CRB3

gene
On this page

Also known as MGC17303

Summary

CRB3 (crumbs cell polarity complex component 3, HGNC:20237) is a protein-coding gene on chromosome 19p13.3, encoding Protein crumbs homolog 3 (Q9BUF7). Involved in the establishment of cell polarity in mammalian epithelial cells.

This gene encodes a member of the Crumbs family of proteins. This gene is widely expressed in epithelial tissues where the encoded protein isoforms play various roles such as the control of cytokinesis and ciliogenesis or the formation of tight junctions. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 92359 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 29 total
  • MANE Select transcript: NM_139161

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20237
Approved symbolCRB3
Namecrumbs cell polarity complex component 3
Location19p13.3
Locus typegene with protein product
StatusApproved
AliasesMGC17303
Ensembl geneENSG00000130545
Ensembl biotypeprotein_coding
OMIM609737
Entrez92359

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000308243, ENST00000356762, ENST00000598494, ENST00000600229

RefSeq mRNA: 3 — MANE Select: NM_139161 NM_139161, NM_174881, NM_174882

CCDS: CCDS12166, CCDS12167

Canonical transcript exons

ENST00000600229 — 4 exons

ExonStartEnd
ENSE0000089540064655456465618
ENSE0000116005864646086464783
ENSE0000151846164642716464350
ENSE0000305355164664666467221

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 96.46.

FANTOM5 (CAGE): breadth broad, TPM avg 2.9679 / max 73.8577, expressed in 497 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1734792.6192483
1734800.3487101

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583496.46gold quality
pharyngeal mucosaUBERON:000035594.84gold quality
mucosa of transverse colonUBERON:000499194.60gold quality
vena cavaUBERON:000408792.94silver quality
kidney epitheliumUBERON:000481992.13gold quality
nasal cavity epitheliumUBERON:000538491.87silver quality
esophagus mucosaUBERON:000246991.46gold quality
upper arm skinUBERON:000426390.90silver quality
body of pancreasUBERON:000115090.78gold quality
parotid glandUBERON:000183190.57silver quality
body of tongueUBERON:001187690.52silver quality
tongueUBERON:000172389.53silver quality
pylorusUBERON:000116689.50silver quality
skin of legUBERON:000151189.46gold quality
skin of abdomenUBERON:000141689.20gold quality
duodenumUBERON:000211489.11gold quality
adult mammalian kidneyUBERON:000008289.10gold quality
amniotic fluidUBERON:000017388.71gold quality
tracheaUBERON:000312688.42gold quality
nippleUBERON:000203087.99gold quality
pancreatic ductal cellCL:000207987.85silver quality
superior surface of tongueUBERON:000737187.84gold quality
zone of skinUBERON:000001487.59gold quality
gingival epitheliumUBERON:000194987.36silver quality
metanephros cortexUBERON:001053387.12gold quality
right lobe of liverUBERON:000111486.97gold quality
pancreasUBERON:000126486.96gold quality
pericardiumUBERON:000240786.81silver quality
lateral nuclear group of thalamusUBERON:000273686.74silver quality
substantia nigra pars reticulataUBERON:000196686.54gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-8142yes124.34
E-ANND-3yes14.78
E-MTAB-9388yes12.97

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HNF4A

miRNA regulators (miRDB)

35 targeting CRB3, 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-5011-5P100.0083.465820
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-590-3P99.9674.346478
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-548AZ-5P99.8369.943230
HSA-MIR-548T-5P99.8369.913220
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-674599.7465.331321
HSA-MIR-410-3P99.2769.982457
HSA-MIR-6852-5P99.1766.692073
HSA-MIR-4999-3P99.1165.55424
HSA-MIR-939-3P98.9765.072347
HSA-MIR-1227-5P98.6565.321549
HSA-MIR-218-1-3P98.6367.97832
HSA-MIR-4722-5P98.4666.341611
HSA-MIR-6838-3P98.4065.88559
HSA-MIR-6864-5P98.3866.591079
HSA-MIR-6742-3P97.9564.501490
HSA-MIR-30C-1-3P97.8066.361499
HSA-MIR-30C-2-3P97.8066.451499
HSA-MIR-6788-5P97.8066.411532
HSA-MIR-4723-3P97.6765.911017

Literature-anchored findings (GeneRIF, showing 19)

  • the Crumbs3-Pals1 complex has a role in development of polarity in mammalian epithelial cells (PMID:12771187)
  • CRB3, through its cytoplasmic domain and its interactors, plays a role in apical membrane morphogenesis and tight junction regulation. (PMID:14718572)
  • The crumbs3 protein plays an important role in epithelial tight junction formation, and also provide the first known functional role for the mammalian Crumbs FERM binding domain. (PMID:15976445)
  • Data show that a novel Crumbs3 isoform regulates cell division and ciliogenesis via importin beta1 interactions. (PMID:17646395)
  • overexpression of human CRB1 and related isoforms, CRB2 and CRB3, had no effect on the levels of presenilin complex components, on NCT maturation or on PS endoproteolysis (PMID:17988153)
  • Morg1 facilitates Par6-aPKC binding to Crb3 for definition of apical identity of epithelial cells. (PMID:23439680)
  • our data demonstrated that CRB3 may be used as a new independent favorable prognostic factor for human ccRCC (PMID:25406012)
  • CRB3A recruits p114RhoGEF and its activator Ehm2 to the cell periphery using both functional motifs of its cytoplasmic tail and increases RhoA activation levels. (PMID:26217016)
  • Data show different intracellular mobility patterns for crumbs 3 proteins Crb3A and Crb3B. (PMID:26975581)
  • we report for the first time that CRB3 acts as an upstream regulator of the Hippo pathway to regulate contact inhibition by recruiting other Hippo molecules, such as Kibra and/or FRMD6, in mammary epithelial cells. (PMID:28079891)
  • CRB3 is an important regulator for breast cancer stemness, which is associated with tamoxifen resistance.Association between CRB3 and beta-catenin expression levels correlates with tamoxifen resistance of breast cancer. (PMID:29602199)
  • We found that CRB3-induced proliferation is epidermal growth factor (EGF)-independent and occurs through a mechanism that involves secretion of the EGF-family ligand, amphiregulin (AREG)..We identified the FBD-containing protein, EPB41L4B, as an essential mediator of CRB3-driven proliferation and observed that the CRB3-dependent changes in endocytic trafficking were also dependent on EPB41L4B (PMID:30440051)
  • CRB3 strongly promotes tumor invasion and metastasis of human colon adenocarcinoma cells. Correlative expression between CRB3 and FGFR1 was consistently detected in primary and metastatic colorectal cancer patient tissues. Taking these together, CRB3 critically accelerates cell migration, namely invasion and metastasis of human colon cancers, through specific interaction to FGFR1 on colon cancer cells. (PMID:30980524)
  • Crumbs protein homolog 3 (CRB3) expression is associated with oestrogen and progesterone receptor positivity in breast cancer. (PMID:31087799)
  • CRB3 DNA methylation negatively correlated with CRB3 mRNA expression. CRB3 DNA methylation was also related to pathologic stage, T stage, N stage, and M stage of ccRCC. (PMID:31147860)
  • Knockout (KO) of apical polarity determinant Crumbs 3 (Crb3) enhances Adeno-associated viruses (AAV) transduction, while overexpression exerts the opposite effect. Crb3 restricts AAV transduction in a serotype- and cell type-specific manner. Increased availability of galactosylated glycans on the surfaces of Crb3 KO cells, but not the universal AAV receptor, leads to increased capsid attachment and enhanced transduction. (PMID:31391273)
  • The Crb3 may promote colon cancer cell migration by regulating the expression of GSLs on the cell surface. (PMID:31500807)
  • Aberrant epithelial polarity cues drive the development of precancerous airway lesions. (PMID:33903236)
  • Fructose-bisphosphatase1 (FBP1) alleviates experimental osteoarthritis by regulating Protein crumbs homolog 3 (CRB3). (PMID:38049890)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCrb3ENSMUSG00000044279
rattus_norvegicusCrb3ENSRNOG00000070099

Paralogs (3): SCARF1 (ENSG00000074660), CRB2 (ENSG00000148204), SCARF2 (ENSG00000244486)

Protein

Protein identifiers

Protein crumbs homolog 3Q9BUF7 (reviewed: Q9BUF7)

All UniProt accessions (1): Q9BUF7

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the establishment of cell polarity in mammalian epithelial cells. Regulates the morphogenesis of tight junctions. Involved in promoting phosphorylation and cytoplasmic retention of transcriptional coactivators YAP1 and WWTR1/TAZ which leads to suppression of TGFB1-dependent transcription of target genes such as CCN2/CTGF, SERPINE1/PAI1, SNAI1/SNAIL1 and SMAD7.

Subunit / interactions. Component of a complex composed of CRB3, PALS1 and PATJ. Interacts (via C-terminus) with PALS1 (via PDZ domain). Interacts with PARD6A. Interacts (via intracellular domain) with EPB41L5. Interacts with WDR83.

Subcellular location. Apical cell membrane. Cell junction. Tight junction.

Tissue specificity. Preferentially expressed in epithelial tissues. Expressed at high levels in lung, kidney, and colon. Expressed at high levels in retina, colon and mammary glands. Moderately expressed in liver, spleen, pancreas and prostate. Moderately to weakly expressed in the placenta. Weakly expressed in skeletal muscle and small intestine.

Domain organisation. The PDZ-binding motif is involved in the interactions with PARD6A and PALS1.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BUF7-11, Ayes
Q9BUF7-22, B

RefSeq proteins (3): NP_631900, NP_777377, NP_777378 (=MANE)

Domains & families (InterPro)

UniProt features (14 total): mutagenesis site 2, topological domain 2, region of interest 2, signal peptide 1, chain 1, splice variant 1, strand 1, transmembrane region 1, short sequence motif 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
5I7ZX-RAY DIFFRACTION1.8

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BUF7-F169.830.14

Functional residue map

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

Glycosylation sites (1): 36

Mutagenesis-validated functional residues (2):

PositionPhenotype
36abolishes n-glycosylation. no effect on localization to the apical cell membrane.
117–120loss of interaction with pard6a and pals1. no effect on interaction with epb41l5.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-420029Tight junction interactions
R-HSA-9705677SARS-CoV-2 targets PDZ proteins in cell-cell junction

MSigDB gene sets: 120 (showing top): GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, AREB6_03, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, AREB6_01, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, KEGG_TIGHT_JUNCTION, HNF1_Q6, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELL_JUNCTION_ORGANIZATION, WANG_LMO4_TARGETS_DN, GOBP_POSITIVE_REGULATION_OF_CELL_JUNCTION_ASSEMBLY

GO Biological Process (4): establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197), protein localization to plasma membrane (GO:0072659), tight junction organization (GO:0120193), positive regulation of cell junction assembly (GO:1901890)

GO Molecular Function (3): SH3 domain binding (GO:0017124), protein domain specific binding (GO:0019904), protein binding (GO:0005515)

GO Cellular Component (12): plasma membrane (GO:0005886), bicellular tight junction (GO:0005923), apical plasma membrane (GO:0016324), cell junction (GO:0030054), subapical complex (GO:0035003), apical junction complex (GO:0043296), extracellular exosome (GO:0070062), tight junction (GO:0070160), membrane (GO:0016020), protein-containing complex (GO:0032991), apical part of cell (GO:0045177), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Cell-cell junction organization1
SARS-CoV-2-host interactions1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
apical junction complex2
cell-cell junction2
establishment or maintenance of apical/basal cell polarity1
protein localization to membrane1
protein localization to cell periphery1
cell-cell junction organization1
cell junction assembly1
positive regulation of cellular component biogenesis1
positive regulation of cellular component organization1
regulation of cell junction assembly1
protein domain specific binding1
protein binding1
binding1
membrane1
cell periphery1
tight junction1
apical part of cell1
plasma membrane region1
plasma membrane protein complex1
extracellular vesicle1
cellular_component1
cell junction1

Protein interactions and networks

STRING

506 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CRB3PALS1Q8N3R9999
CRB3PATJQ8NI35998
CRB3CRB2Q5IJ48904
CRB3EPB41L5Q9HCM4825
CRB3LIN7CQ9NUP9797
CRB3NXNQ6DKJ4760
CRB3EZRP15311735
CRB3LLGL2Q6P1M3724
CRB3TJP1Q07157723
CRB3CNTNAP1P78357682
CRB3PARD3Q8TEW0682
CRB3AMOTQ4VCS5658
CRB3SCRIBQ14160656
CRB3EPB41P11171642
CRB3ZEB1P37275638

IntAct

11 interactions, top by confidence:

ABTypeScore
PALS1Epsi-mi:“MI:0915”(physical association)0.600
PSMA3CRB3psi-mi:“MI:0915”(physical association)0.560
PALS1AMOTL1psi-mi:“MI:0914”(association)0.530
CRB3EPB41L5psi-mi:“MI:0915”(physical association)0.520
EPB41L5CRB3psi-mi:“MI:0915”(physical association)0.520
PALS1CRB3psi-mi:“MI:0915”(physical association)0.400
RAB11FIP5CRB3psi-mi:“MI:0403”(colocalization)0.270

BioGRID (32): CRB3 (Two-hybrid), CRB3 (Reconstituted Complex), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), CRB3 (Two-hybrid), VAMP1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GW64, A0A5F4BST2, A0PJX4, A8MVS5, A8MWV9, B0FP48, E5RIL1, E9PGG2, O14836, O60320, O95998, P09564, Q01113, Q01114, Q13477, Q2KI80, Q2T9R2, Q3TS39, Q3UPR0, Q3URD2, Q4V9L6, Q5FVJ4, Q5M869, Q6A044, Q6UWJ8, Q75VT8, Q864V4, Q8BRJ3, Q8BX43, Q8C503, Q8IVY1, Q8K5A9, Q8N112, Q8NC24, Q8NDY8, Q8QZT4, Q8R138, Q969Z4, Q9BUF7, Q9CQM1

Diamond homologs: A0A5F4BST2, Q8QZT4, Q9BUF7, A0A1F4, A4FV93, D3ZHH1, F1RWC3, O60494, P00744, P07225, P10040, P49013, P53813, Q08761, Q0V8T4, Q28520, Q3KN41, Q5IJ48, Q6DCQ6, Q80YA8, Q8VHS2, Q9NYJ7, Q9NYQ8, Q9TU53, O14594, O35474, O75095, O88516, O88671, P16296, P18168, P55066, P55067, Q05793, Q0V8T7, Q5IS41, Q5ZQU0, Q70E20, Q8TER0, Q90953

SIGNOR signaling

1 interactions.

AEffectBMechanism
CRB3up-regulatesAMOT/MPP5/INADL/LIN7Cbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance23
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

407 predictions. Top by Δscore:

VariantEffectΔscore
19:6464779:GCAAA:Gdonor_gain1.0000
19:6464782:AA:Adonor_gain1.0000
19:6464784:G:GGdonor_gain1.0000
19:6465541:A:AGacceptor_gain1.0000
19:6465543:A:AGacceptor_gain1.0000
19:6465544:G:GTacceptor_gain1.0000
19:6465544:GT:Gacceptor_gain1.0000
19:6465544:GTAC:Gacceptor_gain1.0000
19:6465544:GTACA:Gacceptor_gain1.0000
19:6465617:TGG:Tdonor_loss1.0000
19:6465618:GGTG:Gdonor_loss1.0000
19:6466461:T:TAacceptor_gain1.0000
19:6466461:TGCA:Tacceptor_loss1.0000
19:6466462:GCAGC:Gacceptor_loss1.0000
19:6466464:A:AGacceptor_gain1.0000
19:6466464:AGC:Aacceptor_gain1.0000
19:6466465:G:GCacceptor_gain1.0000
19:6466465:GC:Gacceptor_gain1.0000
19:6466465:GCG:Gacceptor_gain1.0000
19:6466465:GCGT:Gacceptor_gain1.0000
19:6466465:GCGTC:Gacceptor_gain1.0000
19:6466509:T:Aacceptor_gain1.0000
19:6464327:C:Gdonor_gain0.9900
19:6464603:CCCA:Cacceptor_loss0.9900
19:6464604:CCA:Cacceptor_loss0.9900
19:6464605:CA:Cacceptor_loss0.9900
19:6464606:A:Cacceptor_loss0.9900
19:6464607:G:GAacceptor_loss0.9900
19:6465534:A:AGacceptor_gain0.9900
19:6465535:C:Gacceptor_gain0.9900

AlphaMissense

742 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:6466665:T:AL119H0.994
19:6466668:T:AI120N0.991
19:6466668:T:CI120T0.990
19:6466665:T:CL119P0.988
19:6466659:A:TE117V0.986
19:6466668:T:GI120S0.985
19:6466580:G:TG91C0.984
19:6466586:T:CY93H0.983
19:6466580:G:CG91R0.982
19:6466658:G:AE117K0.974
19:6466660:G:CE117D0.974
19:6466660:G:TE117D0.974
19:6466586:T:GY93D0.972
19:6466587:A:GY93C0.970
19:6466592:C:TP95S0.969
19:6466659:A:CE117A0.969
19:6466569:G:CR87P0.968
19:6466662:G:CR118P0.968
19:6466661:C:GR118G0.967
19:6466586:T:AY93N0.966
19:6466593:C:AP95H0.966
19:6466647:T:CL113S0.963
19:6466581:G:TG91V0.960
19:6466532:G:AG75R0.957
19:6466532:G:CG75R0.957
19:6466581:G:AG91D0.956
19:6466659:A:GE117G0.955
19:6466595:A:CS96R0.954
19:6466597:T:AS96R0.954
19:6466597:T:GS96R0.954

dbSNP variants (sampled 300 via entrez): RS1000198635 (19:6463272 G>A), RS1000646940 (19:6462581 G>A), RS1001386900 (19:6464650 G>A), RS1001412854 (19:6461876 G>A), RS1001421289 (19:6467408 T>C,G), RS1002317630 (19:6463742 GC>G), RS1002473038 (19:6466266 G>C), RS1003474893 (19:6465066 G>T), RS1004427090 (19:6463633 G>A), RS1004479449 (19:6463899 T>A), RS1004568393 (19:6463373 A>G), RS1004668734 (19:6467441 C>A), RS1004698440 (19:6467101 C>A,T), RS1005156152 (19:6462172 A>G), RS1005433925 (19:6462218 T>C)

Disease associations

OMIM: gene MIM:609737 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionaffects expression, increases expression4
Air Pollutantsdecreases expression, increases abundance, increases expression2
Cadmium Chloridedecreases expression, increases expression2
Particulate Matterincreases abundance, increases expression, decreases expression2
aristolochic acid Iincreases expression1
sulforaphanedecreases expression1
sodium arseniteincreases expression1
abrineincreases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Amiodaroneincreases expression1
Benzo(a)pyreneaffects methylation1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Estradiolaffects cotreatment, decreases expression1
Leadincreases expression1
Mustard Gasincreases expression1
Smokedecreases expression1
Lactic Aciddecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.