Aliases for CCDC47 Gene

Aliases for CCDC47 Gene

  • Coiled-Coil Domain Containing 47 2 3 5
  • Calumin 2 3 4
  • Coiled-Coil Domain-Containing Protein 47 3 4
  • GK001 2 3
  • MSTP041 3
  • CCDC47 5
  • THNS 3

External Ids for CCDC47 Gene

Previous GeneCards Identifiers for CCDC47 Gene

  • GC17M059177
  • GC17M061822
  • GC17M057190

Summaries for CCDC47 Gene

GeneCards Summary for CCDC47 Gene

CCDC47 (Coiled-Coil Domain Containing 47) is a Protein Coding gene. Diseases associated with CCDC47 include Trichohepatoneurodevelopmental Syndrome and Atypical Choroid Plexus Papilloma. Gene Ontology (GO) annotations related to this gene include calcium ion binding.

UniProtKB/Swiss-Prot Summary for CCDC47 Gene

  • Involved in the regulation of calcium ion homeostasis in the endoplasmic reticulum (PubMed:30401460). Required for proper protein degradation via the ERAD pathway (PubMed:25009997). Has an essential role in the maintenance of endoplasmic reticulum organization during embryogenesis (By similarity).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CCDC47 Gene

Genomics for CCDC47 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CCDC47 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J063771 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 +2.3 2256 5.4 SP1 ZNF207 MYC IKZF1 NCOR1 ZNF600 SSRP1 JUND ZNF580 ZNF592 DDX42 CCDC47 FTSJ3 CEP95 POLG2 SMARCD2 DDX5 CSH2 KPNA2P3 ERN1
GH17J063746 Promoter/Enhancer 0.9 EPDnew Ensembl 250.3 +29.4 29350 1.6 CTCF TOE1 GATAD2B SUZ12 RAD21 ZNF207 ZNF512B TRIM22 CEBPB ZNF444 CCDC47 FTSJ3 LIMD2 PSMC5 ENSG00000125695 STRADA lnc-STRADA-2
GH17J063745 Promoter 0.3 EPDnew 250.3 +30.7 30656 0.1 CCDC47 LIMD2 STRADA ENSG00000125695
GH17J063571 Enhancer 1 Ensembl ENCODE 4.1 +204.1 204051 3.8 LARP7 ZNF600 IKZF1 JUND CEBPB SIX4 CTCF ZNF217 ARNT ELF1 RNU6-288P RF00026-436 FTSJ3 DCAF7 TACO1 CYB561 CCDC47
GH17J063780 Enhancer 1.1 Ensembl ENCODE dbSUPER 0.7 -4.3 -4250 1.6 ZNF600 ZNF10 FEZF1 SIX4 CUX1 NONO ZBTB48 TCF7L2 ZNF189 SMARCE1 FTSJ3 CCDC47 DDX42 piR-61412 PSMC5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC47 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CCDC47

Top Transcription factor binding sites by QIAGEN in the CCDC47 gene promoter:
  • AML1a
  • AREB6
  • Elk-1
  • GR
  • GR-alpha
  • GR-beta
  • LyF-1
  • POU3F1
  • TBP

Genomic Locations for CCDC47 Gene

Latest Assembly
chr17:63,745,255-63,776,351
(GRCh38/hg38)
Size:
31,097 bases
Orientation:
Minus strand

Previous Assembly
chr17:61,822,615-61,850,957
(GRCh37/hg19 by Entrez Gene)
Size:
28,343 bases
Orientation:
Minus strand

chr17:61,822,610-61,853,711
(GRCh37/hg19 by Ensembl)
Size:
31,102 bases
Orientation:
Minus strand

Genomic View for CCDC47 Gene

Genes around CCDC47 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC47 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC47 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC47 Gene

Proteins for CCDC47 Gene

  • Protein details for CCDC47 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96A33-CCD47_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 47
    Protein Accession:
    Q96A33
    Secondary Accessions:
    • B2RAS8
    • D3DU20
    • Q96D00
    • Q96JZ7
    • Q9H3E4
    • Q9NRG3

    Protein attributes for CCDC47 Gene

    Size:
    483 amino acids
    Molecular mass:
    55874 Da
    Quaternary structure:
    • Interacts with VCP, HSPA5, DERL1, DERL2 and SELENOS.
    SequenceCaution:
    • Sequence=AAG39292.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CCDC47 Gene

    Alternative splice isoforms for CCDC47 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCDC47 Gene

Post-translational modifications for CCDC47 Gene

  • Glycosylation at Asn178
  • Ubiquitination at Lys419
  • Modification sites at PhosphoSitePlus

Other Protein References for CCDC47 Gene

No data available for DME Specific Peptides for CCDC47 Gene

Domains & Families for CCDC47 Gene

Gene Families for CCDC47 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CCDC47 Gene

InterPro:
Blocks:
  • Protein of unknown function DUF1682

Suggested Antigen Peptide Sequences for CCDC47 Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain-containing protein 47 (CCD47_HUMAN)
genes like me logo Genes that share domains with CCDC47: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CCDC47 Gene

Function for CCDC47 Gene

Molecular function for CCDC47 Gene

UniProtKB/Swiss-Prot Function:
Involved in the regulation of calcium ion homeostasis in the endoplasmic reticulum (PubMed:30401460). Required for proper protein degradation via the ERAD pathway (PubMed:25009997). Has an essential role in the maintenance of endoplasmic reticulum organization during embryogenesis (By similarity).

Phenotypes From GWAS Catalog for CCDC47 Gene

Gene Ontology (GO) - Molecular Function for CCDC47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005509 calcium ion binding IBA 21873635
GO:0005515 protein binding IPI 21903422
genes like me logo Genes that share ontologies with CCDC47: view
genes like me logo Genes that share phenotypes with CCDC47: view

Human Phenotype Ontology for CCDC47 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CCDC47 Gene

MGI Knock Outs for CCDC47:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC47

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CCDC47 Gene

Localization for CCDC47 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC47 Gene

Endoplasmic reticulum membrane. Rough endoplasmic reticulum membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCDC47 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 1
cytosol 1
plasma membrane 0
peroxisome 0
nucleus 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CCDC47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005791 rough endoplasmic reticulum IEA --
GO:0016020 membrane IEA,HDA 16210410
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CCDC47: view

Pathways & Interactions for CCDC47 Gene

PathCards logo

SuperPathways for CCDC47 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CCDC47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001649 osteoblast differentiation HDA 16210410
GO:0006983 ER overload response IEA --
GO:0007029 endoplasmic reticulum organization IEA --
GO:0009791 post-embryonic development IEA --
GO:0030433 ubiquitin-dependent ERAD pathway IEA --
genes like me logo Genes that share ontologies with CCDC47: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC47 Gene

Drugs & Compounds for CCDC47 Gene

No Compound Related Data Available

Transcripts for CCDC47 Gene

mRNA/cDNA for CCDC47 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC47

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC47 Gene

No ASD Table

Relevant External Links for CCDC47 Gene

GeneLoc Exon Structure for
CCDC47

Expression for CCDC47 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CCDC47 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CCDC47 Gene

This gene is overexpressed in Pancreas (10.9) and Nasal epithelium (9.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CCDC47 Gene



Protein tissue co-expression partners for CCDC47 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CCDC47

SOURCE GeneReport for Unigene cluster for CCDC47 Gene:

Hs.202011

Evidence on tissue expression from TISSUES for CCDC47 Gene

  • Heart(4.5)
  • Liver(4.4)
  • Nervous system(4.2)
  • Muscle(2.4)
  • Kidney(2.2)
genes like me logo Genes that share expression patterns with CCDC47: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC47 Gene

Orthologs for CCDC47 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CCDC47 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CCDC47 29 30
  • 99.93 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CCDC47 29 30
  • 94.69 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CCDC47 29 30
  • 93.51 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ccdc47 29 16 30
  • 92.13 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ccdc47 29
  • 91.65 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia CCDC47 30
  • 90 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CCDC47 30
  • 90 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CCDC47 29 30
  • 81.84 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CCDC47 30
  • 76 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ccdc47 29
  • 79.21 (n)
Str.586 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.16389 29
Zebrafish
(Danio rerio)
Actinopterygii ccdc47 29 30
  • 74.34 (n)
OneToOne
wufd13e11 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1555 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010007 29
  • 51.96 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG17593 29 30
  • 50.95 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ccdc-47 29 30
  • 50.36 (n)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT4G24330 29
  • 45.59 (n)
Rice
(Oryza sativa)
Liliopsida Os05g0432400 29
  • 44.81 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.1616 30
  • 47 (a)
OneToMany
Species where no ortholog for CCDC47 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for CCDC47 Gene

ENSEMBL:
Gene Tree for CCDC47 (if available)
TreeFam:
Gene Tree for CCDC47 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC47: view image
Alliance of Genome Resources:
Additional Orthologs for CCDC47

Paralogs for CCDC47 Gene

No data available for Paralogs for CCDC47 Gene

Variants for CCDC47 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CCDC47 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
993035 Likely Pathogenic: Trichohepatoneurodevelopmental syndrome 63,761,328(-) CTTCT/C
NM_020198.3(CCDC47):c.567_570del (p.Glu190fs)
FRAMESHIFT
rs1269750663 Pathogenic/Likely Pathogenic: Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hair; Trichohepatoneurodevelopmental syndrome; not provided 63,752,334(-) G/A
NM_020198.3(CCDC47):c.1189C>T (p.Arg397Ter)
NONSENSE
rs1568246398 Likely Pathogenic: Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hair; Trichohepatoneurodevelopmental syndrome 63,752,357(-) GA/G
NM_020198.3(CCDC47):c.1165del (p.Ser389fs)
FRAMESHIFT
rs16947066 Benign: not provided 63,752,432(-) G/A
NM_020198.3(CCDC47):c.1094-3C>T
INTRON
rs201808551 Likely Benign: not provided 63,760,906(-) A/C
NM_020198.3(CCDC47):c.735+8T>G
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CCDC47 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CCDC47 Gene

Variant ID Type Subtype PubMed ID
esv2266185 CNV deletion 18987734
nsv1138565 CNV deletion 24896259
nsv833510 CNV loss 17160897

Variation tolerance for CCDC47 Gene

Residual Variation Intolerance Score: 14.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.02; 20.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC47 Gene

Human Gene Mutation Database (HGMD)
CCDC47
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC47
Leiden Open Variation Database (LOVD)
CCDC47

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC47 Gene

Disorders for CCDC47 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CCDC47 Gene - From: OMI, CVR, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CCD47_HUMAN
  • Trichohepatoneurodevelopmental syndrome (THNS) [MIM:618268]: An autosomal recessive complex multisystem disorder characterized by woolly or coarse hair, liver dysfunction, pruritus, dysmorphic features, hypotonia, and global developmental delay. {ECO:0000269 PubMed:30401460}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for CCDC47

genes like me logo Genes that share disorders with CCDC47: view

No data available for Genatlas for CCDC47 Gene

Publications for CCDC47 Gene

  1. Bi-allelic CCDC47 Variants Cause a Disorder Characterized by Woolly Hair, Liver Dysfunction, Dysmorphic Features, and Global Developmental Delay. (PMID: 30401460) Morimoto M … Malicdan MCV (American journal of human genetics 2018) 3 4 72
  2. Contribution of calumin to embryogenesis through participation in the endoplasmic reticulum-associated degradation activity. (PMID: 25009997) Yamamoto S … Kakizawa S (Developmental biology 2014) 2 3 4
  3. Transmembrane insertases and N-glycosylation critically determine synthesis, trafficking, and activity of the nonselective cation channel TRPC6. (PMID: 31266804) Talbot BE … Schlondorff JS (The Journal of biological chemistry 2019) 2 3
  4. Calumin, a novel Ca2+-binding transmembrane protein on the endoplasmic reticulum. (PMID: 17204322) Zhang M … Takeshima H (Cell calcium 2007) 2 3
  5. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4

Products for CCDC47 Gene

Sources for CCDC47 Gene