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LIMS3

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Summary

LIMS3 (LIM zinc finger domain containing 3, HGNC:30047) is a protein-coding gene on chromosome 2q13, encoding LIM and senescent cell antigen-like-containing domain protein 3 (P0CW19).

Predicted to enable metal ion binding activity. Predicted to be located in cytoplasm; focal adhesion; and plasma membrane.

Source: NCBI Gene 96626 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 7 total
  • MANE Select transcript: NM_001394901

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30047
Approved symbolLIMS3
NameLIM zinc finger domain containing 3
Location2q13
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000256977
Ensembl biotypeprotein_coding
Entrez96626

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000437679, ENST00000479168, ENST00000480744, ENST00000482065, ENST00000487150, ENST00000631420

RefSeq mRNA: 2 — MANE Select: NM_001394901 NM_001394901, NM_033514

CCDS: CCDS2084, CCDS92835

Canonical transcript exons

ENST00000480744 — 10 exons

ExonStartEnd
ENSE00001881392109919493109919643
ENSE00003531865109921640109921688
ENSE00003649046109920254109920346
ENSE00003661355109924348109924423
ENSE00003778577109924622109925625
ENSE00003780924109898688109898910
ENSE00003804221109916507109916656
ENSE00003804522109914411109914477
ENSE00003808582109915952109916072
ENSE00003808591109903253109903412

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 89.06.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endometriumUBERON:000129589.06gold quality
stromal cell of endometriumCL:000225586.53gold quality
ascending aortaUBERON:000149684.61gold quality
thoracic aortaUBERON:000151584.23gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.10gold quality
adrenal tissueUBERON:001830380.77gold quality
descending thoracic aortaUBERON:000234580.49gold quality
right uterine tubeUBERON:000130279.05gold quality
fallopian tubeUBERON:000388977.16gold quality
gastrocnemiusUBERON:000138876.59gold quality
hindlimb stylopod muscleUBERON:000425276.04gold quality
muscle of legUBERON:000138375.99gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099175.40gold quality
right coronary arteryUBERON:000162575.22gold quality
left coronary arteryUBERON:000162674.77gold quality
islet of LangerhansUBERON:000000674.57gold quality
popliteal arteryUBERON:000225074.16gold quality
tibial arteryUBERON:000761074.14gold quality
left adrenal gland cortexUBERON:003582573.36gold quality
adrenal glandUBERON:000236973.18gold quality
left uterine tubeUBERON:000130373.13gold quality
apex of heartUBERON:000209872.74gold quality
left adrenal glandUBERON:000123472.49gold quality
right atrium auricular regionUBERON:000663171.39gold quality
placentaUBERON:000198771.19gold quality
heartUBERON:000094870.88gold quality
right adrenal glandUBERON:000123370.77gold quality
metanephros cortexUBERON:001053370.58gold quality
smooth muscle tissueUBERON:000113570.11gold quality
heart left ventricleUBERON:000208469.63gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-6701yes17.10
E-MTAB-6678yes8.02
E-ANND-3yes5.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting LIMS3, 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-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-569699.9872.364487
HSA-MIR-552-5P99.9368.561583
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-627-3P99.9071.423316
HSA-MIR-449299.8768.253611
HSA-MIR-137-3P99.8774.742401
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-76299.5866.611994
HSA-MIR-4524A-5P99.5771.731193
HSA-MIR-4524B-5P99.5771.681195
HSA-MIR-516B-5P99.5666.331495
HSA-MIR-199A-5P99.5169.711107
HSA-MIR-199B-5P99.5169.741098
HSA-MIR-449899.4767.422360
HSA-MIR-429299.1665.571767
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-5001-5P99.0566.761972
HSA-MIR-4699-5P98.9967.501210
HSA-MIR-430398.0168.132304
HSA-MIR-320197.1665.421044
HSA-MIR-1287-5P96.8065.30743

Literature-anchored findings (GeneRIF, showing 1)

  • The full length of its cDNA was 963 bp, with a 354-bp open reading frame (ORF), encoding a 117-amino acid protein. PINCH 2 was a splicing isoform of PINCH. (PMID:17435276)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriolims2ENSDARG00000014976
danio_reriolims1ENSDARG00000026985
mus_musculusLims1ENSMUSG00000019920
rattus_norvegicusLims1ENSRNOG00000037765
drosophila_melanogasterstckFBGN0020249
drosophila_melanogasterZasp67FBGN0036044
caenorhabditis_elegansWBGENE00004030
caenorhabditis_elegansWBGENE00006826

Paralogs (3): LIMS2 (ENSG00000072163), LIMS1 (ENSG00000169756), LIMS4 (ENSG00000256671)

Protein

Protein identifiers

LIM and senescent cell antigen-like-containing domain protein 3 — P0CW19 (reviewed: P0CW19)

Alternative names: Particularly interesting new Cys-His protein 3

All UniProt accessions (3): A0A0J9YXC7, A0A0J9YYC1, P0CW19

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Detected in testis.

Isoforms (2)

UniProt IDNamesCanonical?
P0CW19-11yes
P0CW19-22

RefSeq proteins (2): NP_001381830, NP_277049 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001781Znf_LIMDomain
IPR017351PINCH-1-4-likeFamily

Pfam: PF00412

UniProt features (3 total): chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P0CW19-F173.650.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): MODULE_503, MODULE_195, MODULE_147, MODULE_356, PEDRIOLI_MIR31_TARGETS_UP, TRAYNOR_RETT_SYNDROM_UP, MIR4492, MIR4524A_5P, MIR4524B_5P, GSE11057_NAIVE_VS_EFF_MEMORY_CD4_TCELL_DN, GSE11057_NAIVE_VS_MEMORY_CD4_TCELL_DN, GSE11864_CSF1_VS_CSF1_IFNG_IN_MAC_DN, MIR4699_5P, MIR1287_5P, MANNE_COVID19_NONICU_VS_HEALTHY_DONOR_PLATELETS_DN

GO Biological Process (2): cell surface receptor signaling pathway (GO:0007166), positive regulation of signal transduction (GO:0009967)

GO Molecular Function (2): metal ion binding (GO:0046872), actin binding (GO:0003779)

GO Cellular Component (5): cytoplasm (GO:0005737), plasma membrane (GO:0005886), focal adhesion (GO:0005925), membrane (GO:0016020), anchoring junction (GO:0070161)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
signal transduction2
cellular anatomical structure2
regulation of signal transduction1
positive regulation of cell communication1
positive regulation of signaling1
positive regulation of response to stimulus1
cation binding1
cytoskeletal protein binding1
intracellular anatomical structure1
membrane1
cell periphery1
cell-substrate junction1
cell junction1

Protein interactions and networks

STRING

286 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LIMS3RGPD5Q99666651
LIMS3H3BVE0H3BVE0544
LIMS3RSPH10B2B2RC85447
LIMS3CCDC54Q8NEL0432
LIMS3TSACCQ96A04432
LIMS3C11orf71Q6IPW1417
LIMS3C22orf23Q9BZE7399
LIMS3RIMBP3CA6NJZ7399
LIMS3FSCBQ5H9T9392
LIMS3ZNF404Q494X3375
LIMS3ANKRD7Q92527370
LIMS3NPHP1O15259370
LIMS3CATSPERTQ53TS8370
LIMS3ZC3H6P61129359
LIMS3GKAP1Q5VSY0354

IntAct

2 interactions, top by confidence:

ABTypeScore
ECE1LIMS3psi-mi:“MI:0915”(physical association)0.370

BioGRID (25): LIMS3 (Two-hybrid), LIMS3 (Two-hybrid), LIMS3L (Two-hybrid), LIMS3 (Two-hybrid), LIMS3L (Two-hybrid), LIMS3 (Two-hybrid), LIMS3L (Two-hybrid), LIMS3 (Two-hybrid), LIMS3L (Two-hybrid), LIMS3 (Two-hybrid), LIMS3L (Two-hybrid), LIMS3 (Two-hybrid), LIMS3L (Two-hybrid), LIMS3 (Two-hybrid), LIMS3L (Two-hybrid)

ESM2 similar proteins: B6H6F3, B8NLZ3, C8VDQ4, E5DG73, G4NEB8, O14448, O42794, O54992, O59922, O95259, P0CW19, P0CW20, P25908, P28348, P32023, P52959, P86244, P93025, Q01386, Q03043, Q0U822, Q14123, Q2QYY8, Q2RBR1, Q2UPB6, Q4IJ84, Q4WCV3, Q4WPU8, Q4WQL0, Q4X1A8, Q5RF96, Q5ZKK1, Q60603, Q63421, Q64338, Q6DC61, Q7S1P9, Q7TX80, Q86ZN7, Q8INB9

Diamond homologs: A5H447, P0CW19, P0CW20, P48059, P50464, Q0VA45, Q15942, Q2KJ33, Q7Z4I7, Q91XD2, Q99JW4, A1Z6W3, A1ZA47, B5DEH0, B7ZUL2, E1BKA3, G5E5X0, O42565, O43294, O60711, O74398, O75112, P25791, P25800, P25801, P36202, P49023, P49024, P50212, P50479, P50480, P53406, P53407, P53408, P53409, P70271, Q06BR1, Q07E40, Q09476, Q174I2

SIGNOR signaling

1 interactions.

AEffectBMechanism
LIMS3“form complex”“IPP complex”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance5
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

917 predictions. Top by Δscore:

VariantEffectΔscore
2:109898871:TGA:Tdonor_gain1.0000
2:109898884:G:GTdonor_gain1.0000
2:109898906:AAATT:Adonor_gain1.0000
2:109898907:AATT:Adonor_gain1.0000
2:109898908:ATT:Adonor_gain1.0000
2:109898909:TT:Tdonor_gain1.0000
2:109898910:TG:Tdonor_loss1.0000
2:109898911:G:GGdonor_gain1.0000
2:109898912:TGAG:Tdonor_loss1.0000
2:109903243:C:CAacceptor_gain1.0000
2:109903245:T:TAacceptor_gain1.0000
2:109903251:A:AGacceptor_gain1.0000
2:109903252:G:GAacceptor_gain1.0000
2:109903252:GC:Gacceptor_gain1.0000
2:109903252:GCA:Gacceptor_gain1.0000
2:109903252:GCAA:Gacceptor_gain1.0000
2:109903252:GCAAC:Gacceptor_gain1.0000
2:109903410:GAG:Gdonor_gain1.0000
2:109903413:G:GGdonor_gain1.0000
2:109903414:T:Gdonor_loss1.0000
2:109915939:T:Aacceptor_gain1.0000
2:109915948:A:AGacceptor_gain1.0000
2:109915948:ACAG:Aacceptor_gain1.0000
2:109915949:C:Gacceptor_gain1.0000
2:109915949:CAGG:Cacceptor_loss1.0000
2:109915950:A:AGacceptor_gain1.0000
2:109915950:AG:Aacceptor_gain1.0000
2:109915950:AGGT:Aacceptor_gain1.0000
2:109915951:G:Aacceptor_gain1.0000
2:109915951:G:GAacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1005579223 (2:109918035 C>G,T), RS1018746136 (2:109918055 T>C), RS1045007142 (2:109909210 A>G), RS1046064705 (2:109914514 T>A,C), RS1047215453 (2:109915194 T>C), RS1053971610 (2:109913883 G>A,C), RS112366401 (2:109914018 T>G), RS1132994 (2:109905883 C>T), RS113434358 (2:109917082 T>C), RS113458393 (2:109924100 G>A), RS11491326 (2:109905325 A>G), RS1157015209 (2:109924021 G>A), RS1158051502 (2:109912648 C>A), RS1158189225 (2:109924377 G>A), RS1158381685 (2:109914616 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:187500

GenCC curated gene-disease

Mondo (1): tetralogy of fallot (MONDO:0008542)

Orphanet (1): Tetralogy of Fallot (Orphanet:3303)

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST002929_12Chromium levels6.000000e-06

MeSH disease descriptors (1)

DescriptorNameTree numbers
D013771Tetralogy of FallotC14.240.400.849; C14.280.400.849; C16.131.240.400.849

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

ChemicalActions (top 5)PubMed papers
Doxorubicindecreases expression, increases expression2
CGP 52608affects binding, increases reaction1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
(+)-JQ1 compounddecreases expression1
Arsenic Trioxideincreases expression1
Amiodaroneincreases expression1
Diethylhexyl Phthalateincreases expression1
Plant Oilsincreases expression1
Rifampindecreases expression1
Silicon Dioxideincreases expression1
Tetrachlorodibenzodioxindecreases expression1
Copper Sulfateincreases expression1
Magnetite Nanoparticlesincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01971593PHASE4TERMINATEDThe Effects of Eplerenone on Markers of Myocardial Fibrosis in Adult Congenital Heart Disease
NCT00564993PHASE3TERMINATEDCardiac Function Under Stress for Early Detection of the Right Ventricular Insufficiency After Repair of Tetralogy of Fallot
NCT00848393PHASE2COMPLETEDMeasures to Lower the Stress Response in Pediatric Cardiac Surgery
NCT02010905PHASE2UNKNOWNRight Ventricular Dysfunction in Tetralogy of Fallot: Inhibition of the Renin-angiotensin-aldosterone System
NCT00573066PHASE1COMPLETEDUnderstanding Dexmedetomidine In Infants Post-Operative From Cardiac Surgery
NCT01915277PHASE1COMPLETEDA Phase I Study of Dexmedetomidine Bolus and Infusion in Corrective Infant Cardiac Surgery: Safety and Pharmacokinetics
NCT04713657PHASE1RECRUITINGBeta-blocker Administration for Cardiomyocyte Division
NCT02590679PHASE2/PHASE3UNKNOWNMulti-center Trial of Percutaneous Pulmonary Valve Implantation With Venus-p
NCT05579964PHASE2/PHASE3COMPLETEDThe Role of Dexmedetomidine as Myocardial Protector in Pediatric Cardiac Surgery Total Correction of Tetralogy of Fallot
NCT05186415PHASE1/PHASE2COMPLETEDContrast Enhanced 3D Echocardiographic Quantification of Right Ventricular Volumes in Repaired CHD
NCT07194304EARLY_PHASE1COMPLETEDEffect of Parenteral Alpha-Tocopherol in the Definitive Surgery of Tetralogy of Fallot
NCT00004361Not specifiedCOMPLETEDStudy of the Relationship Between Calcium Levels and Intact Parathyroid Hormone (iPTH) in Adults With Repaired or Palliated Conotruncal Cardiac Defects
NCT00005190Not specifiedCOMPLETEDReproduction and Survival After Cardiac Defect Repair
NCT00112320Not specifiedCOMPLETEDComparison of Two Pulmonary Valve Replacement Methods to Treat Tetralogy of Fallot
NCT00155428Not specifiedUNKNOWNBiomodel in Tetralogy of Fallot
NCT00243776Not specifiedRECRUITINGMolecular and Cellular Characterization of Cardiac Tissue in Postnatal Development
NCT00266188Not specifiedCOMPLETEDFollow up of Post-repair Tetralogy of Fallot
NCT00412685Not specifiedCOMPLETEDMyocardial Contrast Echocardiography in Congenital Heart Disease
NCT00536432Not specifiedCOMPLETEDEarly Re-intervention in Infants and Small Children After Correction of Tetralogy of Fallot
NCT00860327Not specifiedTERMINATEDExamining Developmental Changes in Heart Contractions of Children With Congenital Heart Defects
NCT01419756Not specifiedCOMPLETEDAssessment of Right Ventricular Volume in Tetralogy of Fallott (TOF) Patients
NCT01762124Not specifiedCOMPLETEDStudy of the Native Outflow Tract Transcatheter Pulmonary Valve (TPV)
NCT01824160Not specifiedCOMPLETEDPulmonary Artery Repair With Covered Stents
NCT01941576Not specifiedCOMPLETEDEffects of rhBNP in Pediatrics After Corrective Repair of Tetralogy Of Fallot
NCT02161471Not specifiedCOMPLETEDHaemodynamics and Function of the Atria in Congenital Heart Disease by Cardiovascular Magnetic Resonance
NCT02364934Not specifiedUNKNOWNPharmacokinetics and Pharmacodynamics of Rocuronium in Closed-Loop Infusion System
NCT02534792Not specifiedCOMPLETEDEarly Revalvulation After Fallot Repair Improves Clinical Outcome
NCT02586740Not specifiedCOMPLETEDRetrospective Review of Anesthetic Considerations for Pulmonary Artery Rehabilitation
NCT02643810Not specifiedCOMPLETEDExercise Training in Adults With Corrected Tetralogy of Fallot
NCT02967315Not specifiedCOMPLETEDEffects of Changes in Fluid Status on Right Ventricular Volumes and Function
NCT02968264Not specifiedCOMPLETEDTetralogy of Fallot for Life
NCT02980614Not specifiedUNKNOWN4D Velocity Mapping of the Heart in rTOF Patients
NCT03049995Not specifiedUNKNOWNStress Echo 2020 - The International Stress Echo Study
NCT03130777Not specifiedACTIVE_NOT_RECRUITINGALTERRA: SAPIEN 3 THV With the Alterra Adaptive Prestent
NCT03234582Not specifiedUNKNOWNComparison of RVOT Gradient Under Anaesthesia With Post-operative Gradient in Patients Undergoing TOF Repair
NCT03275844Not specifiedUNKNOWNPhysical Capacity and Activity in Children With Congenital Heart Disease
NCT03441971Not specifiedACTIVE_NOT_RECRUITINGEvaluation of the GORE PV1 Device in Patients With Pulmonary Valve Dysfunction
NCT03470064Not specifiedUNKNOWNEarly Right Ventricular Function After Repair Of Tetralogy Of Fallot , An Evidence Based Study.
NCT03568357Not specifiedUNKNOWNReoxygenation for Cyanotic Pediatric CHD
NCT03634072Not specifiedTERMINATEDPediatric REPlAcement of the PulmonaRy ValvE in Tetralogy of Fallot -
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): tetralogy of fallot

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
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This page pulls from 74 datasets indexed by BioBTree:

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