CUBN

gene
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Also known as IFCRgp280

Summary

CUBN (cubilin, HGNC:2548) is a protein-coding gene on chromosome 10p13, encoding Cubilin (O60494). Endocytic receptor which plays a role in lipoprotein, vitamin and iron metabolism by facilitating their uptake.

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.

Source: NCBI Gene 8029 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Imerslund-Grasbeck syndrome type 1 (Definitive, GenCC) — +2 more curated relationships
  • GWAS associations: 50
  • Clinical variants (ClinVar): 2,582 total — 63 pathogenic, 110 likely-pathogenic
  • Phenotypes (HPO): 40
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_001081

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2548
Approved symbolCUBN
Namecubilin
Location10p13
Locus typegene with protein product
StatusApproved
AliasesIFCR, gp280
Ensembl geneENSG00000107611
Ensembl biotypeprotein_coding
OMIM602997
Entrez8029

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding_CDS_not_defined, 2 retained_intron, 2 protein_coding

ENST00000377823, ENST00000377833, ENST00000433666, ENST00000438254, ENST00000648092, ENST00000649135, ENST00000649933

RefSeq mRNA: 1 — MANE Select: NM_001081 NM_001081

CCDS: CCDS7113

Canonical transcript exons

ENST00000377833 — 67 exons

ExonStartEnd
ENSE000005038951688841716888566
ENSE000006144241687689716877097
ENSE000006144251687437416874503
ENSE000006144261686963616869853
ENSE000006925631689037116890527
ENSE000006927071708816417088345
ENSE000006927081710000517100239
ENSE000006927101710312517103237
ENSE000006927161710964017109735
ENSE000006927191711402717114189
ENSE000006927241712358817123689
ENSE000006927281712912117129250
ENSE000008159791704103317041220
ENSE000008159921712782917127924
ENSE000009259261683125216831417
ENSE000009259271683501416835195
ENSE000009259291684033016840535
ENSE000009259311689899616899183
ENSE000009259321690062516900850
ENSE000009259331690133816901459
ENSE000009259341690396616904115
ENSE000009259441710441917104605
ENSE000009259471710545717105575
ENSE000009259511711091917111050
ENSE000009259571711547117115597
ENSE000009259611712279517122898
ENSE000009854351712676117126799
ENSE000009854371708427117084461
ENSE000009854381707182717071971
ENSE000009854391707142617071604
ENSE000009854401706860517068770
ENSE000009854411706806417068280
ENSE000009854421706550817065638
ENSE000009854431704741417047603
ENSE000009854441704593417046094
ENSE000009854451704500717045188
ENSE000009854471701983317019983
ENSE000009854481699033416990515
ENSE000009854491698410516984279
ENSE000009854501698248416982653
ENSE000009854511695438916954548
ENSE000009854521695227616952389
ENSE000009854531695000116950111
ENSE000009854541694847816948606
ENSE000009854561694003216940237
ENSE000009854571693896316939147
ENSE000009854581693759216937784
ENSE000009854591693308716933284
ENSE000009854601692815716928303
ENSE000009854631685123516851443
ENSE000010987161692558416925774
ENSE000011640271683623516836382
ENSE000011642961708559717085759
ENSE000011928961694723516947367
ENSE000012835941704382717043983
ENSE000014752731682396616825082
ENSE000014754201712964417129811
ENSE000016357031691582116916030
ENSE000016517241691381116913992
ENSE000017151581691503216915172
ENSE000017258761691862216918800
ENSE000017387271684088516841047
ENSE000017458251691996316920137
ENSE000017953431690750816907679
ENSE000017968171690620316906409
ENSE000017991121692524116925424
ENSE000018004801682880516829040

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 95.36.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0096 / max 255.2028, expressed in 221 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
1084810.518963
1084720.2231121
1084710.080324
1084820.075025
2057360.040116
1084840.039922
1084850.01727
1084830.015110

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
adult organismUBERON:000702395.36gold quality
nephron tubuleUBERON:000123194.27gold quality
kidney epitheliumUBERON:000481992.57gold quality
adult mammalian kidneyUBERON:000008291.78gold quality
kidneyUBERON:000211390.84gold quality
renal glomerulusUBERON:000007489.24gold quality
renal medullaUBERON:000036289.11gold quality
metanephric glomerulusUBERON:000473688.59gold quality
cortex of kidneyUBERON:000122586.35gold quality
spermCL:000001983.05gold quality
oocyteCL:000002382.17gold quality
male germ cellCL:000001582.15gold quality
metanephrosUBERON:000008181.82gold quality
right uterine tubeUBERON:000130281.16gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.24gold quality
secondary oocyteCL:000065577.68silver quality
tibial nerveUBERON:000132376.39gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047375.20gold quality
small intestine Peyer’s patchUBERON:000345474.79gold quality
sural nerveUBERON:001548874.46gold quality
left lobe of thyroid glandUBERON:000112073.86gold quality
thyroid glandUBERON:000204673.69gold quality
metanephros cortexUBERON:001053373.55gold quality
right lobe of thyroid glandUBERON:000111973.41gold quality
right testisUBERON:000453473.30gold quality
calcaneal tendonUBERON:000370173.13gold quality
small intestineUBERON:000210872.21gold quality
left testisUBERON:000453371.54gold quality
olfactory bulbUBERON:000226471.36gold quality
type B pancreatic cellCL:000016971.17gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-GEOD-131882yes5820.43
E-CURD-119yes5451.71
E-HCAD-10yes40.25
E-MTAB-7008yes32.56
E-ANND-3yes7.21
E-CURD-135no2266.59

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PPARA, YBX3

miRNA regulators (miRDB)

36 targeting CUBN, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-511-3P99.9968.851467
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-512-3P99.9767.351049
HSA-MIR-302E99.9670.742669
HSA-MIR-6778-3P99.9667.292693
HSA-LET-7C-3P99.9573.422862
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-153-5P99.8973.866317
HSA-MIR-130B-5P99.8368.501888
HSA-MIR-94499.8270.853042
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-3177-5P99.6570.381174
HSA-MIR-443799.5265.291266
HSA-MIR-54399.5269.032595
HSA-MIR-806499.4566.92875
HSA-MIR-807799.1766.67862
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-6755-3P98.6166.90834
HSA-MIR-660-3P98.1466.041434
HSA-MIR-6742-3P97.9564.501490

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Comparative analysis of cobalamin binding kinetics (PMID:11788601)
  • Megalin and cubilin: multifunctional endocytic receptors. A review. (PMID:11994745)
  • proteinuria was due to the lack of cubilin function needed for tubular reabsorption of some, but not all, proteins of the primary urine. (PMID:12687456)
  • cubilin and amnionless are subunits of a novel cubilin/amnionless (cubam) complex (PMID:14576052)
  • the early cubilin expression and its function in protein and cholesterol uptake suggest an important role for cubilin in the development of the peri-implantation embryo (PMID:15616221)
  • Formation of the cubilin recognition site on intrinsic factor (IF) is caused by assembly of two distant domains, which allows the saturated IF protein to be recognized by the receptor. (PMID:15736970)
  • interactions of COBALAMIN BINDING proteins with a number of ligands (PMID:17487979)
  • This review summarizes recent data on the biological function of cubilin and focuses on its implication in embryonic nutrition and central nervous system malformations. (PMID:17979745)
  • light chain endocytosis is predominantly mediated by the megalin-cubilin tandem endocytic receptor and identify endocytosis as a key step in light chain cytotoxicity. (PMID:18448595)
  • results show different expression patterns of megalin and cubulin in calculous gallbladders and acalculous gallbladders suggesting an association with gallstone formation and implying a putative role of the two proteins in cholesterol endocytosis (PMID:18791690)
  • An association study of 45 folate-related genes in spina bifida: Involvement of cubilin (PMID:19161160)
  • Aberrant shedding of megalin and cubilin may contribute to albuminuria in diabetes and to deficiency states of important vitamins and hormones. (PMID:19366958)
  • crystal structure of the complex between IF-Cbl and the cubilin IF-Cbl-binding-region (CUB(5-8)) determined at 3.3 A resolution (PMID:20237569)
  • cubilin gene polymorphisms have an influence on 25(OH)D3 and 1,25(OH)2D3 plasma levels in type 1 diabetes patients (PMID:20398757)
  • There is a missense CUBN variant that associates with levels of albuminuria in both the general population and in individuals with diabetes. (PMID:21355061)
  • megalin and cubilin are involved in the metabolism of vitamin D by reabsorbing vitamin D binding protein; dysfunction of these receptors is likely to be associated with the development of vitamin D deficiency in patients with chronic kidney disease (PMID:21595846)
  • amnionless is essential for the correct luminal expression of cubilin in humans. (PMID:21750092)
  • These data suggest that CUBN is not involved in cleft lip or palate onset in the investigated Italian population (PMID:21781439)
  • A novel 1-bp homozygous deletion of the cubilin was found to be the cause of proteinuria with nephrotic syndrome. (PMID:21903995)
  • used immunocytochemistry and reverse transcription-polymerase chain reaction on laser-captured glomeruli to demonstrate synthesis and expression of cubilin in glomerular podocytes (PMID:22337902)
  • Expression of megalin and cubilin is decreased during experimental endotoxemia, which may contribute to an increase in urine levels of albumin during acute renal failure. (PMID:22437417)
  • CUBN rs7918972 as a novel risk variant for renal function loss (PMID:22574174)
  • Single nucleotide polymorphisms in cubilin gene is associated with iron overload. (PMID:22761678)
  • Our genetic screening of 154 families of patients with inherited cobalamin malabsorption revealed population-specific mutations, mutational hotspots, and functionally distinct regions in the three causal genes: CUBN, AMN, and GIF. (PMID:22929189)
  • The p.I1e2984Val variant of cubulin is part of a larger haplotype in European populations that is almost absent in West Africans. (PMID:23114252)
  • Data suggest that endodermal layer of yolk sac and syncytiotrophoblast/cytotrophoblast cells of placental villi express cubilin mRNA/protein; expression of cubilin mRNA/protein is up-regulated as gestation/placentation progresses. (PMID:23978537)
  • MA is associated with CVD irrespective of the presence of the CUBN risk allele. These results challenge the concept that albuminuria in the setting of this mutation is benign. (PMID:24052458)
  • LOS treatment decreased microalbuminuria induced by Cd apparently through a cubilin receptor-dependent mechanism but independent of megalin. (PMID:24093454)
  • Cubilin haploinsufficiency leads to reduced renal proximal tubular uptake of albumin and apolipoprotein (apo)A-I, significantly increasing urinary loss of albumin and apoA-I. (PMID:24357674)
  • The variant rs11254363 of the CUBN gene was associated with a decreased risk of developing congenital heart disease in Han Chinese populations (PMID:24533076)
  • predisposition to multibacillary leprosy in Vietnam is associated with CUBN and NEBL common variants in the chromosome 10p13 linkage region (PMID:24563210)
  • CUBN was associated with albuminuria in type 2 diabetes patients. (PMID:26631737)
  • The CUBN haplotypes were associated with an altered gastric cancer risk. (PMID:26959381)
  • CUBN SNP rs1801239 (I2984V), previously associated with albuminuria, was significantly associated with T2D-ESRD in blacks. (PMID:27197912)
  • Study identified CUBN as a marker for risk stratification of patients with renal cell carcinoma (RCC). Lack of CUBN expression was significantly associated with early disease progression and poor patient outcome, independent of T-stage, Fuhrman grade and nodal status. Owing to a highly RCC-specific expression profile, CUBN expression also has a potential role in clinical cancer differential diagnostics. (PMID:28052770)
  • Tumoral expression of cubilin is a positive predictive marker for treatment of metastatic renal cell cancer patients with sunitinib and sorafenib. (PMID:28260162)
  • in teens with positive recto-vaginal group B streptococcus colonization, placental mRNA expression of cubilin is lower compared to those who tested negative for this infection (PMID:28622535)
  • Cubilin is involved in 25(OH) vitamin D uptake by adipocytes. (PMID:29186386)
  • Study shows that cubilin mutations (novel and some previously reported) and all previously reported amnionless missense mutations resulted in endoplasmic reticulum retention and completely inhibited amnionless-dependent plasma membrane expression of cubilin. (PMID:29402915)
  • Data indicate the crystal structure of amnionless (AMN) in complex with the amino-terminal region of intrinsic factor-cobalamin receptor (cubilin). (PMID:30523278)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocubnENSDARG00000087013
mus_musculusCubnENSMUSG00000026726
rattus_norvegicusCubnENSRNOG00000029047
drosophila_melanogastertokFBGN0004885
drosophila_melanogasterCubn2FBGN0259140

Paralogs (35): NRXN3 (ENSG00000021645), TLL1 (ENSG00000038295), CP (ENSG00000047457), DCBLD2 (ENSG00000057019), HEPH (ENSG00000089472), TLL2 (ENSG00000095587), NRP1 (ENSG00000099250), PCOLCE (ENSG00000106333), CNTNAP3 (ENSG00000106714), CNTNAP1 (ENSG00000108797), NRXN2 (ENSG00000110076), MEP1A (ENSG00000112818), NRP2 (ENSG00000118257), CUZD1 (ENSG00000138161), MFGE8 (ENSG00000140545), MEP1B (ENSG00000141434), PDGFC (ENSG00000145431), CNTNAP4 (ENSG00000152910), CNTNAP3B (ENSG00000154529), CNTNAP5 (ENSG00000155052), CDCP2 (ENSG00000157211), PCOLCE2 (ENSG00000163710), EDIL3 (ENSG00000164176), NETO1 (ENSG00000166342), BMP1 (ENSG00000168487), PDGFD (ENSG00000170962), NETO2 (ENSG00000171208), CNTNAP2 (ENSG00000174469), NRXN1 (ENSG00000179915), HEPHL1 (ENSG00000181333), F8 (ENSG00000185010), ASTL (ENSG00000188886), F5 (ENSG00000198734), MFRP (ENSG00000235718), CNTNAP3C (ENSG00000283378)

Protein

Protein identifiers

CubilinO60494 (reviewed: O60494)

Alternative names: 460 kDa receptor, Intestinal intrinsic factor receptor, Intrinsic factor-cobalamin receptor, Intrinsic factor-vitamin B12 receptor

All UniProt accessions (2): O60494, H7C480

UniProt curated annotations — full annotation on UniProt →

Function. Endocytic receptor which plays a role in lipoprotein, vitamin and iron metabolism by facilitating their uptake. Acts together with LRP2 to mediate endocytosis of high-density lipoproteins, GC, hemoglobin, ALB, TF and SCGB1A1. Acts together with AMN to mediate endocytosis of the CBLIF-cobalamin complex. Binds to ALB, MB, Kappa and lambda-light chains, TF, hemoglobin, GC, SCGB1A1, APOA1, high density lipoprotein, and the CBLIF-cobalamin complex. Ligand binding requires calcium. Serves as important transporter in several absorptive epithelia, including intestine, renal proximal tubules and embryonic yolk sac. May play an important role in the development of the peri-implantation embryo through internalization of APOA1 and cholesterol. Binds to LGALS3 at the maternal-fetal interface.

Subunit / interactions. Interacts with AMN. Component of the cubam complex composed of one CUBN trimer and one AMN chain. The cubam complex can dimerize. Interacts with LRP2 in a dual-receptor complex in a calcium-dependent manner. Found in a complex with PID1/PCLI1, LRP1 and CUBNI. Interacts with LRP1 and PID1/PCLI1.

Subcellular location. Apical cell membrane. Cell membrane. Membrane. Coated pit. Endosome. Lysosome membrane.

Tissue specificity. Detected in kidney cortex (at protein level). Expressed in kidney proximal tubule cells, placenta, visceral yolk-sac cells and in absorptive intestinal cells. Expressed in the epithelium of intestine and kidney.

Post-translational modifications. The precursor is cleaved by a trans-Golgi proteinase furin, removing a propeptide. N-glycosylated.

Disease relevance. Imerslund-Grasbeck syndrome 1 (IGS1) [MIM:261100] A form of Imerslund-Grasbeck syndrome, a rare autosomal recessive disorder characterized by vitamin B12 deficiency commonly resulting in megaloblastic anemia, which is responsive to parenteral vitamin B12 therapy and appears in infancy or early childhood. Clinical manifestations include failure to thrive, infections and neurological damage. Mild proteinuria, with no signs of kidney disease, is present in about half of the patients. The disease is caused by variants affecting the gene represented in this entry. Proteinuria, chronic benign (PROCHOB) [MIM:618884] An autosomal recessive condition characterized by isolated, non-progressive proteinuria in absence of renal disease and hypertension. Onset of proteinuria is in the first decade of life. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The CUB domains 5 to 8 mediate binding to CBLIF and ALB. CUB domains 1 and 2 mediate interaction with LRP2. The cubam complex is composed of a 400 Angstrom long stem and a globular crown region. The stem region is probably formed by AMN and the CUBN N-terminal region, including the EGF-like domains. The crown is probably formed by the CUBN CUB domains.

RefSeq proteins (1): NP_001072* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000152EGF-type_Asp/Asn_hydroxyl_sitePTM
IPR000742EGFDomain
IPR000859CUB_domDomain
IPR001881EGF-like_Ca-bd_domDomain
IPR009030Growth_fac_rcpt_cys_sfHomologous_superfamily
IPR018097EGF_Ca-bd_CSConserved_site
IPR024731NELL2-like_EGFDomain
IPR035914Sperma_CUB_dom_sfHomologous_superfamily
IPR049883NOTCH1_EGF-likeDomain

Pfam: PF00008, PF00431, PF07645, PF12947

UniProt features (281 total): disulfide bond 66, sequence variant 64, glycosylation site 47, strand 36, domain 34, binding site 19, turn 4, helix 3, sequence conflict 2, signal peptide 1, propeptide 1, chain 1, region of interest 1, site 1, modified residue 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6GJEX-RAY DIFFRACTION2.3
3KQ4X-RAY DIFFRACTION3.3

Predicted structure (AlphaFold)

No AlphaFold model available for O60494 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 35–36 (cleavage; by furin)

Ligand- & substrate-binding residues (19): 980; 988; 1027; 1029; 1030; 1096; 1105; 1146; 1148; 1149; 1213; 1221

Post-translational modifications (1): 3008

Disulfide bonds (66): 136–147, 141–156, 158–167, 174–190, 184–199, 201–210, 267–280, 274–289, 292–303, 353–366, 360–376, 399–409, 404–418, 420–429, 436–447, 441–456, 458–467, 474–500, 527–549, 590–616 …

Glycosylation sites (47): 3295, 3357, 3430, 3457, 3533, 3576, 105, 428, 482, 711, 749, 781, 857, 957, 984, 1092, 1168, 1217, 1285, 1307 …

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-196791Vitamin D (calciferol) metabolism
R-HSA-3359462Defective AMN causes MGA1
R-HSA-3359463Defective CUBN causes MGA1
R-HSA-8964011HDL clearance
R-HSA-9758881Uptake of dietary cobalamins into enterocytes

MSigDB gene sets: 243 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, SHEPARD_BMYB_MORPHOLINO_UP, GOCC_VACUOLAR_MEMBRANE, GOCC_CELL_SURFACE, GOBP_VESICLE_MEDIATED_TRANSPORT, BROWNE_HCMV_INFECTION_48HR_DN, TCF4_Q5, chr10p13, GOBP_COBALAMIN_METABOLIC_PROCESS, GOBP_TETRAPYRROLE_METABOLIC_PROCESS, GOBP_VITAMIN_TRANSPORT, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPOPROTEIN_LOCALIZATION, GOCC_APICAL_PLASMA_MEMBRANE

GO Biological Process (12): tissue homeostasis (GO:0001894), receptor-mediated endocytosis (GO:0006898), cholesterol metabolic process (GO:0008203), cobalamin metabolic process (GO:0009235), response to bacterium (GO:0009617), cobalamin transport (GO:0015889), lipoprotein transport (GO:0042953), establishment of localization in cell (GO:0051649), lipid metabolic process (GO:0006629), endocytosis (GO:0006897), steroid metabolic process (GO:0008202), protein transport (GO:0015031)

GO Molecular Function (7): calcium ion binding (GO:0005509), cobalamin binding (GO:0031419), signaling receptor activity (GO:0038023), cargo receptor activity (GO:0038024), protein homodimerization activity (GO:0042803), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (21): lysosomal membrane (GO:0005765), endosome (GO:0005768), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), cytosol (GO:0005829), plasma membrane (GO:0005886), clathrin-coated pit (GO:0005905), membrane (GO:0016020), apical plasma membrane (GO:0016324), endocytic vesicle (GO:0030139), extrinsic component of external side of plasma membrane (GO:0031232), brush border membrane (GO:0031526), microvillus membrane (GO:0031528), lysosomal lumen (GO:0043202), signaling receptor complex (GO:0043235), extracellular exosome (GO:0070062), cytoplasm (GO:0005737), lysosome (GO:0005764), brush border (GO:0005903), cell projection membrane (GO:0031253), apical part of cell (GO:0045177)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Defects in cobalamin (B12) metabolism2
Metabolism of steroids1
Plasma lipoprotein clearance1
Cobalamin (Cbl, vitamin B12) transport and metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
endomembrane system4
cytoplasm3
cellular anatomical structure3
vesicle-mediated transport2
lysosome2
cytoplasmic vesicle2
intracellular membrane-bounded organelle2
membrane2
apical part of cell2
plasma membrane region2
cell projection membrane2
microvillus2
multicellular organismal-level homeostasis1
anatomical structure homeostasis1
endocytosis1
sterol metabolic process1
secondary alcohol metabolic process1
tetrapyrrole metabolic process1
response to other organism1
vitamin transport1
nitrogen compound transport1
protein transport1
lipoprotein localization1
establishment of localization1
cellular localization1
primary metabolic process1
vesicle budding from membrane1
membrane invagination1
import into cell1
lipid metabolic process1
transport1
intracellular protein localization1
establishment of protein localization1
metal ion binding1
vitamin binding1
tetrapyrrole binding1
heterocyclic compound binding1
molecular transducer activity1
molecular_function1
molecular adaptor activity1

Protein interactions and networks

STRING

1174 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CUBNAMNQ9BXJ7999
CUBNLRP2P98164999
CUBNALBP02768992
CUBNCBLIFP27352984
CUBNAPOA1P02647972
CUBNGCP02774970
CUBNCLCN5P51795868
CUBNSLC9A3P48764835
CUBNDAB2P98082811
CUBNCBLP22681806
CUBNHPP00737747
CUBNTCN2P20062706
CUBNAMBPP00977704
CUBNTCN1P20061671
CUBNPLB1Q6P1J6669

IntAct

9 interactions, top by confidence:

ABTypeScore
AMNCUBNpsi-mi:“MI:0407”(direct interaction)0.600
AMNCUBNpsi-mi:“MI:0915”(physical association)0.600
CBLIFCUBNpsi-mi:“MI:0407”(direct interaction)0.560
CUBNCUBNpsi-mi:“MI:0915”(physical association)0.400
LMP2WWP2psi-mi:“MI:0914”(association)0.350
RRP1BYY2psi-mi:“MI:0914”(association)0.350

BioGRID (10): CUBN (Affinity Capture-Western), GIF (Reconstituted Complex), CUBN (Reconstituted Complex), CUBN (Affinity Capture-MS), CUBN (Affinity Capture-MS), CUBN (Reconstituted Complex), CUBN (Protein-peptide), LRP1 (Affinity Capture-Western), PID1 (Affinity Capture-Western), CUBN (Two-hybrid)

ESM2 similar proteins: A0A1D5NSM8, A0A1L8HYT7, A2AJX4, B1AUH1, B3DK56, B3EX02, E2RK30, E9PZ36, F1RWC3, F8W3R9, O54767, O60494, O70244, P08922, P08F94, P20239, P47984, P56677, P79953, P86091, P97435, P98072, P98073, P98074, Q0IIH7, Q0V8T3, Q0V8T5, Q2QI47, Q3UZ09, Q5VYJ5, Q63132, Q66TN7, Q6DIV5, Q6YI48, Q769J6, Q78DX7, Q7M761, Q7RTY7, Q7RTY8, Q7RTZ1

Diamond homologs: A0A0C5PRQ1, A0FKN6, A0JNA2, A8Q2D1, C6K2K4, C9D7R3, D2KBH9, D5FM34, D5FM37, D5FM38, K7Z9Q9, O16977, O17264, O35276, O35375, O43897, O57382, O57460, O60462, O60494, O70244, P07584, P0DM61, P0DM62, P13497, P28825, P28826, P31579, P31580, P31581, P42674, P55112, P55113, P55114, P55115, P84748, P91828, P98060, P98061, P98068

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

2582 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic63
Likely pathogenic110
Uncertain significance1249
Likely benign653
Benign246

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1072126NM_001081.4(CUBN):c.7013del (p.Gly2338fs)Pathogenic
1074985NM_001081.4(CUBN):c.7051G>T (p.Gly2351Ter)Pathogenic
1075676NM_001081.4(CUBN):c.2191_2192del (p.Thr731fs)Pathogenic
1076401NM_001081.4(CUBN):c.1892del (p.Thr631fs)Pathogenic
1179177NM_001081.4(CUBN):c.796G>T (p.Glu266Ter)Pathogenic
1322176NM_001081.4(CUBN):c.10233G>A (p.Trp3411Ter)Pathogenic
1427549NM_001081.4(CUBN):c.8684_8687del (p.Ser2895fs)Pathogenic
1444492NM_001081.4(CUBN):c.424C>T (p.Gln142Ter)Pathogenic
1444519NM_001081.4(CUBN):c.7802G>A (p.Trp2601Ter)Pathogenic
1705570NM_001081.4(CUBN):c.4689T>A (p.Cys1563Ter)Pathogenic
1992848NM_001081.4(CUBN):c.9783del (p.Thr3261_Leu3262insTer)Pathogenic
2009822NM_001081.4(CUBN):c.8049del (p.Lys2683fs)Pathogenic
2032699NM_001081.4(CUBN):c.5701G>T (p.Glu1901Ter)Pathogenic
2104999NM_001081.4(CUBN):c.794dup (p.Asp265fs)Pathogenic
2193032NM_001081.4(CUBN):c.10557_10558del (p.Gly3520fs)Pathogenic
2423663NC_000010.10:g.(?16961942)(16970322_?)delPathogenic
2628983NM_001081.4(CUBN):c.8355del (p.Asp2786fs)Pathogenic
2718935NM_001081.4(CUBN):c.10520C>A (p.Ser3507Ter)Pathogenic
2721529NM_001081.4(CUBN):c.5856del (p.Lys1954fs)Pathogenic
2731233NM_001081.4(CUBN):c.3138del (p.Ala1047fs)Pathogenic
2736019NM_001081.4(CUBN):c.6118C>T (p.Arg2040Ter)Pathogenic
2793997NM_001081.4(CUBN):c.7145_7146del (p.Asp2381_Phe2382insTer)Pathogenic
2859831NM_001081.4(CUBN):c.3578G>A (p.Trp1193Ter)Pathogenic
2958744NM_001081.4(CUBN):c.8165del (p.Pro2722fs)Pathogenic
30291NM_001081.4(CUBN):c.3329+1G>TPathogenic
3220910NM_001081.4(CUBN):c.591C>G (p.Tyr197Ter)Pathogenic
3235994NM_001081.4(CUBN):c.4042G>T (p.Gly1348Ter)Pathogenic
3235995NM_001081.4(CUBN):c.6297_6298insT (p.Arg2100Ter)Pathogenic
3244830NC_000010.10:g.(?17151619)(17157616_?)delPathogenic
3255214NM_001081.4(CUBN):c.10009_10012del (p.Leu3337fs)Pathogenic

SpliceAI

10556 predictions. Top by Δscore:

VariantEffectΔscore
10:16828799:A:ACdonor_gain1.0000
10:16828800:C:CCdonor_gain1.0000
10:16828803:A:ACdonor_gain1.0000
10:16828803:ACGC:Adonor_gain1.0000
10:16828804:C:CAdonor_gain1.0000
10:16828804:CG:Cdonor_gain1.0000
10:16828804:CGCC:Cdonor_gain1.0000
10:16828804:CGCCT:Cdonor_gain1.0000
10:16829036:ACATC:Aacceptor_gain1.0000
10:16829037:CATC:Cacceptor_gain1.0000
10:16829037:CATCC:Cacceptor_gain1.0000
10:16829038:ATC:Aacceptor_gain1.0000
10:16829038:ATCCT:Aacceptor_loss1.0000
10:16829039:TC:Tacceptor_gain1.0000
10:16829040:CC:Cacceptor_gain1.0000
10:16829040:CCT:Cacceptor_loss1.0000
10:16829041:C:CCacceptor_gain1.0000
10:16829042:T:Aacceptor_loss1.0000
10:16835197:T:Cacceptor_gain1.0000
10:16840883:A:ACdonor_gain1.0000
10:16840883:ACTGT:Adonor_gain1.0000
10:16840884:C:CTdonor_gain1.0000
10:16840884:CTGTC:Cdonor_gain1.0000
10:16841048:C:CCacceptor_gain1.0000
10:16869630:TCTTA:Tdonor_loss1.0000
10:16869631:CTTA:Cdonor_loss1.0000
10:16869632:TTA:Tdonor_loss1.0000
10:16869633:TACCC:Tdonor_loss1.0000
10:16869634:A:ACdonor_gain1.0000
10:16869635:C:CCdonor_gain1.0000

AlphaMissense

23998 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:16913904:C:AW2480C0.995
10:16913904:C:GW2480C0.995
10:16982565:C:AW1538C0.995
10:16982565:C:GW1538C0.995
10:17104436:C:GC467S0.995
10:17104437:A:TC467S0.995
10:17114157:C:AW251C0.995
10:17114157:C:GW251C0.995
10:16828952:C:AW3539C0.994
10:16828952:C:GW3539C0.994
10:16828997:G:CS3524R0.994
10:16828997:G:TS3524R0.994
10:16828999:T:GS3524R0.994
10:16954409:A:CF1612C0.994
10:16954409:A:GF1612S0.994
10:16990434:C:GC1417S0.994
10:16990435:A:GC1417R0.994
10:16990435:A:TC1417S0.994
10:17100021:C:AW583C0.993
10:17100021:C:GW583C0.993
10:17109711:C:GC347S0.993
10:17109712:A:TC347S0.993
10:16928172:C:GA2086P0.992
10:16937640:A:GW1960R0.992
10:16937640:A:TW1960R0.992
10:16939058:A:GW1880R0.992
10:16939058:A:TW1880R0.992
10:16947324:G:CS1751R0.992
10:16947324:G:TS1751R0.992
10:16947326:T:GS1751R0.992

dbSNP variants (sampled 300 via entrez): RS1000013462 (10:16859348 T>C), RS1000014802 (10:17035894 T>C), RS1000019204 (10:16930248 A>G), RS1000042237 (10:17059628 A>G), RS1000047222 (10:16881802 T>A), RS1000058298 (10:17009560 C>G), RS1000058949 (10:17113782 C>A), RS1000065646 (10:17047080 T>A), RS1000067320 (10:16895769 G>A), RS1000071251 (10:16958553 G>A), RS1000077750 (10:17000265 C>A,G), RS1000080493 (10:16901983 A>G), RS1000117887 (10:16988775 A>G), RS1000128299 (10:17000424 C>G,T), RS1000139621 (10:16857185 G>A)

Disease associations

OMIM: gene MIM:602997 | disease phenotypes: MIM:261100, MIM:618884

GenCC curated gene-disease

DiseaseClassificationInheritance
Imerslund-Grasbeck syndrome type 1DefinitiveAutosomal recessive
proteinuria, chronic benignStrongAutosomal recessive
Imerslund-Grasbeck syndromeSupportiveAutosomal recessive

Mondo (7): Imerslund-Grasbeck syndrome (MONDO:0009853), proteinuria, chronic benign (MONDO:0030042), Imerslund-Grasbeck syndrome type 1 (MONDO:0100156), proteinuria (MONDO:0003634), chronic kidney disease (MONDO:0005300), focal segmental glomerulosclerosis (MONDO:0100313), autism spectrum disorder (MONDO:0005258)

Orphanet (2): Imerslund-Gräsbeck syndrome (Orphanet:35858), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

40 total (30 of 40 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000083Renal insufficiency
HP:0000093Proteinuria
HP:0000206Glossitis
HP:0000707Abnormality of the nervous system
HP:0000726Dementia
HP:0000750Delayed speech and language development
HP:0000980Pallor
HP:0001252Hypotonia
HP:0001289Confusion
HP:0001508Failure to thrive
HP:0001649Tachycardia
HP:0001824Weight loss
HP:0001873Thrombocytopenia
HP:0001875Decreased total neutrophil count
HP:0001876Pancytopenia
HP:0001889Megaloblastic anemia
HP:0001892Abnormal bleeding
HP:0001923Reticulocytosis
HP:0001972Macrocytic anemia
HP:0002013Vomiting
HP:0002019Constipation
HP:0002376Developmental regression
HP:0002721Immunodeficiency
HP:0002907Microscopic hematuria
HP:0003401Paresthesia
HP:0003474Somatic sensory dysfunction
HP:0004396Poor appetite
HP:0004821Hypersegmentation of neutrophil nuclei
HP:0004823Anisopoikilocytosis

GWAS associations

50 associations (top):

StudyTraitp-value
GCST000337_26Quantitative traits6.000000e-06
GCST000358_2Folate pathway vitamin levels1.000000e-06
GCST000483_3Folate pathway vitamin levels3.000000e-09
GCST000891_4Whole-brain volume3.000000e-06
GCST000988_1Urinary albumin excretion1.000000e-11
GCST002087_11Homocysteine levels8.000000e-10
GCST002087_15Homocysteine levels8.000000e-10
GCST002221_72Cholesterol, total3.000000e-11
GCST002559_4Vitamin B levels in ischemic stroke2.000000e-13
GCST002919_3Colorectal cancer7.000000e-08
GCST002937_2Molybdenum levels3.000000e-07
GCST003253_1Microalbuminuria1.000000e-10
GCST003254_2Urinary albumin-to-creatinine ratio in non-diabetics4.000000e-06
GCST003255_8Urinary albumin-to-creatinine ratio2.000000e-10
GCST003774_1Urinary albumin-to-creatinine ratio2.000000e-08
GCST004235_38Total cholesterol levels5.000000e-11
GCST004616_78Platelet distribution width6.000000e-17
GCST005387_2Binge eating behaviour in bipolar disorder1.000000e-07
GCST006463_14Urinary albumin excretion (no hypertensive medication)1.000000e-51
GCST006463_15Urinary albumin excretion (no hypertensive medication)4.000000e-09
GCST006463_16Urinary albumin excretion (no hypertensive medication)3.000000e-84
GCST006586_24Urinary albumin excretion2.000000e-92
GCST006586_25Urinary albumin excretion3.000000e-11
GCST006586_26Urinary albumin excretion9.000000e-09
GCST006586_27Urinary albumin excretion2.000000e-107
GCST007202_3High density lipoprotein cholesterol levels1.000000e-06
GCST007718_1Urinary albumin-to-creatinine ratio1.000000e-51
GCST007718_2Urinary albumin-to-creatinine ratio1.000000e-40
GCST007718_3Urinary albumin-to-creatinine ratio4.000000e-62
GCST008610_2Proteinuria3.000000e-15

EFO canonical traits (14, from GWAS)

EFO IDTrait name
EFO:0006336diastolic blood pressure
EFO:0004620vitamin B12 measurement
EFO:0005089whole-brain volume
EFO:0004285albuminuria
EFO:0004578homocysteine measurement
EFO:0004574total cholesterol measurement
EFO:0007778urinary albumin to creatinine ratio
EFO:0007984platelet component distribution width
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004531urate measurement
EFO:0005420grey matter volume measurement
EFO:0010408triacylglycerol 50:1 measurement
EFO:0009963bipolar I disorder
EFO:0007985platelet crit

MeSH disease descriptors (4)

DescriptorNameTree numbers
D005923Glomerulosclerosis, Focal SegmentalC12.050.351.968.419.570.363.640; C12.200.777.419.570.363.660; C12.950.419.570.363.640
D007676Kidney Failure, ChronicC12.050.351.968.419.780.750.500; C12.200.777.419.780.750.500; C12.950.419.780.750.500; C23.550.291.500.906.500
D011507ProteinuriaC12.050.351.968.934.734; C12.200.777.934.734; C12.950.934.734; C23.888.942.750
C538556Imerslund-Grasbeck syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases methylation2
Valproic Aciddecreases expression, increases methylation2
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aincreases methylation, decreases methylation, affects cotreatment1
sodium arseniteincreases expression1
ochratoxin Adecreases acetylation1
entinostatincreases expression1
(+)-JQ1 compounddecreases expression1
Sunitinibdecreases expression1
Zoledronic Acidincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Methamphetamineaffects response to substance1
N-Nitrosopyrrolidinedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Vitamin K 3decreases expression1

Cellosaurus cell lines

4 cell lines: 3 finite cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B3YUWG2625Finite cell lineMale
CVCL_B3Z4WG3086Finite cell lineMale
CVCL_B4EFWG3705Finite cell line
CVCL_C0LPGM28311Transformed cell lineFemale

Clinical trials (associated diseases)

163 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00067990PHASE4COMPLETEDAngiotensin II Blockade for Chronic Allograft Nephropathy
NCT00234871PHASE4COMPLETEDTarka® vs. Lotrel® in Hypertensive, Diabetic Subjects With Renal Disease (TANDEM)
NCT00241085PHASE4COMPLETEDEffect of Valsartan on Proteinuria in Patients With Hypertension and Diabetes Mellitus
NCT00369538PHASE4SUSPENDEDSpecific Blockage of Angiotensine 2 and Podocyturia in Glomerular Nephropathies With Hypertension and Proteinuria
NCT00508898PHASE4WITHDRAWNThe Efficacy and Safety of Calcitriol for the Treatment of Lupus Nephritis and Persistent Proteinuria
NCT00550095PHASE4COMPLETEDTo Assess the Effects of Valsartan on Albuminuria/Proteinuria in Hypertensive Patients With Type 2 Diabetes Mellitus
NCT00674596PHASE4COMPLETEDThe Effect of Renin Angiotensin System Blockage (RAS) Blockade On PTX3 Levels In Diabetic Patients With Proteinuria
NCT00858299PHASE4UNKNOWNThe Change of Urinary Angiotensinogen Excretion After Valsartan Treatment in Patients With Persistent Proteinuria
NCT00893425PHASE4COMPLETEDEffect of Renin Angiotensin System Blockade on the Fas Antigen (CD95) and Asymmetric Dimethylarginine (ADMA) Levels in Type-2 Diabetic Patients With Proteinuria
NCT00921570PHASE4COMPLETEDThe Effects of Renin Angiotensin System Blockage (RAS), Calcium Channel Blocker and Combined Drugs on TWEAK, PTX3 and FMD Levels in Diabetic Proteinuric Patients With Hypertension
NCT00961207PHASE4TERMINATEDTriple Blockade of the Renin Angiotensin Aldosterone System in Diabetic (Type 1&2) Proteinuric Patients
NCT01169857PHASE4WITHDRAWNVelcade for Proliferative Lupus Nephritis
NCT01219413PHASE4COMPLETEDInfluence of Aliskiren on Proteinuria
NCT01386554PHASE4COMPLETEDActhar for Treatment of Proteinuria in Membranous Nephropathy Patients
NCT01512862PHASE4UNKNOWNAnti-proteinuric Effect of Calcitriol in Non-diabetic Kidney Disease Patients
NCT01541267PHASE4COMPLETEDThe Effect of Various Types of the Renin-angiotensin-aldosterone System Blockade on Proteinuria
NCT01637259PHASE4COMPLETEDMARCH Renal Substudy
NCT01703234PHASE4COMPLETEDFGF-23 and Endothelial Dysfunction in Diabetic Proteinuric Patients
NCT01820832PHASE4UNKNOWNOral Calcitriol for Reduction of Mild Proteinuria in Patients With CKD
NCT01827202PHASE4COMPLETEDRAS Quantification in Patients With Aliskiren or Candesartan
NCT02057523PHASE4TERMINATEDActhar as Rescue Therapy for Transplant Glomerulopathy in Kidney Transplant Recipients
NCT02063100PHASE4UNKNOWNEfficacy and Safety of Shenyankangfu Tablets for Primary Glomerulonephritis
NCT02382523PHASE4WITHDRAWNActhar on Proteinuria in IgA Nephropathy Patients
NCT02522650PHASE4UNKNOWNA Crossover Pilot Study of the Effect of Amiloride on Proteinuria
NCT03195023PHASE4UNKNOWNEffect of RAS Blockers on CKD Progression in Elderly Patients With Non Proteinuric Nephropathies (PROERCAN01)
NCT03550859PHASE4UNKNOWNHMG-CoA Reductase add-on in Chronic Kidney Disease Patients With Proteinuria
NCT03983551PHASE4COMPLETEDComparing the Renal Effect of Dipeptidyl-peptidase 4 Inhibitors and Sulfonylureas
NCT04531397PHASE4WITHDRAWNEfficacy and Safety of Dapagliflozin in Children With Proteinuric Chronic Kidney Disease
NCT04534270PHASE4COMPLETEDEfficacy and Safety of Dapagliflozin in Children With Proteinuria
NCT06374043PHASE4COMPLETEDDecentralized N=1 Study: A Feasible Approach to Evaluate Individual Therapy Response to Dapagliflozin.
NCT07030894PHASE4RECRUITINGNefecon and Ambrisentan in IgA Nephropathy
NCT07219121PHASE4RECRUITINGSparsentan in Posttransplant Immunoglobulin A Nephropathy or Focal Segmental Glomerulosclerosis
NCT07358520PHASE4NOT_YET_RECRUITINGClinical Study on the Use of Huaier Granules for the Treatment of Proteinuria Related to Bevacizumab and Anlotinib in Lung Cancer Patients
NCT00073710PHASE4COMPLETEDStudy to Evaluate the Effects of Zemplar Injection and Calcijex on Intestinal Absorption of Calcium
NCT00125593PHASE4COMPLETEDStudy of Heart and Renal Protection
NCT00132431PHASE4COMPLETEDSTART: Sensipar Treatment Algorithm to Reach K/DOQI Targets in Chronic Kidney Disease Subjects With Secondary Hyperparathyroidism
NCT00155246PHASE4COMPLETEDEfficacy of Pentoxifylline on Chronic Kidney Disease
NCT00175149PHASE4TERMINATEDActive Vitamin D Effect on Left Ventricular Hypertrophy
NCT00184769PHASE4COMPLETEDGrowth Hormone Treatment in Infants Aged 1 to 2 Years With Chronic Renal Insufficiency (CRI) and Growth Retardation.
NCT00190580PHASE4COMPLETEDKanagawa Valsartan Trial (KVT): Effects of Valsartan on Renal and Cardiovascular Disease