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    CUBN cubilin [ Homo sapiens (human) ]

    Gene ID: 8029, updated on 17-Jun-2024

    Summary

    Official Symbol
    CUBNprovided by HGNC
    Official Full Name
    cubilinprovided by HGNC
    Primary source
    HGNC:HGNC:2548
    See related
    Ensembl:ENSG00000107611 MIM:602997; AllianceGenome:HGNC:2548
    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
    IGS; IFCR; IGS1; MGA1; gp280
    Summary
    Cubilin (CUBN) acts as a receptor for intrinsic factor-vitamin B12 complexes. The role of receptor is supported by the presence of 27 CUB domains. Cubulin is located within the epithelium of intestine and kidney. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in kidney (RPKM 65.4) and small intestine (RPKM 9.4) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CUBN in Genome Data Viewer
    Location:
    10p13
    Exon count:
    71
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (16823966..17129811, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (16842423..17148343, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (16865965..17171810, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene Ras suppressor protein 1 Neighboring gene uncharacterized LOC124902384 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:16801281-16801433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:16829435-16829935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3104 Neighboring gene uncharacterized LOC105376435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3107 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:16864864-16865015 Neighboring gene MPRA-validated peak881 silencer Neighboring gene MPRA-validated peak882 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:16933270-16934469 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:16942960-16943677 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:16970960-16971553 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:17010389-17010952 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:17026880-17027039 Neighboring gene GATA motif-containing MPRA enhancer 283 Neighboring gene Sharpr-MPRA regulatory region 1431 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:17104252-17105451 Neighboring gene MPRA-validated peak883 silencer Neighboring gene MPRA-validated peak884 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:17157167-17158366 Neighboring gene tRNA aspartic acid methyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2181 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:17268719-17268933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2182 Neighboring gene VIM antisense RNA 1 Neighboring gene vimentin

    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
    Imerslund-Grasbeck syndrome type 1
    MedGen: C4016819 OMIM: 261100 GeneReviews: Not available
    Compare labs
    Proteinuria, chronic benign
    MedGen: C5394384 OMIM: 618884 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
    EBI GWAS Catalog
    CUBN is a gene locus for albuminuria.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial.
    EBI GWAS Catalog
    Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
    EBI GWAS Catalog
    Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations.
    EBI GWAS Catalog
    Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
    EBI GWAS Catalog
    Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ90055, FLJ90747

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables cargo receptor activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables cargo receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cargo receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables cobalamin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cobalamin metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cobalamin transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cobalamin transport TAS
    Traceable Author Statement
    more info
     
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipoprotein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in receptor-mediated endocytosis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in response to bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in tissue homeostasis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in apical plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in brush border membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in brush border membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in clathrin-coated pit IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extrinsic component of external side of plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in microvillus membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    part_of receptor complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    cubilin
    Names
    460 kDa receptor
    cubilin (intrinsic factor-cobalamin receptor)
    intestinal intrinsic factor receptor
    intrinsic factor-vitamin B12 receptor

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008967.1 RefSeqGene

      Range
      5001..310852
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_540

    mRNA and Protein(s)

    1. NM_001081.4NP_001072.2  cubilin precursor

      See identical proteins and their annotated locations for NP_001072.2

      Status: REVIEWED

      Source sequence(s)
      AC067747, AF034611, AL365215, AL731551, BP270790, BP271329
      Consensus CDS
      CCDS7113.1
      UniProtKB/Swiss-Prot
      B0YIZ4, O60494, Q5VTA6, Q96RU9
      UniProtKB/TrEMBL
      Q7LC53
      Related
      ENSP00000367064.4, ENST00000377833.10
      Conserved Domains (7) summary
      smart00179
      Location:305348
      EGF_CA; Calcium-binding EGF-like domain
      cd00041
      Location:16201733
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      cd00054
      Location:170210
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00431
      Location:19782088
      CUB; CUB domain
      pfam12947
      Location:353387
      EGF_3; EGF domain
      cd22201
      Location:32135
      cubilin_NTD; N-terminal domain of cubilin and similar proteins
      cl00049
      Location:10481157
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      16823966..17129811 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011519710.3XP_011518012.1  cubilin isoform X2

      Conserved Domains (2) summary
      cd00041
      Location:274387
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam00431
      Location:632742
      CUB; CUB domain
    2. XM_011519709.3XP_011518011.1  cubilin isoform X1

      Conserved Domains (3) summary
      cd00041
      Location:282395
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam00431
      Location:640750
      CUB; CUB domain
      cl00049
      Location:245
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    3. XM_011519711.4XP_011518013.1  cubilin isoform X3

      Conserved Domains (2) summary
      cd00041
      Location:234347
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam00431
      Location:592702
      CUB; CUB domain
    4. XM_011519708.3XP_011518010.1  cubilin isoform X4

      Conserved Domains (6) summary
      smart00179
      Location:263304
      EGF_CA; Calcium-binding EGF-like domain
      cd00041
      Location:16201733
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      cd00054
      Location:170210
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam00431
      Location:19782088
      CUB; CUB domain
      pfam12947
      Location:353387
      EGF_3; EGF domain
      cl00049
      Location:10481157
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      16842423..17148343 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366803.1XP_054222778.1  cubilin isoform X2

    2. XM_054366802.1XP_054222777.1  cubilin isoform X1

    3. XM_054366804.1XP_054222779.1  cubilin isoform X3