 45.3 +207.9 207858 0.4 POLR2A REST CNTLN GC09M017401 GC09P017217
GH09J017082 Enhancer 0.5 ENCODE 20.5 -52.4 -52401 0.4 CTCF ZBTB6 ZNF10 RCOR1 ZIC2 CNTLN RPS29P33 RN7SL720P LOC105375983
GH09J017057 Enhancer 0.4 ENCODE 11.2 -76.9 -76948 0.9 JUND CEBPA HNF4A CNTLN RN7SL720P RPS29P33 LOC105375983
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNTLN on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CNTLN gene promoter:
  • FOXO1a
  • FOXO1
  • FOXF2
  • Nkx2-5
  • Elk-1
  • c-Ets-1
  • FOXD3
  • ATF-2

Genomic Locations for CNTLN Gene

Genomic Locations for CNTLN Gene
368,942 bases
Plus strand
368,942 bases
Plus strand

Genomic View for CNTLN Gene

Genes around CNTLN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CNTLN Gene

Proteins for CNTLN Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A5Z2X6
    • Q5VYJ0
    • Q8N1G9
    • Q9HAJ5

    Protein attributes for CNTLN Gene

    1405 amino acids
    Molecular mass:
    161603 Da
    Quaternary structure:
    • Interacts with CEP250 and CEP68. Interacts with NEK2; the interaction leads to phosphorylation of CNTLN.
    • Sequence=BAA91052.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB13850.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for CNTLN Gene


neXtProt entry for CNTLN Gene

Post-translational modifications for CNTLN Gene

No data available for DME Specific Peptides for CNTLN Gene

Domains & Families for CNTLN Gene

Gene Families for CNTLN Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CNTLN Gene

Suggested Antigen Peptide Sequences for CNTLN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for CNTLN Gene

Function for CNTLN Gene

Molecular function for CNTLN Gene

UniProtKB/Swiss-Prot Function:
Required for centrosome cohesion and recruitment of CEP68 to centrosomes.

Phenotypes From GWAS Catalog for CNTLN Gene

Gene Ontology (GO) - Molecular Function for CNTLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0019901 protein kinase binding IPI 24554434
GO:0019904 protein domain specific binding IPI 24554434
GO:0030674 protein binding, bridging IMP 24554434
genes like me logo Genes that share ontologies with CNTLN: view
genes like me logo Genes that share phenotypes with CNTLN: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

Localization for CNTLN Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNTLN Gene

Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole. Note=Colocalizes with gamma-tubulin during interphase and mitosis. Appears to associate with the mother centriole during G1 phase and with daughter centrioles towards G1/S phase (By similarity). Localizes to the proximal ends of the centrioles (PubMed:24554434). Levels are high at interphase centrosomes but are reduced on mitotic spindle poles (PubMed:24554434). {ECO:0000250 UniProtKB:A9ZSY0, ECO:0000269 PubMed:24554434}.

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 CNTLN gene
Compartment Confidence
extracellular 5
cytoskeleton 5
nucleus 5
cytosol 5
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (3)
  • Cytosol (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CNTLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 24554434
GO:0005813 centrosome IDA --
GO:0005814 centriole IEA,IDA 24554434
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with CNTLN: view

Pathways & Interactions for CNTLN Gene

SuperPathways for CNTLN Gene

No Data Available

Gene Ontology (GO) - Biological Process for CNTLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010457 centriole-centriole cohesion IMP 24554434
GO:0033365 protein localization to organelle IMP 24554434
genes like me logo Genes that share ontologies with CNTLN: view

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

Drugs & Compounds for CNTLN Gene

No Compound Related Data Available

Transcripts for CNTLN Gene

Unigene Clusters for CNTLN Gene

Centlein, centrosomal protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23
SP3: -

Relevant External Links for CNTLN Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CNTLN Gene

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

Protein differential expression in normal tissues from HIPED for CNTLN Gene

This gene is overexpressed in Platelet (36.5), Plasma (12.9), and Urinary Bladder (12.8).

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

NURSA nuclear receptor signaling pathways regulating expression of CNTLN Gene:


SOURCE GeneReport for Unigene cluster for CNTLN Gene:


Evidence on tissue expression from TISSUES for CNTLN Gene

  • Stomach(4)
genes like me logo Genes that share expression patterns with CNTLN: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CNTLN Gene

Orthologs for CNTLN Gene

This gene was present in the common ancestor of chordates.

Orthologs for CNTLN Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CNTLN 34 33
  • 98.96 (n)
(Bos Taurus)
Mammalia CNTLN 34 33
  • 89.91 (n)
(Canis familiaris)
Mammalia CNTLN 34 33
  • 89.69 (n)
(Mus musculus)
Mammalia Cntln 16 34 33
  • 82.1 (n)
(Rattus norvegicus)
Mammalia Cntln 33
  • 81.32 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 69 (a)
-- 34
  • 59 (a)
(Monodelphis domestica)
Mammalia CNTLN 34
  • 49 (a)
(Gallus gallus)
Aves C9ORF39 33
  • 68.03 (n)
-- 34
  • 62 (a)
-- 34
  • 56 (a)
(Anolis carolinensis)
Reptilia CNTLN 34
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cntln 33
  • 61.78 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.4694 33
(Danio rerio)
Actinopterygii si:ch211-2i17.1 33
  • 52.5 (n)
cntln 34
  • 36 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 30 (a)
Species where no ortholog for CNTLN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for CNTLN Gene

Gene Tree for CNTLN (if available)
Gene Tree for CNTLN (if available)
Evolutionary constrained regions (ECRs) for CNTLN: view image

Paralogs for CNTLN Gene

(4) SIMAP similar genes for CNTLN Gene using alignment to 3 proteins:

  • C9J1F9_HUMAN
  • J3KN33_HUMAN
genes like me logo Genes that share paralogs with CNTLN: view

No data available for Paralogs for CNTLN Gene

Variants for CNTLN Gene

Sequence variations from dbSNP and Humsavar for CNTLN Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000006664 -- 17,175,781(+) T/G genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000010459 -- 17,388,436(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000011270 -- 17,252,623(+) T/C genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000023909 -- 17,181,887(+) C/T genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000031175 -- 17,213,579(+) G/T genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
esv2422265 CNV duplication 17116639
esv2661216 CNV deletion 23128226
esv2666854 CNV deletion 23128226
esv2738244 CNV deletion 23290073
esv27469 CNV loss 19812545
esv27473 CNV loss 19812545
esv2764141 CNV loss 21179565
esv3304113 CNV mobile element insertion 20981092
esv3336164 CNV insertion 20981092
esv3544609 CNV deletion 23714750
esv3544610 CNV deletion 23714750
esv3544612 CNV deletion 23714750
esv3573158 CNV loss 25503493
esv3619834 CNV loss 21293372
esv3619835 CNV loss 21293372
esv3619836 CNV loss 21293372
esv3619837 CNV loss 21293372
esv3619839 CNV loss 21293372
esv3619840 CNV loss 21293372
esv3619842 CNV loss 21293372
esv3619843 CNV loss 21293372
esv3891627 CNV loss 25118596
esv3891628 CNV loss 25118596
esv3891629 CNV loss 25118596
nsv1015524 CNV loss 25217958
nsv1030291 CNV loss 25217958
nsv1031269 CNV loss 25217958
nsv1074844 CNV deletion 25765185
nsv1077094 CNV deletion 25765185
nsv1129301 CNV insertion 24896259
nsv1146643 CNV deletion 26484159
nsv416983 CNV deletion 16902084
nsv466269 CNV gain 19166990
nsv466270 CNV loss 19166990
nsv466273 CNV loss 19166990
nsv471287 CNV gain 18288195
nsv477833 CNV novel sequence insertion 20440878
nsv510184 OTHER sequence alteration 20534489
nsv522698 CNV loss 19592680
nsv523411 CNV gain 19592680
nsv526787 CNV loss 19592680
nsv613693 CNV gain 21841781
nsv613694 CNV loss 21841781
nsv613695 CNV loss 21841781
nsv613696 CNV loss 21841781
nsv613697 CNV loss 21841781
nsv613698 CNV loss 21841781
nsv613699 CNV loss 21841781
nsv957716 CNV deletion 24416366

Variation tolerance for CNTLN Gene

Residual Variation Intolerance Score: 89.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.99; 93.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNTLN Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CNTLN Gene

MalaCards: The human disease database

(7) MalaCards diseases for CNTLN Gene - From: HGMD and DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search CNTLN in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CNTLN

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CNTLN: view

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

Publications for CNTLN Gene

  1. Centlein mediates an interaction between C-Nap1 and Cep68 to maintain centrosome cohesion. (PMID: 24554434) Fang G … Yuan L (Journal of cell science 2014) 3 4 58
  2. Genome-wide association study of lung function decline in adults with and without asthma. (PMID: 22424883) Imboden M … Probst-Hensch NM (The Journal of allergy and clinical immunology 2012) 3 44 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2. (PMID: 19648919) Song H … Gayther SA (Nature genetics 2009) 3 44 58

Products for CNTLN Gene

Sources for CNTLN Gene

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