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Aliases for CCDC115 Gene

Aliases for CCDC115 Gene

  • Coiled-Coil Domain Containing 115 2 3 5
  • Coiled-Coil Domain-Containing Protein 115 3
  • CDG2O 3
  • Ccp1 3

External Ids for CCDC115 Gene

Previous GeneCards Identifiers for CCDC115 Gene

  • GC02M130814
  • GC02M131095
  • GC02M123385

Summaries for CCDC115 Gene

Entrez Gene Summary for CCDC115 Gene

  • The protein encoded by this gene has been observed to localize to the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) and coat protein complex I (COPI) vesicles in some human cells. The encoded protein shares some homology with the yeast V-ATPase assembly factor Vma22p, and the orthologous protein in mouse promotes cell proliferation and suppresses cell death. Defects in this gene are a cause of congenital disorder of glycosylation, type IIo in humans. [provided by RefSeq, Mar 2016]

GeneCards Summary for CCDC115 Gene

CCDC115 (Coiled-Coil Domain Containing 115) is a Protein Coding gene. Diseases associated with CCDC115 include Congenital Disorder Of Glycosylation, Type Iio and Congenital Disorder Of Glycosylation, Type Ii.

UniProtKB/Swiss-Prot for CCDC115 Gene

  • Accessory component of the proton-transporting vacuolar (V)-ATPase protein pump involved in intracellular iron homeostasis. In aerobic conditions, required for intracellular iron homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent proteasomal degradation. Necessary for endolysosomal acidification and lysosomal degradation (PubMed:28296633). May be involved in Golgi homeostasis (PubMed:26833332).

Additional gene information for CCDC115 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCDC115 Gene

Genomics for CCDC115 Gene

GeneHancer (GH) Regulatory Elements for CCDC115 Gene

Promoters and enhancers for CCDC115 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
GH02J130341 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.2 219 3 HDGF HNRNPUL1 PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 PIR60541 IMP4 GC02P130344 CCDC115 SMPD4 PTPN18
GH02J130797 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 2.4 -455.1 -455145 1.8 ATF1 ZFP64 ARID4B SIN3A DMAP1 ZBTB7B ZNF48 SLC30A9 ZNF121 GLIS2 CCDC115 CYCSP8 ARHGEF4 GC02P130573
GH02J130389 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 1.7 -48.4 -48387 2.8 PKNOX1 ATF1 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 ZNF143 SP5 LOC105373618 PTPN18 FAR2P2 AMER3 CCDC115 PIR36289
GH02J130336 Enhancer 1.3 Ensembl ENCODE 0.7 +4.5 4503 3.5 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A ZNF2 IRF4 POLR2B ZNF766 TRE-TTC1-1 SMPD4 PTPN18 RAB6C-AS1 CCDC115 IMP4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC115 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CCDC115 gene promoter:
  • MIF-1
  • MyoD
  • SRF (504 AA)
  • SRF
  • CREB
  • deltaCREB
  • Pax-4a
  • MAZR
  • ATF6
  • PPAR-alpha

Genomic Locations for CCDC115 Gene

Genomic Locations for CCDC115 Gene
chr2:130,337,933-130,342,810
(GRCh38/hg38)
Size:
4,878 bases
Orientation:
Minus strand
chr2:131,095,814-131,099,922
(GRCh37/hg19)
Size:
4,109 bases
Orientation:
Minus strand

Genomic View for CCDC115 Gene

Genes around CCDC115 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC115 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC115 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC115 Gene

Proteins for CCDC115 Gene

  • Protein details for CCDC115 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96NT0-CC115_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 115
    Protein Accession:
    Q96NT0
    Secondary Accessions:
    • B4DJ47
    • Q9BR88

    Protein attributes for CCDC115 Gene

    Size:
    180 amino acids
    Molecular mass:
    19761 Da
    Quaternary structure:
    • Accessory component of the multisubunit proton-transporting vacuolar (V)-ATPase protein pump.

    Alternative splice isoforms for CCDC115 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCDC115 Gene

Post-translational modifications for CCDC115 Gene

  • Ubiquitination at posLast=4444
  • Modification sites at PhosphoSitePlus

Other Protein References for CCDC115 Gene

No data available for DME Specific Peptides for CCDC115 Gene

Domains & Families for CCDC115 Gene

Gene Families for CCDC115 Gene

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

Protein Domains for CCDC115 Gene

ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CCDC115: view

No data available for UniProtKB/Swiss-Prot for CCDC115 Gene

Function for CCDC115 Gene

Molecular function for CCDC115 Gene

UniProtKB/Swiss-Prot Function:
Accessory component of the proton-transporting vacuolar (V)-ATPase protein pump involved in intracellular iron homeostasis. In aerobic conditions, required for intracellular iron homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent proteasomal degradation. Necessary for endolysosomal acidification and lysosomal degradation (PubMed:28296633). May be involved in Golgi homeostasis (PubMed:26833332).

Gene Ontology (GO) - Molecular Function for CCDC115 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051082 unfolded protein binding IBA --
genes like me logo Genes that share ontologies with CCDC115: view
genes like me logo Genes that share phenotypes with CCDC115: view

Human Phenotype Ontology for CCDC115 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for CCDC115 Gene

Localization for CCDC115 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC115 Gene

Endosome. Lysosome. Endoplasmic reticulum-Golgi intermediate compartment. Cytoplasmic vesicle, COPI-coated vesicle. Endoplasmic reticulum.

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 CCDC115 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
endosome 4
nucleus 3
lysosome 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CCDC115 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005768 endosome IEA --
GO:0005783 endoplasmic reticulum IDA,IEA 28296633
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment IEA,IDA 26833332
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with CCDC115: view

Pathways & Interactions for CCDC115 Gene

SuperPathways for CCDC115 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CCDC115 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006879 cellular iron ion homeostasis IMP 28296633
GO:0007042 lysosomal lumen acidification IMP 28296633
GO:0036295 cellular response to increased oxygen levels IMP 28296633
GO:1905146 lysosomal protein catabolic process IMP 28296633
genes like me logo Genes that share ontologies with CCDC115: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC115 Gene

Drugs & Compounds for CCDC115 Gene

No Compound Related Data Available

Transcripts for CCDC115 Gene

mRNA/cDNA for CCDC115 Gene

Unigene Clusters for CCDC115 Gene

Coiled-coil domain containing 115:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC115 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d · 7e
SP1: - - -
SP2: - - - - - -
SP3: - - - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - -
SP6: - - - -
SP7: - -
SP8:
SP9:
SP10:

Relevant External Links for CCDC115 Gene

GeneLoc Exon Structure for
CCDC115
ECgene alternative splicing isoforms for
CCDC115

Expression for CCDC115 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCDC115 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CCDC115 Gene

This gene is overexpressed in Synovial fluid (29.7), Peripheral blood mononuclear cells (10.8), Kidney (8.2), and Bone (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CCDC115 Gene



NURSA nuclear receptor signaling pathways regulating expression of CCDC115 Gene:

CCDC115

SOURCE GeneReport for Unigene cluster for CCDC115 Gene:

Hs.104203

mRNA Expression by UniProt/SwissProt for CCDC115 Gene:

Q96NT0-CC115_HUMAN
Tissue specificity: Expressed throughout the brain.

Evidence on tissue expression from TISSUES for CCDC115 Gene

  • Nervous system(4.8)
  • Eye(4.4)
genes like me logo Genes that share expression patterns with CCDC115: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC115 Gene

Orthologs for CCDC115 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CCDC115 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CCDC115 34 33
  • 99.81 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CCDC115 34 33
  • 84.44 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LOC614882 33
  • 81.7 (n)
CCDC115 34
  • 77 (a)
OneToMany
-- 34
  • 68 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Ccdc115 33
  • 80.38 (n)
mouse
(Mus musculus)
Mammalia Ccdc115 16 34 33
  • 80 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 45 (a)
OneToMany
-- 34
  • 41 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia CCDC115 34
  • 38 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii zgc:113121 33
  • 53.01 (n)
CCDC115 34
  • 37 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 27 (a)
OneToOne
Species where no ortholog for CCDC115 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • 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 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)

Evolution for CCDC115 Gene

ENSEMBL:
Gene Tree for CCDC115 (if available)
TreeFam:
Gene Tree for CCDC115 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC115: view image

Paralogs for CCDC115 Gene

No data available for Paralogs for CCDC115 Gene

Variants for CCDC115 Gene

Sequence variations from dbSNP and Humsavar for CCDC115 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs751325113 pathogenic, CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIo, Congenital disorders of glycosylation type II, Congenital disorder of glycosylation 2O (CDG2O) [MIM:616828] 130,342,034(-) A/G coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs869025583 pathogenic, CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIo, Congenital disorders of glycosylation type II, Congenital disorder of glycosylation 2O (CDG2O) [MIM:616828] 130,342,095(-) C/A 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs752919660 uncertain-significance, not provided 130,342,125(-) T/C genic_upstream_transcript_variant, initiator_codon_variant, intron_variant, missense_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1000095126 -- 130,341,416(-) C/T intron_variant
rs1000327396 -- 130,344,162(-) A/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CCDC115 Gene

Variant ID Type Subtype PubMed ID
dgv2032n106 OTHER inversion 24896259
dgv4073n100 CNV gain 25217958
dgv475n27 CNV gain 19166990
dgv7079n54 CNV loss 21841781
dgv7080n54 CNV gain 21841781
dgv7083n54 CNV loss 21841781
esv2751826 CNV gain 17911159
esv2759092 CNV gain+loss 17122850
esv2760631 CNV gain+loss 21179565
esv2763387 CNV loss 21179565
esv3584065 CNV loss 25503493
esv3592450 CNV loss 21293372
esv3592451 CNV gain 21293372
esv3592452 CNV loss 21293372
esv3592453 CNV gain 21293372
esv3893326 CNV gain 25118596
nsv1001073 CNV gain 25217958
nsv1005664 CNV loss 25217958
nsv1147463 OTHER inversion 26484159
nsv428403 CNV loss 18775914
nsv459274 CNV loss 19166990
nsv459341 CNV loss 19166990
nsv470485 CNV gain 18288195
nsv520559 CNV gain+loss 19592680
nsv583046 CNV loss 21841781
nsv583113 CNV gain 21841781
nsv583132 CNV gain 21841781
nsv583133 CNV loss 21841781
nsv7327 OTHER inversion 18451855
nsv818080 CNV gain 17921354
nsv998333 CNV gain+loss 25217958

Variation tolerance for CCDC115 Gene

Residual Variation Intolerance Score: 50.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.63; 13.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC115 Gene

Human Gene Mutation Database (HGMD)
CCDC115
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC115

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC115 Gene

Disorders for CCDC115 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CCDC115 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CC115_HUMAN
  • Congenital disorder of glycosylation 2O (CDG2O) [MIM:616828]: A form of congenital disorder of glycosylation, a genetically heterogeneous group of autosomal recessive, multisystem disorders caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. CDG2O is characterized by hepatosplenomegaly, liver failure, hypotonia, and psychomotor disability. {ECO:0000269 PubMed:26833332}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CCDC115

genes like me logo Genes that share disorders with CCDC115: view

No data available for Genatlas for CCDC115 Gene

Publications for CCDC115 Gene

  1. CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation. (PMID: 26833332) Jansen JC … Lefeber DJ (American journal of human genetics 2016) 2 3 4 58
  2. The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels. (PMID: 28296633) Miles AL … Nathan JA (eLife 2017) 3 4 58
  3. Regulation of cell proliferation and apoptosis in neuroblastoma cells by ccp1, a FGF2 downstream gene. (PMID: 21118521) Pellicano F … Iwata T (BMC cancer 2010) 2 3 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for CCDC115 Gene

Sources for CCDC115 Gene

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