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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
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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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