This gene encodes an eye lens-specific protein found at the junctions of lens fiber cells, where it may contribute to cell junctional organization. It acts as a receptor for calmodulin, and may play an important role in both lens development and cataractogenesis. Mutations in this gene have been associated with cataract formation. Alternatively spliced transcript variants encod... See more...

Aliases for LIM2 Gene

Aliases for LIM2 Gene

  • Lens Intrinsic Membrane Protein 2 2 3 5
  • MP19 2 3 4
  • Lens Intrinsic Membrane Protein 2, 19kDa 2 3
  • Lens Fiber Membrane Intrinsic Protein 3 4
  • MP17 2 3
  • MP18 3 4
  • MP20 3 4
  • Lens Intrinsic Membrane Protein 2 (19kD) 2
  • CTRCT19 3
  • LIM2 5

External Ids for LIM2 Gene

Previous GeneCards Identifiers for LIM2 Gene

  • GC19M052513
  • GC19M052244
  • GC19M056559
  • GC19M056574
  • GC19M051887
  • GC19M048215

Summaries for LIM2 Gene

Entrez Gene Summary for LIM2 Gene

  • This gene encodes an eye lens-specific protein found at the junctions of lens fiber cells, where it may contribute to cell junctional organization. It acts as a receptor for calmodulin, and may play an important role in both lens development and cataractogenesis. Mutations in this gene have been associated with cataract formation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

GeneCards Summary for LIM2 Gene

LIM2 (Lens Intrinsic Membrane Protein 2) is a Protein Coding gene. Diseases associated with LIM2 include Cataract 19, Multiple Types and Cataract. Gene Ontology (GO) annotations related to this gene include structural constituent of eye lens. An important paralog of this gene is CLDND2.

UniProtKB/Swiss-Prot Summary for LIM2 Gene

  • Present in the thicker 16-17 nm junctions of mammalian lens fiber cells, where it may contribute to cell junctional organization. Acts as a receptor for calmodulin. May play an important role in both lens development and cataractogenesis.

Gene Wiki entry for LIM2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LIM2 Gene

Genomics for LIM2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LIM2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J051386 Promoter/Enhancer 1.1 EPDnew ENCODE CraniofacialAtlas 250.7 +0.4 376 1.4 IKZF1 FOXA2 SAP130 ETV4 RARA TEAD3 SOX5 NR2F1 RFX1 NR2F6 HSALNG0127211 LIM2 LOC105372446 C19orf84 NKG7
GH19J051388 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 0.7 -2.2 -2248 3.2 TBP IKZF1 SMAD5 ZIC2 THAP11 GTF2E2 VEZF1 SMAD4 SAP130 TRIM25 C19orf84 HSALNG0127212 SHANK1 SYT3 IGLON5 LRRC4B LIM2 LOC105372446
GH19J051380 Enhancer 1 Ensembl ENCODE 0.4 +7.0 7010 1.2 IKZF1 ZNF610 ARNT ZFP91 ZNF316 ADNP FOSL1 PRDM10 NFE2 MLLT1 LIM2 NKG7 LOC105372446 HSALNG0127210
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIM2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LIM2

Top Transcription factor binding sites by QIAGEN in the LIM2 gene promoter:
  • HSF1 (long)
  • HSF1short
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • Pax-5
  • Pax-6
  • POU3F1

Genomic Locations for LIM2 Gene

Latest Assembly
chr19:51,379,909-51,387,974
(GRCh38/hg38)
Size:
8,066 bases
Orientation:
Minus strand

Previous Assembly
chr19:51,883,163-51,891,228
(GRCh37/hg19 by Entrez Gene)
Size:
8,066 bases
Orientation:
Minus strand

chr19:51,883,163-51,891,214
(GRCh37/hg19 by Ensembl)
Size:
8,052 bases
Orientation:
Minus strand

Genomic View for LIM2 Gene

Genes around LIM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIM2 Gene

Proteins for LIM2 Gene

  • Protein details for LIM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P55344-LMIP_HUMAN
    Recommended name:
    Lens fiber membrane intrinsic protein
    Protein Accession:
    P55344
    Secondary Accessions:
    • Q6B083
    • Q9BXD0
    • Q9HAR5

    Protein attributes for LIM2 Gene

    Size:
    173 amino acids
    Molecular mass:
    19674 Da
    Quaternary structure:
    • Seems to be associated with itself or another lens membrane component via disulfide bonds.

    Alternative splice isoforms for LIM2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIM2 Gene

Post-translational modifications for LIM2 Gene

  • Glycosylation at Trp43, Trp61, and Asn62
  • Modification sites at PhosphoSitePlus

Other Protein References for LIM2 Gene

No data available for DME Specific Peptides for LIM2 Gene

Domains & Families for LIM2 Gene

Gene Families for LIM2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for LIM2 Gene

InterPro:
Blocks:
  • PMP-22/EMP/MP20 family
  • Lens fibre membrane intrinsic protein (LMIP) signature
ProtoNet:

Suggested Antigen Peptide Sequences for LIM2 Gene

GenScript: Design optimal peptide antigens:
  • MP20 (LMIP_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P55344

UniProtKB/Swiss-Prot:

LMIP_HUMAN :
  • Belongs to the PMP-22/EMP/MP20 family.
Family:
  • Belongs to the PMP-22/EMP/MP20 family.
genes like me logo Genes that share domains with LIM2: view

Function for LIM2 Gene

Molecular function for LIM2 Gene

UniProtKB/Swiss-Prot Function:
Present in the thicker 16-17 nm junctions of mammalian lens fiber cells, where it may contribute to cell junctional organization. Acts as a receptor for calmodulin. May play an important role in both lens development and cataractogenesis.
GENATLAS Biochemistry:
major intrinsic protein of lens fiber,2 (MP19),with water channel properties

Phenotypes From GWAS Catalog for LIM2 Gene

Gene Ontology (GO) - Molecular Function for LIM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005212 structural constituent of eye lens IEA --
genes like me logo Genes that share ontologies with LIM2: view
genes like me logo Genes that share phenotypes with LIM2: view

Human Phenotype Ontology for LIM2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for research

  • Taconic Biosciences Mouse Models for LIM2

miRNA for LIM2 Gene

miRTarBase miRNAs that target LIM2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIM2

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for LIM2 Gene

Localization for LIM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIM2 Gene

Membrane. Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LIM2 gene
Compartment Confidence
plasma membrane 4
cytoskeleton 2
nucleus 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for LIM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction NAS 2584203
GO:0031982 vesicle IEA --
genes like me logo Genes that share ontologies with LIM2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LIM2 Gene

Pathways & Interactions for LIM2 Gene

PathCards logo

SuperPathways for LIM2 Gene

No Data Available

Interacting Proteins for LIM2 Gene

STRING Interaction Network Preview (showing top 2 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000221973 P55344-LMIP_HUMAN for LIM2 Gene via STRING IID

Gene Ontology (GO) - Biological Process for LIM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002088 lens development in camera-type eye IEA --
GO:0007043 cell-cell junction assembly NAS 2584203
GO:0043010 camera-type eye development IEA --
genes like me logo Genes that share ontologies with LIM2: view

No data available for Pathways by source and SIGNOR curated interactions for LIM2 Gene

Drugs & Compounds for LIM2 Gene

(2) Additional Compounds for LIM2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LIM2: view

Transcripts for LIM2 Gene

mRNA/cDNA for LIM2 Gene

2 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIM2

Alternative Splicing Database (ASD) splice patterns (SP) for LIM2 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5
SP1: -
SP2:
SP3:

Relevant External Links for LIM2 Gene

GeneLoc Exon Structure for
LIM2

Expression for LIM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LIM2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LIM2 Gene

This gene is overexpressed in Whole Blood (x40.7).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LIM2

SOURCE GeneReport for Unigene cluster for LIM2 Gene:

Hs.162754

mRNA Expression by UniProt/SwissProt for LIM2 Gene:

P55344-LMIP_HUMAN
Tissue specificity: Eye lens specific.

Evidence on tissue expression from TISSUES for LIM2 Gene

  • Eye(4.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LIM2 Gene

Germ Layers:
  • ectoderm
Systems:
  • nervous
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • peripheral nervous system
genes like me logo Genes that share expression patterns with LIM2: view

Primer products for research

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for LIM2 Gene

Orthologs for LIM2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LIM2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LIM2 30 31
  • 99.53 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LIM2 30 31
  • 91.33 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LIM2 30 31
  • 90.94 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lim2 30
  • 89.21 (n)
Mouse
(Mus musculus)
Mammalia Lim2 30 17 31
  • 88.63 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LIM2 31
  • 76 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LIM2 31
  • 73 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LIM2 31
  • 64 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lim2 30
  • 74.57 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.17586 30
Zebrafish
(Danio rerio)
Actinopterygii lim2.5 30 31
  • 73.41 (n)
OneToMany
lim2.4 31
  • 67 (a)
OneToMany
lim2.1 31
  • 65 (a)
OneToMany
lim2.3 31
  • 63 (a)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1612 30
Species where no ortholog for LIM2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LIM2 Gene

ENSEMBL:
Gene Tree for LIM2 (if available)
TreeFam:
Gene Tree for LIM2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIM2: view image

Paralogs for LIM2 Gene

Paralogs for LIM2 Gene

genes like me logo Genes that share paralogs with LIM2: view

Variants for LIM2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LIM2 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
893018 Uncertain Significance: Cataract 19, multiple types 51,387,270(-) G/A
NM_001161748.2(LIM2):c.174C>T (p.Ile58=)
SYNONYMOUS
893019 Uncertain Significance: Cataract 19, multiple types 51,387,303(-) C/G
NM_001161748.2(LIM2):c.141G>C (p.Leu47=)
SYNONYMOUS
893020 Uncertain Significance: Cataract 19, multiple types 51,387,344(-) A/T
NM_001161748.2(LIM2):c.100T>A (p.Ser34Thr)
MISSENSE
893201 Uncertain Significance: Cataract 19, multiple types 51,379,910(-) A/G
NM_001161748.2(LIM2):c.*291T>C
THREE_PRIME_UTR
893202 Uncertain Significance: Cataract 19, multiple types 51,379,956(-) T/C
NM_001161748.2(LIM2):c.*245A>G
THREE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LIM2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LIM2 Gene

Variant ID Type Subtype PubMed ID
nsv1140251 OTHER inversion 24896259

Variation tolerance for LIM2 Gene

Residual Variation Intolerance Score: 18.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.02; 20.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIM2 Gene

Human Gene Mutation Database (HGMD)
LIM2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIM2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIM2 Gene

Disorders for LIM2 Gene

MalaCards: The human disease database

(11) MalaCards diseases for LIM2 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
cataract 19, multiple types
  • ctrct19
cataract
  • cataracts
cataract 44
  • ctrct44
early-onset non-syndromic cataract
cylindrical spirals myopathy
  • myotonic myopathy with cylindrical spirals
- elite association - COSMIC cancer census association via MalaCards
Search LIM2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LMIP_HUMAN
  • Cataract, multiple types 19 (CTRCT19) [MIM:615277]: An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. {ECO:0000269 PubMed:11917274}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for LIM2

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LIM2: view

No data available for Genatlas for LIM2 Gene

Publications for LIM2 Gene

  1. A missense mutation in LIM2 causes autosomal recessive congenital cataract. (PMID: 18596884) Ponnam SP … Kannabiran C (Molecular vision 2008) 3 23 74
  2. A missense mutation in the LIM2 gene is associated with autosomal recessive presenile cataract in an inbred Iraqi Jewish family. (PMID: 11917274) Pras E … Pras E (American journal of human genetics 2002) 3 4 74
  3. Identification of a lens-specific cis-acting element within the basal promoter of the human lens intrinsic membrane protein MP19 gene (LIM2). (PMID: 15968979) Hsu H … Church RL (Sheng wu gong cheng xue bao = Chinese journal of biotechnology 2004) 3 23
  4. Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants. (PMID: 12107413) Wistow G … Peterson K (Molecular vision 2002) 3 4
  5. MP20, the second most abundant lens membrane protein and member of the tetraspanin superfamily, joins the list of ligands of galectin-3. (PMID: 11532191) Gonen T … Kistler J (BMC cell biology 2001) 3 23

Products for LIM2 Gene

Sources for LIM2 Gene