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    CCDC115 coiled-coil domain containing 115 [ Homo sapiens (human) ]

    Gene ID: 84317, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CCDC115provided by HGNC
    Official Full Name
    coiled-coil domain containing 115provided by HGNC
    Primary source
    HGNC:HGNC:28178
    See related
    Ensembl:ENSG00000136710 MIM:613734; AllianceGenome:HGNC:28178
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ccp1; CDG2O
    Summary
    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]
    Expression
    Ubiquitous expression in ovary (RPKM 17.0), thyroid (RPKM 15.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC115 in Genome Data Viewer
    Location:
    2q21.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (130337933..130342681, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (130771857..130776605, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (131095506..131100254, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene tektin 4 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:131089968-131090518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16525 Neighboring gene tRNA-Glu (anticodon TTC) 1-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16527 Neighboring gene IMP U3 small nucleolar ribonucleoprotein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11957 Neighboring gene protein tyrosine phosphatase non-receptor type 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:131129403-131130030

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Modifier locus mapping of a transgenic F2 mouse population identifies CCDC115 as a novel aggressive prostate cancer modifier gene in humans. Winter JM, et al. BMC Genomics, 2018 Jun 11. PMID 29890952, Free PMC Article
    2. CCDC115-CDG: A new rare and misleading inherited cause of liver disease. Girard M, et al. Mol Genet Metab, 2018 Jul. PMID 29759592
    3. Genetic screens reveal CCDC115 as a modulator of erythroid iron and heme trafficking. Sobh A, et al. Am J Hematol, 2020 Sep. PMID 32510613
    4. Regulation of cell proliferation and apoptosis in neuroblastoma cells by ccp1, a FGF2 downstream gene. Pellicano F, et al. BMC Cancer, 2010 Nov 30. PMID 21118521, Free PMC Article
    5. Defective Lipid Droplet-Lysosome Interaction Causes Fatty Liver Disease as Evidenced by Human Mutations in TMEM199 and CCDC115. Larsen LE, et al. Cell Mol Gastroenterol Hepatol, 2022. PMID 34626841, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Defective Lipid Droplet-Lysosome Interaction Causes Fatty Liver Disease as Evidenced by Human Mutations in TMEM199 and CCDC115.
      Title: Defective Lipid Droplet-Lysosome Interaction Causes Fatty Liver Disease as Evidenced by Human Mutations in TMEM199 and CCDC115.
    2. Genetics of Wilson disease and Wilson-like phenotype in a clinical series from eastern Spain.
      Title: Genetics of Wilson disease and Wilson-like phenotype in a clinical series from eastern Spain.
    3. Genetic screens reveal CCDC115 as a modulator of erythroid iron and heme trafficking.
      Title: Genetic screens reveal CCDC115 as a modulator of erythroid iron and heme trafficking.
    4. CCDC115 mutation is associated with Congenital disorders of glycosylation causing liver disease.
      Title: CCDC115-CDG: A new rare and misleading inherited cause of liver disease.
    5. CCDC115 is associated with less aggressive prostate cancer in humans.
      Title: Modifier locus mapping of a transgenic F2 mouse population identifies CCDC115 as a novel aggressive prostate cancer modifier gene in humans.
    6. Vacuolar H+ ATPase (V-ATPase), the key proton pump for endo-lysosomal acidification, and two previously uncharacterised V-ATPase assembly factors, TMEM199 and CCDC115, stabilise HIF1alpha in aerobic conditions.
      Title: The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels.
    7. Our study reveals CCDC115 deficiency as a disorder of Golgi homeostasis that can be readily identified via screening for abnormal glycosylation in plasma.
      Title: CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    CCDC115-CDG
    MedGen: C4225191 OMIM: 616828 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30131, FLJ34877, MGC12981

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables unfolded protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to increased oxygen levels IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular iron ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lysosomal lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lysosomal protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vacuolar proton-transporting V-type ATPase complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in COPI-coated vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum-Golgi intermediate compartment IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA PubMed 
    part_of vacuolar proton-transporting V-type ATPase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 115

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_046779.1 RefSeqGene

      Range
      5647..9878
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001321118.1 → NP_001308047.1  coiled-coil domain-containing protein 115 isoform b

      Status: REVIEWED

      Source sequence(s)
      AA831631, BC006429, DC340780
      Consensus CDS
      CCDS82512.1
      UniProtKB/TrEMBL
      B8ZZ99
      Related
      ENSP00000387301.1, ENST00000409127.1

    2. NM_001321119.2 → NP_001308048.2  coiled-coil domain-containing protein 115 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC132479

    3. NM_032357.4 → NP_115733.2  coiled-coil domain-containing protein 115 isoform a

      See identical proteins and their annotated locations for NP_115733.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AA831631, BC006429, DB025106
      Consensus CDS
      CCDS2159.1
      UniProtKB/Swiss-Prot
      B4DJ47, Q96NT0, Q9BR88
      Related
      ENSP00000259229.2, ENST00000259229.7

    RNA

    1. NR_104471.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' most exon and contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA831631, AK295922, BC006429, DC340780
      Related
      ENST00000651709.1

    2. NR_135548.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AA831631, AK295922, BC006429, DB025106

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      130337933..130342681 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      130771857..130776605 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96NT0.1 GenPept UniProtKB/Swiss-Prot:Q96NT0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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