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CCBE1 collagen and calcium binding EGF domains 1 [ Homo sapiens (human) ]

Gene ID: 147372, updated on 2-Nov-2024

Summary

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Official Symbol
CCBE1provided by HGNC
Official Full Name
collagen and calcium binding EGF domains 1provided by HGNC
Primary source
HGNC:HGNC:29426
See related
Ensembl:ENSG00000183287 MIM:612753; AllianceGenome:HGNC:29426
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HKLLS1
Summary
This gene is thought to function in extracellular matrix remodeling and migration. It is predominantly expressed in the ovary, but down regulated in ovarian cancer cell lines and primary carcinomas, suggesting its role as a tumour suppressor. Mutations in this gene have been associated with Hennekam lymphangiectasia-lymphedema syndrome, a generalized lymphatic dysplasia in humans. [provided by RefSeq, Mar 2010]
Expression
Biased expression in ovary (RPKM 14.7), lung (RPKM 5.5) and 8 other tissues See more
Orthologs
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Genomic context

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See CCBE1 in Genome Data Viewer
Location:
18q21.32
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (59430939..59697721, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (59632718..59900788, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (57098171..57364655, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9496 Neighboring gene lectin, mannose binding 1 Neighboring gene uncharacterized LOC107985156 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:57053866-57054862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:57122524-57123295 Neighboring gene meiotic recombination hotspot N Neighboring gene ReSE screen-validated silencer GRCh37_chr18:57139771-57139930 Neighboring gene meiotic recombination hotspot L Neighboring gene NANOG hESC enhancer GRCh37_chr18:57214689-57215202 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:57373821-57374004 Neighboring gene ACTB pseudogene 3 Neighboring gene ribosomal protein S26 pseudogene 54 Neighboring gene glutamate dehydrogenase 1 pseudogene 4

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. Multilocus analysis of GAW15 NARAC chromosome 18 case-control data. Browning SR, et al. BMC Proc, 2007. PMID 18466450, Free PMC Article
  2. A Multiplex Kindred with Hennekam Syndrome due to Homozygosity for a CCBE1 Mutation that does not Prevent Protein Expression. Jackson CC, et al. J Clin Immunol, 2016 Jan. PMID 26686525, Free PMC Article
  3. CCBE1 promotes GIST development through enhancing angiogenesis and mediating resistance to imatinib. Tian GA, et al. Sci Rep, 2016 Aug 10. PMID 27506146, Free PMC Article
  4. Collagen and calcium-binding EGF domains 1 is frequently inactivated in ovarian cancer by aberrant promoter hypermethylation and modulates cell migration and survival. Barton CA, et al. Br J Cancer, 2010 Jan 5. PMID 19935792, Free PMC Article
  5. Clinical significance of CCBE1 expression in lung cancer. Li P, et al. Mol Med Rep, 2018 Feb. PMID 29207117, Free PMC Article

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The promotion of non-small cell lung cancer progression by collagen and calcium binding EGF domain 1 is mediated through the regulation of ERK/JNK/P38 phosphorylation by reactive oxygen species.
    Title: The promotion of non-small cell lung cancer progression by collagen and calcium binding EGF domain 1 is mediated through the regulation of ERK/JNK/P38 phosphorylation by reactive oxygen species.
  2. Neovascularization directed by CAVIN1/CCBE1/VEGFC confers TMZ-resistance in glioblastoma.
    Title: Neovascularization directed by CAVIN1/CCBE1/VEGFC confers TMZ-resistance in glioblastoma.
  3. The YAP-TEAD4 complex promotes tumor lymphangiogenesis by transcriptionally upregulating CCBE1 in colorectal cancer.
    Title: The YAP-TEAD4 complex promotes tumor lymphangiogenesis by transcriptionally upregulating CCBE1 in colorectal cancer.
  4. CCBE1 promotes mitochondrial fusion by inhibiting the TGFbeta-DRP1 axis to prevent the progression of hepatocellular carcinoma.
    Title: CCBE1 promotes mitochondrial fusion by inhibiting the TGFβ-DRP1 axis to prevent the progression of hepatocellular carcinoma.
  5. The Lymphangiogenic Factor CCBE1 Promotes Angiogenesis and Tumor Growth in Colorectal Cancer.
    Title: The Lymphangiogenic Factor CCBE1 Promotes Angiogenesis and Tumor Growth in Colorectal Cancer.
  6. Hsa_circ_0076931 suppresses malignant biological properties, down-regulates miR-6760-3p through direct binding, and up-regulates CCBE1 in glioma.
    Title: Hsa_circ_0076931 suppresses malignant biological properties, down-regulates miR-6760-3p through direct binding, and up-regulates CCBE1 in glioma.
  7. miR-942-5p Inhibits Proliferation, Metastasis, and Epithelial-Mesenchymal Transition in Colorectal Cancer by Targeting CCBE1.
    Title: miR-942-5p Inhibits Proliferation, Metastasis, and Epithelial-Mesenchymal Transition in Colorectal Cancer by Targeting CCBE1.
  8. A Novel RNA-Seq-Based Model for Preoperative Prediction of Lymph Node Metastasis in Oral Squamous Cell Carcinoma.
    Title: A Novel RNA-Seq-Based Model for Preoperative Prediction of Lymph Node Metastasis in Oral Squamous Cell Carcinoma.
  9. Next-generation sequencing of 9 Chinese children with early-onset protein-losing enteropathy showed causative CCBE1 mutations (c.521C>T/c.271C>T) in 1 case.
    Title: Phenotype and Genotype of a Cohort of Chinese Children with Early-Onset Protein-Losing Enteropathy.
  10. Efficient activation of the lymphangiogenic growth factor VEGF-C requires the C-terminal domain of VEGF-C and the N-terminal domain of CCBE1.
    Title: Efficient activation of the lymphangiogenic growth factor VEGF-C requires the C-terminal domain of VEGF-C and the N-terminal domain of CCBE1.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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
Hennekam lymphangiectasia-lymphedema syndrome 1
MedGen: C4012050 OMIM: 235510 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association analysis accounting for environmental factors through propensity-score matching: application to stressful live events in major depressive disorder.
EBI GWAS Catalog
Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment.
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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ30681, MGC50861

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables collagen binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protease binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in lung development IEA
Inferred from Electronic Annotation
more info
  
involved_in lymphangiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lymphangiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in lymphatic endothelial cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of angiogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of endothelial cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of lymphangiogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of protein processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of vascular endothelial growth factor production IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of vascular endothelial growth factor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in respiratory system process IEA
Inferred from Electronic Annotation
more info
  
involved_in sprouting angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in venous blood vessel morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
collagen and calcium-binding EGF domain-containing protein 1
Names
full of fluid protein homolog

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.

Genomic

  1. NG_016990.1 RefSeqGene

    Range
    4990..271474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1209

mRNA and Protein(s)

  1. NM_133459.4 → NP_597716.1  collagen and calcium-binding EGF domain-containing protein 1 precursor

    See identical proteins and their annotated locations for NP_597716.1

    Status: REVIEWED

    Source sequence(s)
    AB075863, AC010776, AC016229
    Consensus CDS
    CCDS32838.1
    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    UniProtKB/TrEMBL
    A0A3B3IRL6
    Related
    ENSP00000404464.2, ENST00000439986.9
    Conserved Domains (1) summary
    smart00179
    Location:134 → 175
    EGF_CA; Calcium-binding EGF-like domain

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    59430939..59697721 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451091.2 → XP_024306859.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    UniProtKB/TrEMBL
    A0A3B3IRL6
    Related
    ENSP00000497183.1, ENST00000649564.1
    Conserved Domains (1) summary
    smart00179
    Location:134 → 175
    EGF_CA; Calcium-binding EGF-like domain

  2. XM_017025557.2 → XP_016881046.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8Q3WKU1, A0A8Q3WKU2
    Related
    ENSP00000512259.1, ENST00000695904.1

  3. XM_047437302.1 → XP_047293258.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19

  4. XM_047437301.1 → XP_047293257.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8Q3WKU1

  5. XM_017025558.2 → XP_016881047.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X3

    Related
    ENSP00000512255.1, ENST00000695903.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    59632718..59900788 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054318206.1 → XP_054174181.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

  2. XM_054318207.1 → XP_054174182.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19

  3. XM_054318208.1 → XP_054174183.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19

  4. XM_054318209.1 → XP_054174184.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6UXH8.1 GenPept UniProtKB/Swiss-Prot:Q6UXH8

Gene LinkOut

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

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