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CEP164 Gene(Protein Coding)

Centrosomal Protein 164

GCID:
GC11P117314
GIFtS:
48
Genes Participants
UDN Logo

Aliases for CEP164 Gene

Aliases for CEP164 Gene

  • Centrosomal Protein 164 2 3 5
  • Centrosomal Protein 164kDa 2 3
  • NPHP15 3 4
  • Centrosomal Protein Of 164 KDa 3
  • KIAA1052 4
  • Cep164 4

External Ids for CEP164 Gene

Previous GeneCards Identifiers for CEP164 Gene

  • GC11P116704
  • GC11P117198
  • GC11P113132

Summaries for CEP164 Gene

Entrez Gene Summary for CEP164 Gene

  • This gene encodes a centrosomal protein involved in microtubule organization, DNA damage response, and chromosome segregation. The encoded protein is required for assembly of primary cilia and localizes to mature centrioles. Defects in this gene are a cause of nephronophthisis-related ciliopathies. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

GeneCards Summary for CEP164 Gene

CEP164 (Centrosomal Protein 164) is a Protein Coding gene. Diseases associated with CEP164 include Nephronophthisis 15 and Senior-Loken Syndrome 1. Among its related pathways are Organelle biogenesis and maintenance and Regulation of PLK1 Activity at G2/M Transition.

UniProtKB/Swiss-Prot for CEP164 Gene

  • Plays a role in microtubule organization and/or maintenance for the formation of primary cilia (PC), a microtubule-based structure that protrudes from the surface of epithelial cells. Plays a critical role in G2/M checkpoint and nuclear divisions. A key player in the DNA damage-activated ATR/ATM signaling cascade since it is required for the proper phosphorylation of H2AX, RPA, CHEK2 and CHEK1. Plays a critical role in chromosome segregation, acting as a mediator required for the maintenance of genomic stability through modulation of MDC1, RPA and CHEK1.

Gene Wiki entry for CEP164 Gene

Additional gene information for CEP164 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CEP164 Gene

Genomics for CEP164 Gene

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GeneHancer (GH) Regulatory Elements for CEP164 Gene

Promoters and enhancers for CEP164 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11I117314 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 550.8 +1.2 1213 2.6 PKNOX1 ZFP64 ARID4B SIN3A ZNF2 ZNF48 YY1 ETS1 GLIS2 ZNF143 BACE1 CEP164 GC11P117316 GC11M117315 ENSG00000250699
GH11I117327 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.4 +13.7 13661 2.2 HDGF PKNOX1 ARNT ARID4B SIN3A ZBTB7B YY1 POLR2B ZNF766 ZNF207 ENSG00000250699 CEP164 RNF214 BUD13 ZPR1 PCSK7 ENSG00000252992 BACE1 GC11M117336
GH11I117036 Enhancer 1.1 Ensembl ENCODE dbSUPER 15.4 -276.9 -276904 1.5 ZNF146 INSM2 ZNF140 FEZF1 HIC1 ZNF121 ZNF366 SCRT2 ZNF600 TCF7L2 RPS27P19 GC11M117036 RNF214 APOA1 CEP164 LOC653303 BUD13 ENSG00000224077 SIK3 TAGLN
GH11I116470 Enhancer 0.7 ENCODE 15.4 -841.9 -841859 3.5 JUN ZNF140 CEBPG TEAD3 FOSL1 ZNF366 PRDM10 TRIM24 FOS ATF7 CEP164 RNF214 BUD13 LINC02151 GC11P116229
GH11I116458 Enhancer 0.7 ENCODE 14.9 -854.6 -854589 2.7 CTCF MEIS2 LEF1 PKNOX1 ARNT FEZF1 ZNF335 FOXM1 CTBP1 POLR2A CEP164 RNF214 LINC02151 GC11P116229
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CEP164 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CEP164 gene promoter:

Genomic Locations for CEP164 Gene

Genomic Locations for CEP164 Gene
chr11:117,314,557-117,413,268
(GRCh38/hg38)
Size:
98,712 bases
Orientation:
Plus strand
chr11:117,185,273-117,283,984
(GRCh37/hg19)

Genomic View for CEP164 Gene

Genes around CEP164 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CEP164 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CEP164 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CEP164 Gene

Proteins for CEP164 Gene

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  • Protein details for CEP164 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPV0-CE164_HUMAN
    Recommended name:
    Centrosomal protein of 164 kDa
    Protein Accession:
    Q9UPV0
    Secondary Accessions:
    • Q6PKH9
    • Q7Z2X9
    • Q9NVS0
    • Q9UFJ6

    Protein attributes for CEP164 Gene

    Size:
    1460 amino acids
    Molecular mass:
    164314 Da
    Quaternary structure:
    • Interacts (via N-terminus) with ATRIP. Interacts with ATM, ATR and MDC1. Interacts with XPA (via N-terminus) upon UV irradiation. Interacts with CEP83, CCDC92, TTBK2, DVL3, NPHP3 and weakly with NPHP4.
    SequenceCaution:
    • Sequence=AAH00602.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAH54015.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA83004.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA91677.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAB56023.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CEP164 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CEP164 Gene

Protein Expression for CEP164 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CEP164 Gene

  • Phosphorylation at Ser-186 is induced upon DNA-damage caused by treatment with IR irradiation, UV irradiation, hydroxyurea or amphidicolin. Also MDC1-mediated chromatin remodeling is critical for DNA damage-induced phosphorylation.
  • Ubiquitination at Lys1359 and posLast=13621362

Other Protein References for CEP164 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CEP164 Gene

Domains & Families for CEP164 Gene

Gene Families for CEP164 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CEP164 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CEP164 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CEP164: view

No data available for UniProtKB/Swiss-Prot for CEP164 Gene

Function for CEP164 Gene

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Molecular function for CEP164 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in microtubule organization and/or maintenance for the formation of primary cilia (PC), a microtubule-based structure that protrudes from the surface of epithelial cells. Plays a critical role in G2/M checkpoint and nuclear divisions. A key player in the DNA damage-activated ATR/ATM signaling cascade since it is required for the proper phosphorylation of H2AX, RPA, CHEK2 and CHEK1. Plays a critical role in chromosome segregation, acting as a mediator required for the maintenance of genomic stability through modulation of MDC1, RPA and CHEK1.

Phenotypes From GWAS Catalog for CEP164 Gene

Gene Ontology (GO) - Molecular Function for CEP164 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22863007
genes like me logo Genes that share ontologies with CEP164: view
genes like me logo Genes that share phenotypes with CEP164: view

Human Phenotype Ontology for CEP164 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CEP164 Gene

MGI Knock Outs for CEP164:

Animal Model Products

miRNA for CEP164 Gene

miRTarBase miRNAs that target CEP164

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CEP164 Gene

Localization for CEP164 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CEP164 Gene

Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole. Nucleus. Note=Localizes specifically to very distally located appendage structures on the mature centriole from which initiate PC formation (PubMed:26337392). Persisted at centrioles throughout mitosis. Expressed in chromatin-enriched nuclear fraction of HeLa cells. In response to DNA damage, it translocates to nuclear foci that contain the DNA damage response proteins KAT5/TIP60 and CHEK1. {ECO:0000269 PubMed:26337392}.

Subcellular locations from

COMPARTMENTS
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 CEP164 gene
Compartment Confidence
extracellular 5
cytoskeleton 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (4)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CEP164 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA,IDA 22664934
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA 21399614
genes like me logo Genes that share ontologies with CEP164: view

Pathways & Interactions for CEP164 Gene

genes like me logo Genes that share pathways with CEP164: view

Gene Ontology (GO) - Biological Process for CEP164 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000086 G2/M transition of mitotic cell cycle TAS --
GO:0006281 DNA repair IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0007049 cell cycle IEA --
GO:0010389 regulation of G2/M transition of mitotic cell cycle TAS --
genes like me logo Genes that share ontologies with CEP164: view

No data available for SIGNOR curated interactions for CEP164 Gene

Drugs & Compounds for CEP164 Gene

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No Compound Related Data Available

Transcripts for CEP164 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CEP164 Gene

(32) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(118) Selected AceView cDNA sequences:
(14) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CEP164 Gene

Centrosomal protein 164kDa:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CEP164 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 ^ 24a ·
SP1:
SP2: - - - - - - - - - - - - - -
SP3:
SP4:
SP5:

ExUns: 24b ^ 25a · 25b · 25c · 25d ^ 26 ^ 27a · 27b · 27c ^ 28a · 28b
SP1: -
SP2: - - - - -
SP3: - -
SP4:
SP5: -

Relevant External Links for CEP164 Gene

GeneLoc Exon Structure for
CEP164
ECgene alternative splicing isoforms for
CEP164

Expression for CEP164 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CEP164 Gene

mRNA expression in normal human tissues for CEP164 Gene
mRNA expression by GTEx for CEP164 GenemRNA expression by BioGPS for CEP164 Gene

Protein differential expression in normal tissues from HIPED for CEP164 Gene

This gene is overexpressed in Fetal gut (21.7), Liver (14.4), and Colon (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CEP164 Gene



NURSA nuclear receptor signaling pathways regulating expression of CEP164 Gene:

CEP164

SOURCE GeneReport for Unigene cluster for CEP164 Gene:

Hs.504009

mRNA Expression by UniProt/SwissProt for CEP164 Gene:

Q9UPV0-CE164_HUMAN
Tissue specificity: Expressed in several cell lines.

Evidence on tissue expression from TISSUES for CEP164 Gene

  • Nervous system(4.3)
  • Skin(4.2)
  • Blood(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CEP164 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • nervous
  • skeletal muscle
  • urinary
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • pituitary gland
Thorax:
  • heart
Abdomen:
  • kidney
  • liver
  • pancreas
Pelvis:
  • urinary bladder
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
genes like me logo Genes that share expression patterns with CEP164: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for CEP164 Gene

Orthologs for CEP164 Gene

This gene was present in the common ancestor of animals.

Orthologs for CEP164 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia CEP164 33 34
  • 99.09 (n)
dog
(Canis familiaris)
 Mammalia CEP164 33 34
  • 82.2 (n)
cow
(Bos Taurus)
 Mammalia CEP164 33 34
  • 81.71 (n)
rat
(Rattus norvegicus)
 Mammalia Cep164 33
  • 76.22 (n)
mouse
(Mus musculus)
 Mammalia Cep164 33 16 34
  • 73.81 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 51 (a)
 OneToMany
-- 34
  • 46 (a)
 OneToMany
-- 34
  • 22 (a)
 OneToMany
oppossum
(Monodelphis domestica)
 Mammalia CEP164 34
  • 42 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CEP164 33 34
  • 60.84 (n)
lizard
(Anolis carolinensis)
 Reptilia CEP164 34
  • 32 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia cep164 33
  • 52.06 (n)
zebrafish
(Danio rerio)
 Actinopterygii CABZ01087562.1 34
  • 75 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta CG9170 34
  • 17 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.12255 33
Species where no ortholog for CEP164 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)
  • 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 CEP164 Gene

ENSEMBL:
Gene Tree for CEP164 (if available)
TreeFam:
Gene Tree for CEP164 (if available)

Paralogs for CEP164 Gene

(1) SIMAP similar genes for CEP164 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for CEP164 Gene

genes like me logo Genes that share paralogs with CEP164: view

No data available for Paralogs for CEP164 Gene

Variants for CEP164 Gene

Sequence variations from dbSNP and Humsavar for CEP164 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs112209873 uncertain-significance, likely-benign, not specified, Nephronophthisis 15 117,381,729(+) C/G/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs115051850 benign, not specified, Nephronophthisis 15 117,409,796(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs117083334 benign, not specified, Nephronophthisis 15 117,381,721(+) A/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs142545580 likely-benign, Nephronophthisis 15 117,395,011(+) A/G genic_downstream_transcript_variant, intron_variant, non_coding_transcript_variant
rs143512199 likely-benign, Nephronophthisis 15 117,382,910(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for CEP164 Gene

Variant ID Type Subtype PubMed ID
esv2678884 CNV deletion 23128226
esv2745118 CNV deletion 23290073
esv2745120 CNV deletion 23290073
esv3627849 CNV gain 21293372
esv3627850 CNV gain 21293372
esv3627851 CNV loss 21293372
esv3627853 CNV loss 21293372
nsv1038815 CNV gain 25217958
nsv1040918 CNV gain 25217958
nsv1052364 CNV gain 25217958
nsv39581 CNV deletion 16902084
nsv477444 CNV novel sequence insertion 20440878
nsv517908 CNV loss 19592680
nsv972074 CNV duplication 23825009

Variation tolerance for CEP164 Gene

Residual Variation Intolerance Score: 81.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.82; 91.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CEP164 Gene

Human Gene Mutation Database (HGMD)
CEP164
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CEP164

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CEP164 Gene

Disorders for CEP164 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CEP164 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
nephronophthisis 15
  • nphp15
senior-loken syndrome 1
  • slsn1
nephronophthisis
  • medullary cystic disease
spinocerebellar ataxia 11
  • sca11
leber congenital amaurosis
  • lca
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CE164_HUMAN
  • Nephronophthisis 15 (NPHP15) [MIM:614845]: An autosomal recessive disorder characterized by the association of nephronophthisis with Leber congenital amaurosis and retinal degeneration, often resulting in blindness during childhood. Additional features include seizures, cerebellar vermis hypoplasia, facial dysmorphism, bronchiectasis and liver failure. Nephronophthisis is a chronic tubulo-interstitial nephritis that progresses to end-stage renal failure. {ECO:0000269 PubMed:22863007}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CEP164

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CEP164: view

No data available for Genatlas for CEP164 Gene

Publications for CEP164 Gene

  1. UV-dependent interaction between Cep164 and XPA mediates localization of Cep164 at sites of DNA damage and UV sensitivity. (PMID: 19197159) Pan YR … Lee EY (Cell cycle (Georgetown, Tex.) 2009) 3 4 22 58
  2. Cep164 is a mediator protein required for the maintenance of genomic stability through modulation of MDC1, RPA, and CHK1. (PMID: 18283122) Sivasubramaniam S … Lee EY (Genes & development 2008) 3 4 22 58
  3. Cep164, a novel centriole appendage protein required for primary cilium formation. (PMID: 17954613) Graser S … Nigg EA (The Journal of cell biology 2007) 3 4 22 58
  4. Proteomic characterization of the human centrosome by protein correlation profiling. (PMID: 14654843) Andersen JS … Mann M (Nature 2003) 2 3 4 58
  5. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58

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