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

Gene ID: 57003, updated on 3-Nov-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 multi-pass transmembrane protein insertion into ER membrane. Located in endoplasmic reticulum membrane. Part of multi-pass translocon complex and protein folding chaperone complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in colon (RPKM 44.7), duodenum (RPKM 34.8) and 25 other tissues See more
Orthologs
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Genomic context

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See CCDC47 in Genome Data Viewer
Location:
17q23.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63745255..63773597, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64616174..64644500, complement)
RS_2024_09 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 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 (133) 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_2024_08

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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