CGN

gene
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Also known as KIAA1319

Summary

CGN (cingulin, HGNC:17429) is a protein-coding gene on chromosome 1q21.3, encoding Cingulin (Q9P2M7). Probably plays a role in the formation and regulation of the tight junction (TJ) paracellular permeability barrier.

Enables cadherin binding activity. Predicted to be involved in microtubule cytoskeleton organization. Predicted to act upstream of or within bicellular tight junction assembly and epithelial cell morphogenesis. Located in bicellular tight junction and plasma membrane.

Source: NCBI Gene 57530 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 223 total
  • MANE Select transcript: NM_020770

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17429
Approved symbolCGN
Namecingulin
Location1q21.3
Locus typegene with protein product
StatusApproved
AliasesKIAA1319
Ensembl geneENSG00000143375
Ensembl biotypeprotein_coding
OMIM609473
Entrez57530

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 14 protein_coding, 3 retained_intron

ENST00000271636, ENST00000416743, ENST00000427934, ENST00000464886, ENST00000467998, ENST00000473377, ENST00000502442, ENST00000505188, ENST00000879038, ENST00000879039, ENST00000879040, ENST00000879041, ENST00000928061, ENST00000928062, ENST00000928063, ENST00000928064, ENST00000962862

RefSeq mRNA: 1 — MANE Select: NM_020770 NM_020770

CCDS: CCDS999

Canonical transcript exons

ENST00000271636 — 21 exons

ExonStartEnd
ENSE00000959670151520166151520266
ENSE00000959671151520414151520483
ENSE00000959672151520596151520691
ENSE00000959674151524226151524358
ENSE00000959675151524674151524886
ENSE00000959676151525642151525790
ENSE00000959680151530489151530746
ENSE00000959681151532402151532572
ENSE00000959682151533975151534136
ENSE00000959683151535042151535131
ENSE00001436343151529350151529559
ENSE00001436384151529909151530115
ENSE00001596393151511387151511515
ENSE00003463739151536237151536345
ENSE00003501439151536730151536893
ENSE00003562037151535780151535898
ENSE00003568370151526975151527107
ENSE00003604275151535600151535683
ENSE00003653528151537205151538692
ENSE00003786637151523434151523561
ENSE00003796769151518506151519392

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 98.79.

FANTOM5 (CAGE): breadth broad, TPM avg 2.5339 / max 63.5436, expressed in 622 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
52291.6297525
52280.6394313
52300.2648158

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207998.79gold quality
ileal mucosaUBERON:000033197.68gold quality
mucosa of transverse colonUBERON:000499197.29gold quality
right uterine tubeUBERON:000130295.75gold quality
body of pancreasUBERON:000115095.29gold quality
rectumUBERON:000105294.91gold quality
right lobe of liverUBERON:000111494.80gold quality
metanephros cortexUBERON:001053393.56gold quality
duodenumUBERON:000211493.25gold quality
upper lobe of left lungUBERON:000895292.80gold quality
right lungUBERON:000216792.29gold quality
lower esophagus mucosaUBERON:003583492.26gold quality
sural nerveUBERON:001548892.17gold quality
secondary oocyteCL:000065592.01gold quality
pancreasUBERON:000126491.95gold quality
olfactory segment of nasal mucosaUBERON:000538691.95gold quality
upper lobe of lungUBERON:000894891.91gold quality
skin of legUBERON:000151191.77gold quality
jejunal mucosaUBERON:000039991.51gold quality
minor salivary glandUBERON:000183091.49gold quality
liverUBERON:000210791.18gold quality
oviduct epitheliumUBERON:000480491.13gold quality
skin of abdomenUBERON:000141690.98gold quality
right hemisphere of cerebellumUBERON:001489090.84gold quality
cerebellar hemisphereUBERON:000224590.33gold quality
cerebellar cortexUBERON:000212990.10gold quality
transverse colonUBERON:000115789.76gold quality
oocyteCL:000002389.50gold quality
colonic mucosaUBERON:000031789.50gold quality
small intestine Peyer’s patchUBERON:000345489.42gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes11.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting CGN, 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-4533100.0069.482758
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-3162-3P100.0065.37363
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-3689D100.0066.141181
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-3163100.0077.238605
HSA-MIR-511-3P99.9968.851467
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-453199.9969.703181
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-477599.9875.006394
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-807599.9767.20962
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-9-3P99.9670.882068
HSA-MIR-391099.9571.132227
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-345-3P99.8970.231421
HSA-MIR-391999.8769.452489

Literature-anchored findings (GeneRIF, showing 10)

  • Cingulin (KIAA1319 protein) is localized in the cytoplasmic domain of vertebrate epithelial tight junctions, and it interacts with other tight junction proteins such as ZO-1, and with the actomyosin cytoskeleton. (PMID:11042084)
  • Results indicate that cells underwent EMT exhibited overactive TGFbeta signaling and loss of expression of the CDH1, CGN, CLDN4, and KLK10 genes as a result of hypermethylation of their corresponding promoter regions. (PMID:20086175)
  • Co-imunoprecipitation and confocal microscopy experiments also revealed the tight junction protein cingulin as a new interacting partner of Ubn-1 (PMID:22245583)
  • MgcRacGAP colocalizes with CGN and CGNL1 at TJs and forms a complex and interacts directly in vitro with CGN and CGNL1. (PMID:24807907)
  • Cingulin modulates barrier function in endothelium. (PMID:26821949)
  • Down-regulation of Cingulin Augments Thrombin-induced Endothelial Barrier Disruption. (PMID:27590342)
  • Phosphorylated cingulin localises GEF-H1 at tight junctions to protect vascular barriers in blood endothelial cells. (PMID:34345888)
  • miR-1270 enhances the proliferation, migration, and invasion of osteosarcoma via targeting cingulin. (PMID:34873899)
  • Cingulin regulates hair cell cuticular plate morphology and is required for hearing in human and mouse. (PMID:37691516)
  • The Roles and Regulatory Mechanisms of Tight Junction Protein Cingulin and Transcription Factor Forkhead Box Protein O1 in Human Lung Adenocarcinoma A549 Cells and Normal Lung Epithelial Cells. (PMID:38338691)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocgnaENSDARG00000055607
danio_reriocgnbENSDARG00000058690
mus_musculusCgnENSMUSG00000068876

Paralogs (44): MYH13 (ENSG00000006788), MYO16 (ENSG00000041515), MYO9A (ENSG00000066933), MYO3B (ENSG00000071909), MYH7B (ENSG00000078814), MYO15A (ENSG00000091536), MYH7 (ENSG00000092054), MYO3A (ENSG00000095777), MYO9B (ENSG00000099331), MYH9 (ENSG00000100345), MYH14 (ENSG00000105357), MYH1 (ENSG00000109061), MYH3 (ENSG00000109063), MYH2 (ENSG00000125414), MYO1B (ENSG00000128641), MYO5C (ENSG00000128833), CGNL1 (ENSG00000128849), MYH8 (ENSG00000133020), MYH10 (ENSG00000133026), MYH11 (ENSG00000133392), MYO18B (ENSG00000133454), CCDC102A (ENSG00000135736), MYO1G (ENSG00000136286), MYO7A (ENSG00000137474), MYO1F (ENSG00000142347), TMF1 (ENSG00000144747), MYH15 (ENSG00000144821), MYO10 (ENSG00000145555), CCDC102B (ENSG00000150636), MYO1E (ENSG00000157483), CCDC158 (ENSG00000163749), MYO1A (ENSG00000166866), MYO5B (ENSG00000167306), MYO7B (ENSG00000169994), MYO1H (ENSG00000174527), MYO1D (ENSG00000176658), MYO18A (ENSG00000196535), MYO6 (ENSG00000196586), MYO5A (ENSG00000197535), MYH6 (ENSG00000197616)

Protein

Protein identifiers

CingulinQ9P2M7 (reviewed: Q9P2M7)

All UniProt accessions (4): Q9P2M7, A2A3M4, A6PVU7, H0Y4A8

UniProt curated annotations — full annotation on UniProt →

Function. Probably plays a role in the formation and regulation of the tight junction (TJ) paracellular permeability barrier.

Subunit / interactions. Homodimer. Interacts with TJP1/ZO1. Interacts with SPEF1.

Subcellular location. Cell junction. Tight junction.

Tissue specificity. Localized on the cytoplasmic face of tight junctions of polarized epithelia and some endothelia. Expressed in pancreas, kidney, liver and lung, but not in skeletal muscle, placenta, brain or heart.

Domain organisation. Deletion of the TJP1/ZO1 interaction motif (ZIM) decreases but does not abolish colocalization with TJP1/ZO1.

Miscellaneous. May be due to an intron retention.

Similarity. Belongs to the cingulin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9P2M7-11yes
Q9P2M7-22

RefSeq proteins (1): NP_065821* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002928Myosin_tailDomain

Pfam: PF01576

UniProt features (35 total): modified residue 18, region of interest 8, compositionally biased region 3, splice variant 2, chain 1, short sequence motif 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P2M7-F170.440.39

Functional residue map

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

Post-translational modifications (18): 95, 96, 135, 137, 140, 155, 165, 214, 217, 258, 276, 338, 351, 579, 712, 1175, 1176, 1182

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2173791TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)

MSigDB gene sets: 144 (showing top): REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX, ATACCTC_MIR202, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, KEGG_TIGHT_JUNCTION, TGACCTY_ERR1_Q2, CHX10_01, USF_C, NFKB_Q6, GTGCCTT_MIR506, TCF4_Q5, CEBP_Q2, NKX62_Q2, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, WANG_LMO4_TARGETS_DN, USF_01

GO Biological Process (1): microtubule cytoskeleton organization (GO:0000226)

GO Molecular Function (4): actin binding (GO:0003779), microtubule binding (GO:0008017), cadherin binding (GO:0045296), protein binding (GO:0005515)

GO Cellular Component (5): plasma membrane (GO:0005886), bicellular tight junction (GO:0005923), myosin complex (GO:0016459), cell junction (GO:0030054), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Signaling by TGF-beta Receptor Complex1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoskeleton organization1
microtubule-based process1
cytoskeletal protein binding1
tubulin binding1
cell adhesion molecule binding1
binding1
membrane1
cell periphery1
apical junction complex1
tight junction1
actin cytoskeleton1
protein-containing complex1
cellular anatomical structure1
cell junction1

Protein interactions and networks

STRING

975 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CGNTJP2Q9UDY2999
CGNTJP1Q07157998
CGNTJP3O95049997
CGNOCLNQ16625995
CGNMARVELD2Q8N4S9987
CGNAFDNP55196975
CGNF11RQ9Y624963
CGNARHGEF2Q92974947
CGNA0A087WZG4A0A087WZG4923
CGNARHGEF18Q6ZSZ5923
CGNRACGAP1Q9H0H5919
CGNSYMPKQ92797854
CGNMPDZO75970854
CGNASH1LQ9NR48847
CGNPLEKHA7Q6IQ23783

IntAct

292 interactions, top by confidence:

ABTypeScore
YWHAHABLIM1psi-mi:“MI:0914”(association)0.800
CGNYWHAQpsi-mi:“MI:0914”(association)0.710
CGNYWHAEpsi-mi:“MI:0914”(association)0.710
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
YWHABBLTP3Bpsi-mi:“MI:2364”(proximity)0.610
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
YWHAQIGLC7psi-mi:“MI:0914”(association)0.530
YWHAZBLTP3Bpsi-mi:“MI:0914”(association)0.530
YWHABPLEKHG3psi-mi:“MI:0914”(association)0.480
YWHAQPLEKHG3psi-mi:“MI:0914”(association)0.480
L1TD1PARP1psi-mi:“MI:0914”(association)0.460
ESR2FBLL1psi-mi:“MI:0914”(association)0.460
CGNSNX27psi-mi:“MI:0407”(direct interaction)0.440
CGNRHPN1psi-mi:“MI:0407”(direct interaction)0.440
CGNPATJpsi-mi:“MI:0407”(direct interaction)0.440
CGNPDZD2psi-mi:“MI:0407”(direct interaction)0.440
CGNTAMALINpsi-mi:“MI:0407”(direct interaction)0.440
CGNAPBA3psi-mi:“MI:0407”(direct interaction)0.440
AHNAKCGNpsi-mi:“MI:0407”(direct interaction)0.440
CGNAPBA1psi-mi:“MI:0407”(direct interaction)0.440
CGNAPBA2psi-mi:“MI:0407”(direct interaction)0.440
CGNARHGEF11psi-mi:“MI:0407”(direct interaction)0.440
CGNCARD11psi-mi:“MI:0407”(direct interaction)0.440
CGNCASKpsi-mi:“MI:0407”(direct interaction)0.440
CGNWHRNpsi-mi:“MI:0407”(direct interaction)0.440
WHRNCGNpsi-mi:“MI:0407”(direct interaction)0.440

BioGRID (198): CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Affinity Capture-MS), CGN (Proximity Label-MS), CGN (Proximity Label-MS), YWHAZ (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8QCI3, A0JMK8, A3KGV1, A7YH32, A9X1A5, B0KWC9, B6MFW3, B8JK76, G5E861, G9G127, O35550, O35551, P59242, P85120, Q15276, Q3V6T2, Q502I3, Q5BJF6, Q5RG45, Q5SNZ0, Q5TZ80, Q5ZJ27, Q5ZKK5, Q66GS9, Q66KE8, Q6AYX5, Q6DIX6, Q6NRB0, Q6P402, Q6P5D4, Q6PGZ0, Q6VGS5, Q6ZU80, Q7TMK6, Q80UF4, Q80YF0, Q80YT7, Q86SQ7, Q8BIL5, Q8CJ99

Diamond homologs: A7YH32, A9X1A5, B0KWC9, B1MTG4, B1WB65, B3EX63, P14105, P59242, Q0VF96, Q1L8T5, Q6AW69, Q99105, Q9P2M7, Q9PTD7, P35579, Q258K2, P10587, P35580, P35749, P12844, O08638, P35748, Q27991, Q61879, Q62812, Q63862, Q6URW6, Q7Z406, Q8VDD5, Q99323, Q9JLT0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 179 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex949.1×2e-11
Activation of BAD and translocation to mitochondria743.3×9e-09
SARS-CoV-1 targets host intracellular signalling and regulatory pathways738.2×2e-08
Activation of BH3-only proteins728.3×2e-07
RHO GTPases activate PKNs1025.8×9e-10
Intrinsic Pathway for Apoptosis716.7×7e-06
FOXO-mediated transcription513.7×6e-04
Neurexins and neuroligins812.8×7e-06

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity620.9×2e-04
regulation of postsynaptic membrane neurotransmitter receptor levels720.8×4e-05
protein targeting613.2×1e-03
negative regulation of translation78.2×4e-03
cellular response to insulin stimulus77.1×7e-03
intracellular protein localization95.6×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance193
Likely benign11
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2777 predictions. Top by Δscore:

VariantEffectΔscore
1:151511513:AGGGT:Adonor_loss1.0000
1:151511514:GG:Gdonor_gain1.0000
1:151511515:GG:Gdonor_gain1.0000
1:151511516:G:Cdonor_loss1.0000
1:151511516:G:GGdonor_gain1.0000
1:151518501:TCTA:Tacceptor_loss1.0000
1:151518502:CTAG:Cacceptor_loss1.0000
1:151518503:TA:Tacceptor_loss1.0000
1:151518504:A:AGacceptor_gain1.0000
1:151518504:AGG:Aacceptor_loss1.0000
1:151518505:G:Aacceptor_loss1.0000
1:151518505:G:GGacceptor_gain1.0000
1:151520165:GTTC:Gacceptor_gain1.0000
1:151520262:GAGGG:Gdonor_gain1.0000
1:151520264:GGG:Gdonor_gain1.0000
1:151520264:GGGGT:Gdonor_loss1.0000
1:151520265:GGG:Gdonor_gain1.0000
1:151520266:GGTG:Gdonor_loss1.0000
1:151520267:GTGA:Gdonor_loss1.0000
1:151520268:T:Gdonor_loss1.0000
1:151520412:A:AGacceptor_gain1.0000
1:151520413:G:GGacceptor_gain1.0000
1:151520413:GA:Gacceptor_gain1.0000
1:151520413:GAA:Gacceptor_gain1.0000
1:151520594:AGAT:Aacceptor_gain1.0000
1:151520595:GATG:Gacceptor_gain1.0000
1:151523431:CA:Cacceptor_loss1.0000
1:151523432:A:ACacceptor_loss1.0000
1:151523432:A:AGacceptor_gain1.0000
1:151523433:G:GGacceptor_gain1.0000

AlphaMissense

7764 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000081141 (1:151531089 C>T), RS1000092828 (1:151512989 G>A), RS1000264401 (1:151516891 G>A), RS1000361976 (1:151509998 TAA>T,TA,TAAA,TAAAA), RS1000396748 (1:151509883 TAAA>T,TAA,TAAAA), RS1000455130 (1:151513191 C>A), RS1000503726 (1:151513538 C>T), RS1000541504 (1:151536936 G>A), RS1000594811 (1:151529326 A>G), RS1000807834 (1:151523245 A>G), RS1000947518 (1:151527234 G>A), RS1000957308 (1:151527575 G>A), RS1001086290 (1:151519843 A>G), RS1001149383 (1:151532878 C>T), RS1001309705 (1:151526461 C>A)

Disease associations

OMIM: gene MIM:609473 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST005951_38Body mass index4.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004340body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

50 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, decreases methylation, affects cotreatment6
Estradioldecreases expression, increases reaction, affects binding, increases expression, affects cotreatment4
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment, decreases expression3
Benzo(a)pyrenedecreases expression, decreases methylation3
Tobacco Smoke Pollutionaffects expression, decreases expression, increases expression3
Cyclosporinedecreases expression3
Particulate Matterdecreases expression, increases abundance, increases expression3
methylmercuric chlorideaffects cotreatment, increases expression2
Air Pollutantsincreases abundance, increases expression, decreases expression2
Phenobarbitalaffects expression, decreases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Aflatoxin B1affects expression, decreases expression, increases methylation2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
propionaldehydeincreases expression1
bisphenol Adecreases expression1
sodium arsenatedecreases expression, increases abundance1
afimoxifenedecreases expression, decreases reaction1
butyraldehydeincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
pentanalincreases expression1
dorsomorphinaffects cotreatment, increases expression1
5-(2,4-dihydroxy-5-isopropylphenyl)-4-(4-morpholin-4-ylmethylphenyl)isoxazole-3-carboxylic acid ethylamidedecreases expression1
bisphenol Sdecreases methylation1
jinfukangdecreases expression, affects cotreatment1
LDN 193189decreases expression, affects cotreatment1
Rosiglitazonedecreases expression1
Temozolomideincreases expression1
Zoledronic Aciddecreases expression1
Acetaminophendecreases 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.