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    CCDC38 coiled-coil domain containing 38 [ Homo sapiens (human) ]

    Gene ID: 120935, updated on 11-Apr-2024

    Summary

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    Official Symbol
    CCDC38provided by HGNC
    Official Full Name
    coiled-coil domain containing 38provided by HGNC
    Primary source
    HGNC:HGNC:26843
    See related
    Ensembl:ENSG00000165972 AllianceGenome:HGNC:26843
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward testis (RPKM 5.9) See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q23.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (95867048..95943233, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (95843468..95919803, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (96260826..96336392, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SNRPF divergent transcript Neighboring gene long intergenic non-protein coding RNA 2410 Neighboring gene MPRA-validated peak1901 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96243941 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96244864 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96249988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96252439-96253054 Neighboring gene small nuclear ribonucleoprotein polypeptide F Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96301545-96302055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96302056-96302565 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:96322471-96322972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96350128-96350641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96350642-96351154 Neighboring gene amidohydrolase domain containing 1 Neighboring gene AMDHD1 eExon liver enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96363883-96364528 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:96364529-96365174 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31139 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96379806 Neighboring gene histidine ammonia-lyase

    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
    • 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. Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction. Wain LV, et al. PLoS Genet, 2014 May. PMID 24786987, Free PMC Article
    2. Proteomic analysis of mammalian sperm cells identifies new components of the centrosome. Firat-Karalar EN, et al. J Cell Sci, 2014 Oct 1. PMID 25074808, Free PMC Article
    3. Lupus nephritis susceptibility loci in women with systemic lupus erythematosus. Chung SA, et al. J Am Soc Nephrol, 2014 Dec. PMID 24925725, Free PMC Article
    4. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Soler Artigas M, et al. Nat Genet, 2011 Sep 25. PMID 21946350, Free PMC Article
    5. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. Hancock DB, et al. PLoS Genet, 2012. PMID 23284291, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. strongest signal of association with smoking resistance for a non-synonymous SNP in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells
      Title: Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
    EBI GWAS Catalog

    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

    • FLJ40089

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ubiquitin-modified histone reader activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in acrosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intraciliary anterograde transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sperm flagellum assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in manchette IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sperm flagellum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sperm head IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 38

    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.

    mRNA and Protein(s)

    1. NM_182496.3 → NP_872302.2  coiled-coil domain-containing protein 38

      See identical proteins and their annotated locations for NP_872302.2

      Status: VALIDATED

      Source sequence(s)
      AK097408, BC095479
      Consensus CDS
      CCDS9056.1
      UniProtKB/Swiss-Prot
      Q502W7, Q8N835
      Related
      ENSP00000345470.3, ENST00000344280.8
      Conserved Domains (1) summary
      pfam13863
      Location:112 → 230
      DUF4200; Domain of unknown function (DUF4200)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      95867048..95943233 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011537883.3 → XP_011536185.1  coiled-coil domain-containing protein 38 isoform X1

      See identical proteins and their annotated locations for XP_011536185.1

      UniProtKB/Swiss-Prot
      Q502W7, Q8N835
      Conserved Domains (1) summary
      pfam13863
      Location:112 → 230
      DUF4200; Domain of unknown function (DUF4200)

    2. XM_047428281.1 → XP_047284237.1  coiled-coil domain-containing protein 38 isoform X2

    3. XM_011537888.4 → XP_011536190.1  coiled-coil domain-containing protein 38 isoform X3

    4. XM_011537889.2 → XP_011536191.1  coiled-coil domain-containing protein 38 isoform X4

      Conserved Domains (1) summary
      pfam13863
      Location:112 → 230
      DUF4200; Domain of unknown function (DUF4200)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      95843468..95919803 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371059.1 → XP_054227034.1  coiled-coil domain-containing protein 38 isoform X1

    2. XM_054371060.1 → XP_054227035.1  coiled-coil domain-containing protein 38 isoform X2

    3. XM_054371061.1 → XP_054227036.1  coiled-coil domain-containing protein 38 isoform X3

    4. XM_054371062.1 → XP_054227037.1  coiled-coil domain-containing protein 38 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q502W7.1 GenPept UniProtKB/Swiss-Prot:Q502W7

    Gene LinkOut

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

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