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CUBN cubilin [ Homo sapiens (human) ]

Gene ID: 8029, updated on 3-Jun-2018
Official Symbol
CUBNprovided by HGNC
Official Full Name
cubilinprovided by HGNC
Primary source
HGNC:HGNC:2548
See related
Ensembl:ENSG00000107611 MIM:602997; Vega:OTTHUMG00000017741
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
IFCR; 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
See CUBN in Genome Data Viewer
Location:
10p13
Exon count:
71
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (16823966..17130492, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (16865965..17171816, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4915 Neighboring gene Ras suppressor protein 1 Neighboring gene uncharacterized LOC105376435 Neighboring gene GATA motif-containing MPRA enhancer 283 Neighboring gene tRNA aspartic acid methyltransferase 1 Neighboring gene VIM antisense RNA 1 Neighboring gene vimentin

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Megaloblastic anemia due to inborn errors of metabolism
MedGen: C1306856 OMIM: 261100 GeneReviews: Not available
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NHGRI GWAS Catalog

Description
Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
NHGRI GWA Catalog
CUBN is a gene locus for albuminuria.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial.
NHGRI GWA Catalog
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
NHGRI GWA Catalog
Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations.
NHGRI GWA Catalog
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway.
NHGRI GWA Catalog
  • Cobalamin (Cbl, vitamin B12) transport and metabolism, organism-specific biosystem (from REACTOME)
    Cobalamin (Cbl, vitamin B12) transport and metabolism, organism-specific biosystemVitamin B12 (cobalamin, Cbl) is a water-soluble vitamin with a key role in blood formation and normal functioning of the brain and nervous system. Cbl consists of a planar corrin ring coordinating wi...
  • Defective AMN causes hereditary megaloblastic anemia 1, organism-specific biosystem (from REACTOME)
    Defective AMN causes hereditary megaloblastic anemia 1, organism-specific biosystemDefects in AMN cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Norwegian type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Norwegian cases described by Imerslund were du...
  • Defective CUBN causes hereditary megaloblastic anemia 1, organism-specific biosystem (from REACTOME)
    Defective CUBN causes hereditary megaloblastic anemia 1, organism-specific biosystemDefects in the CUBN gene cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Finnish type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Finnish cases described by Grasbeck et...
  • Defects in cobalamin (B12) metabolism, organism-specific biosystem (from REACTOME)
    Defects in cobalamin (B12) metabolism, organism-specific biosystemCobalamin (Cbl, vitamin B12) is a nutrient essential for normal functioning of the brain and nervous system and for the formation of blood. Cbl-dependent methionine synthase (MTR) is required for con...
  • Defects in vitamin and cofactor metabolism, organism-specific biosystem (from REACTOME)
    Defects in vitamin and cofactor metabolism, organism-specific biosystemVitamins are essential nutrients, required in small amounts from the diet for the normal growth and development of a multicellular organism. Where there is vitamin deficiency, either by poor diet or ...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of metabolism, organism-specific biosystem (from REACTOME)
    Diseases of metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • HDL-mediated lipid transport, organism-specific biosystem (from REACTOME)
    HDL-mediated lipid transport, organism-specific biosystemHDL particles play a central role in the reverse transport of cholesterol, the process by which cholesterol in tissues other than the liver is returned to the liver for conversion to bile salts and e...
  • Lipid digestion, mobilization, and transport, organism-specific biosystem (from REACTOME)
    Lipid digestion, mobilization, and transport, organism-specific biosystemProcesses annotated here include the digestion of dietary lipids, sterol uptake, the formation and turnover of lipoproteins (chylomicrons, VLDL, LDL, and HDL), and the mobilization of fatty acids thr...
  • Lipoprotein metabolism, organism-specific biosystem (from REACTOME)
    Lipoprotein metabolism, organism-specific biosystemBecause of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport ...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of fat-soluble vitamins, organism-specific biosystem (from REACTOME)
    Metabolism of fat-soluble vitamins, organism-specific biosystemVitamins A, D, E, and K are classified as fat-soluble. Metabolic pathways by which dietary precursors of vitamins A (Harrison 2005) and K(Shearer et al. 2012) are converted to active forms, and by wh...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, classified according to their solubility, either fat-soluble or water-soluble, that are either not synthesized or synthesized only in limited amount...
  • Metabolism of water-soluble vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of water-soluble vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only ...
  • Vitamin B12 Metabolism, organism-specific biosystem (from WikiPathways)
    Vitamin B12 Metabolism, organism-specific biosystem
    Vitamin B12 Metabolism
  • Vitamin D (calciferol) metabolism, organism-specific biosystem (from REACTOME)
    Vitamin D (calciferol) metabolism, organism-specific biosystemVitamin D3 (cholecalciferol) is a steroid hormone that plays a role in regulating calcium and bone metabolism. It is obtained from the diet and produced in the skin by photolysis of 7-dehydrocholeste...
  • Vitamin digestion and absorption, organism-specific biosystem (from KEGG)
    Vitamin digestion and absorption, organism-specific biosystemVitamins are a diverse and chemically unrelated group of organic substances that share a common feature of being essential for normal health and well-being. They catalyze numerous biochemical reactio...
  • Vitamin digestion and absorption, conserved biosystem (from KEGG)
    Vitamin digestion and absorption, conserved biosystemVitamins are a diverse and chemically unrelated group of organic substances that share a common feature of being essential for normal health and well-being. They catalyze numerous biochemical reactio...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ90055, FLJ90747

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
cobalamin binding IEA
Inferred from Electronic Annotation
more info
 
drug binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
transporter activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cholesterol metabolic process IEA
Inferred from Electronic Annotation
more info
 
cobalamin metabolic process TAS
Traceable Author Statement
more info
 
cobalamin transport TAS
Traceable Author Statement
more info
PubMed 
high-density lipoprotein particle clearance TAS
Traceable Author Statement
more info
 
lipoprotein transport IEA
Inferred from Electronic Annotation
more info
 
receptor-mediated endocytosis NAS
Non-traceable Author Statement
more info
PubMed 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
tissue homeostasis NAS
Non-traceable Author Statement
more info
PubMed 
vitamin D metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
apical plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
brush border membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
brush border membrane NAS
Non-traceable Author Statement
more info
PubMed 
clathrin-coated pit IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
endocytic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
endosome membrane TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extrinsic component of external side of plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
lysosomal lumen TAS
Traceable Author Statement
more info
 
lysosomal membrane IEA
Inferred from Electronic Annotation
more info
 
membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
Preferred Names
cubilin
Names
460 kDa receptor
cubilin (intrinsic factor-cobalamin receptor)
cubilin precursor variant 1
cubilin precursor variant 2
cubilin precursor variant 3
intestinal intrinsic factor receptor
intrinsic factor-vitamin B12 receptor

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_001081.3NP_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
    O60494
    Related
    ENSP00000367064.4, OTTHUMP00000019220, ENST00000377833.8, OTTHUMT00000047009
    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.

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    16823966..17130492 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519710.2XP_011518012.1  cubilin isoform X3

    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_011519709.2XP_011518011.1  cubilin isoform X2

    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_011519711.3XP_011518013.1  cubilin isoform X4

    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_011519708.2XP_011518010.1  cubilin isoform X1

    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.
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