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    CCDC47 coiled-coil domain containing 47 [ Homo sapiens (human) ]

    Gene ID: 57003, updated on 5-May-2024

    Summary

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    Official Symbol
    CCDC47provided by HGNC
    Official Full Name
    coiled-coil domain containing 47provided by HGNC
    Primary source
    HGNC:HGNC:24856
    See related
    Ensembl:ENSG00000108588 MIM:618260; AllianceGenome:HGNC:24856
    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
    Also known as
    THNS; GK001; MSTP041
    Summary
    Enables protein folding chaperone and ribosome binding activity. Involved in ERAD pathway; endoplasmic reticulum calcium ion homeostasis; and protein insertion into ER membrane. Located in endoplasmic reticulum. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in colon (RPKM 44.7), duodenum (RPKM 34.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17q23.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63745255..63773597, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64616174..64644500, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (61822615..61850957, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61777898-61778483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61778484-61779068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8829 Neighboring gene uncharacterized LOC729683 Neighboring gene LIM domain containing 2 Neighboring gene Sharpr-MPRA regulatory region 9817 Neighboring gene STE20 related adaptor alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61817285-61817784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8830 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61850832-61851416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8831 Neighboring gene DEAD-box helicase 42 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:61897185-61898384 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:61904136-61905335 Neighboring gene FtsJ RNA 2'-O-methyltransferase 3 Neighboring gene proteasome 26S subunit, ATPase 5

    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. Bi-allelic CCDC47 Variants Cause a Disorder Characterized by Woolly Hair, Liver Dysfunction, Dysmorphic Features, and Global Developmental Delay. Morimoto M, et al. Am J Hum Genet, 2018 Nov 1. PMID 30401460, Free PMC Article
    2. An intramembrane chaperone complex facilitates membrane protein biogenesis. Chitwood PJ, et al. Nature, 2020 Aug. PMID 32814900, Free PMC Article
    3. Mechanism of an intramembrane chaperone for multipass membrane proteins. Smalinskaitė L, et al. Nature, 2022 Nov. PMID 36261528, Free PMC Article
    4. Calumin, a novel Ca2+-binding transmembrane protein on the endoplasmic reticulum. Zhang M, et al. Cell Calcium, 2007 Jul. PMID 17204322
    5. Substrate-driven assembly of a translocon for multipass membrane proteins. Sundaram A, et al. Nature, 2022 Nov. PMID 36261522, Free PMC Article

    See all (107) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. these findings suggested that calumin serves to maintain the yolk sac integrity through participation in the ERAD activity, contributing to embryonic development.
      Title: Contribution of calumin to embryogenesis through participation in the endoplasmic reticulum-associated degradation activity.
    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
    Trichohepatoneurodevelopmental syndrome
    MedGen: C4748898 OMIM: 618268 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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr HIV-1 Vpr is identified to have a physical interaction with coiled-coil domain containing 47 (CCDC47) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein folding chaperone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ER overload response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in multi-pass transmembrane protein insertion into ER membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in osteoblast differentiation HDA PubMed 
    involved_in post-embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein folding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein insertion into ER membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    part_of multi-pass translocon complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of multi-pass translocon complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of protein folding chaperone complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in rough endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PAT complex subunit CCDC47
    Names
    Calumin
    coiled-coil domain-containing protein 47

    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_020198.3 → NP_064583.2  PAT complex subunit CCDC47 precursor

      See identical proteins and their annotated locations for NP_064583.2

      Status: VALIDATED

      Source sequence(s)
      AF226054, AK027844, BC001300, DB222124
      Consensus CDS
      CCDS11643.1
      UniProtKB/Swiss-Prot
      B2RAS8, D3DU20, Q96A33, Q96D00, Q96JZ7, Q9H3E4, Q9NRG3
      Related
      ENSP00000225726.5, ENST00000225726.10
      Conserved Domains (2) summary
      PRK05901
      Location:18 → 115
      PRK05901; RNA polymerase sigma factor; Provisional
      pfam07946
      Location:135 → 467
      DUF1682; Protein of unknown function (DUF1682)

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      63745255..63773597 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005257527.3 → XP_005257584.1  PAT complex subunit CCDC47 isoform X1

      See identical proteins and their annotated locations for XP_005257584.1

      UniProtKB/Swiss-Prot
      B2RAS8, D3DU20, Q96A33, Q96D00, Q96JZ7, Q9H3E4, Q9NRG3
      Conserved Domains (2) summary
      PRK05901
      Location:18 → 115
      PRK05901; RNA polymerase sigma factor; Provisional
      pfam07946
      Location:135 → 467
      DUF1682; Protein of unknown function (DUF1682)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      64616174..64644500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316708.1 → XP_054172683.1  PAT complex subunit CCDC47 isoform X1

      UniProtKB/Swiss-Prot
      B2RAS8, D3DU20, Q96A33, Q96D00, Q96JZ7, Q9H3E4, Q9NRG3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96A33.1 GenPept UniProtKB/Swiss-Prot:Q96A33

    Gene LinkOut

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

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