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

Gene ID: 147372, updated on 30-Jun-2024

Summary

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

See CCBE1 in Genome Data Viewer
Location:
18q21.32
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (59430939..59697721, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (59632718..59900788, complement)
105.20220307 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_133459.4NP_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:134175
    EGF_CA; Calcium-binding EGF-like domain

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_000018.10 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_024451091.2XP_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:134175
    EGF_CA; Calcium-binding EGF-like domain
  2. XM_017025557.2XP_016881046.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8Q3WKU1, A0A8Q3WKU2
    Related
    ENSP00000512259.1, ENST00000695904.1
  3. XM_047437302.1XP_047293258.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    UniProtKB/TrEMBL
    A0A3B3IRL6
  4. XM_047437301.1XP_047293257.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8Q3WKU1, A0A8Q3WKU2
  5. XM_017025558.2XP_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_054318206.1XP_054174181.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8Q3WKU2
  2. XM_054318207.1XP_054174182.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    UniProtKB/TrEMBL
    A0A3B3IRL6
  3. XM_054318208.1XP_054174183.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X2

    UniProtKB/Swiss-Prot
    Q6MZX5, Q6UXH8, Q86SS2, Q8TF19
    UniProtKB/TrEMBL
    A0A3B3IRL6
  4. XM_054318209.1XP_054174184.1  collagen and calcium-binding EGF domain-containing protein 1 isoform X3