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Aliases for LIMS2 Gene

Aliases for LIMS2 Gene

  • LIM Zinc Finger Domain Containing 2 2 3 5
  • Particularly Interesting New Cys-His Protein 2 2 3 4
  • LIM And Senescent Cell Antigen-Like Domains 2 2 3
  • LIM-Type Zinc Finger Domains 2 2 3
  • PINCH-2 3 4
  • PINCH2 3 4
  • LIM And Senescent Cell Antigen-Like-Containing Domain Protein 2 3
  • ILK-Binding Protein 3
  • LIM-Like Protein 2 4
  • LGMD2W 3

External Ids for LIMS2 Gene

Previous GeneCards Identifiers for LIMS2 Gene

  • GC02M125694
  • GC02M126320
  • GC02M128300
  • GC02M128489
  • GC02M128112
  • GC02M120702
  • GC02M128395

Summaries for LIMS2 Gene

Entrez Gene Summary for LIMS2 Gene

  • This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

GeneCards Summary for LIMS2 Gene

LIMS2 (LIM Zinc Finger Domain Containing 2) is a Protein Coding gene. Diseases associated with LIMS2 include Muscular Dystrophy, Limb-Girdle, Type 2W and Muscular Dystrophy. Among its related pathways are ERK Signaling and EphB-EphrinB Signaling. An important paralog of this gene is LIMS1.

UniProtKB/Swiss-Prot for LIMS2 Gene

  • Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Plays a role in modulating cell spreading and migration.

Additional gene information for LIMS2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIMS2 Gene

Genomics for LIMS2 Gene

GeneHancer (GH) Regulatory Elements for LIMS2 Gene

Promoters and enhancers for LIMS2 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
GH02I127674 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 550.4 +6.2 6180 1.6 CTCF KLF1 SAP130 SUZ12 ZNF48 RAD21 ZNF335 ZFHX2 GLIS2 PATZ1 LIMS2 POLR2D PIR47712
GH02I127663 Promoter/Enhancer 1.2 EPDnew Ensembl dbSUPER 550.4 +17.8 17797 1.8 RING1 POLR2A SUZ12 RCOR1 EZH2 LIMS2 ERCC3 WDR33 GPR17 PIR47712
GH02I127681 Promoter/Enhancer 1 EPDnew Ensembl dbSUPER 550.8 +0.2 171 0.4 NR2F2 LIMS2 PIR47712
GH02I127648 Promoter/Enhancer 0.7 EPDnew dbSUPER 550.3 +33.5 33536 0.1 LIMS2 GPR17 PIR41862 GC02P127671
GH02I127507 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.3 +172.1 172078 4.9 PKNOX1 SIN3A FEZF1 ZNF2 ATF7 FOS REST TSHZ1 MAFF SMARCA4 SFT2D3 ENSG00000236682 MYO7B RNU4-48P LIMS2 ERCC3 IWS1 ENSG00000231731 AMMECR1L MAP3K2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LIMS2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LIMS2 gene promoter:

Genomic Locations for LIMS2 Gene

Genomic Locations for LIMS2 Gene
chr2:127,638,381-127,681,786
(GRCh38/hg38)
Size:
43,406 bases
Orientation:
Minus strand
chr2:128,395,956-128,439,360
(GRCh37/hg19)

Genomic View for LIMS2 Gene

Genes around LIMS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIMS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIMS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIMS2 Gene

Proteins for LIMS2 Gene

  • Protein details for LIMS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z4I7-LIMS2_HUMAN
    Recommended name:
    LIM and senescent cell antigen-like-containing domain protein 2
    Protein Accession:
    Q7Z4I7
    Secondary Accessions:
    • A6NLH0
    • B4DMV1
    • F5H6E6
    • Q7Z4I2
    • Q7Z4I6
    • Q7Z4I8
    • Q8NFE7
    • Q9HA13

    Protein attributes for LIMS2 Gene

    Size:
    341 amino acids
    Molecular mass:
    38916 Da
    Quaternary structure:
    • Interacts with TGFB1I1 (By similarity). Interacts with integrin-linked protein kinase 1 (ILK) via the first LIM domain, and in competition with LIMS1. Part of the heterotrimeric IPP complex composed of integrin-linked kinase (ILK), LIMS1 or LIMS2, and PARVA.
    SequenceCaution:
    • Sequence=AAM77350.1; Type=Frameshift; Positions=331; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LIMS2 Gene

    Alternative splice isoforms for LIMS2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIMS2 Gene

Post-translational modifications for LIMS2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LIMS2 Gene

Domains & Families for LIMS2 Gene

Gene Families for LIMS2 Gene

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

Protein Domains for LIMS2 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LIMS2: view

No data available for UniProtKB/Swiss-Prot for LIMS2 Gene

Function for LIMS2 Gene

Molecular function for LIMS2 Gene

UniProtKB/Swiss-Prot Function:
Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Plays a role in modulating cell spreading and migration.

Phenotypes From GWAS Catalog for LIMS2 Gene

Gene Ontology (GO) - Molecular Function for LIMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIMS2: view
genes like me logo Genes that share phenotypes with LIMS2: view

Human Phenotype Ontology for LIMS2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LIMS2 Gene

MGI Knock Outs for LIMS2:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LIMS2 Gene

Localization for LIMS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIMS2 Gene

Nucleus. Cell junction, focal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side.

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 LIMS2 gene
Compartment Confidence
cytosol 5
plasma membrane 3
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Focal adhesion sites (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LIMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IEA --
GO:0005925 focal adhesion IEA,IDA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with LIMS2: view

Pathways & Interactions for LIMS2 Gene

genes like me logo Genes that share pathways with LIMS2: view

Pathways by source for LIMS2 Gene

1 Qiagen pathway for LIMS2 Gene

Gene Ontology (GO) - Biological Process for LIMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034329 cell junction assembly TAS --
GO:0043066 negative regulation of apoptotic process IEA --
GO:0045216 cell-cell junction organization IEA --
GO:0050680 negative regulation of epithelial cell proliferation IEA --
GO:0098609 cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with LIMS2: view

No data available for SIGNOR curated interactions for LIMS2 Gene

Drugs & Compounds for LIMS2 Gene

No Compound Related Data Available

Transcripts for LIMS2 Gene

Unigene Clusters for LIMS2 Gene

LIM and senescent cell antigen-like domains 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIMS2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b · 12c · 12d · 12e ^ 13a · 13b ^ 14a · 14b ·
SP1: - - - - - -
SP2: - - - - - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - - - - - -
SP7: - - - - - - -
SP8: - - - - -
SP9: - - -
SP10: - - - - - - - - - - - -
SP11: -
SP12: - -
SP13: -
SP14: - - - -
SP15:
SP16:
SP17: -

ExUns: 14c ^ 15a · 15b ^ 16a · 16b · 16c · 16d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15: - -
SP16:
SP17:

Relevant External Links for LIMS2 Gene

GeneLoc Exon Structure for
LIMS2
ECgene alternative splicing isoforms for
LIMS2

Expression for LIMS2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIMS2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LIMS2 Gene

This gene is overexpressed in Colon - Sigmoid (x5.5).

Protein differential expression in normal tissues from HIPED for LIMS2 Gene

This gene is overexpressed in Cardia (13.5), Urinary Bladder (12.3), Colon (9.5), Rectum (8.5), Prostate (8.2), and Uterus (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LIMS2 Gene



Protein tissue co-expression partners for LIMS2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LIMS2 Gene:

LIMS2

SOURCE GeneReport for Unigene cluster for LIMS2 Gene:

Hs.469881

Evidence on tissue expression from TISSUES for LIMS2 Gene

  • Nervous system(4.6)
  • Lung(4.3)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with LIMS2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIMS2 Gene

Orthologs for LIMS2 Gene

This gene was present in the common ancestor of animals.

Orthologs for LIMS2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LIMS2 33 34
  • 99.5 (n)
oppossum
(Monodelphis domestica)
Mammalia LIMS2 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LIMS2 33 34
  • 91.77 (n)
cow
(Bos Taurus)
Mammalia LIMS2 33 34
  • 91.57 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LIMS2 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lims2 33 16 34
  • 88.76 (n)
rat
(Rattus norvegicus)
Mammalia Lims2 33
  • 87.73 (n)
chicken
(Gallus gallus)
Aves LIMS2 33 34
  • 83.53 (n)
lizard
(Anolis carolinensis)
Reptilia LIMS2 34
  • 86 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta stck 34
  • 63 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea unc-97 34
  • 58 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11312 34
  • 63 (a)
OneToMany
Species where no ortholog for LIMS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for LIMS2 Gene

ENSEMBL:
Gene Tree for LIMS2 (if available)
TreeFam:
Gene Tree for LIMS2 (if available)

Paralogs for LIMS2 Gene

Pseudogenes.org Pseudogenes for LIMS2 Gene

genes like me logo Genes that share paralogs with LIMS2: view

Variants for LIMS2 Gene

Sequence variations from dbSNP and Humsavar for LIMS2 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs115961120 benign, not specified, Muscular dystrophy, limb-girdle, type 2W 127,640,153(-) G/A/C/T genic_downstream_transcript_variant, intron_variant
rs11900522 benign, Muscular dystrophy, limb-girdle, type 2W 127,654,492(-) C/G/T coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs143117627 benign, Muscular dystrophy, limb-girdle, type 2W 127,657,535(-) G/A/T coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs144872986 likely-benign, Muscular dystrophy, limb-girdle, type 2W 127,657,421(-) G/A coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs145123078 likely-benign, benign, not specified, Muscular dystrophy, limb-girdle, type 2W 127,643,047(-) G/A/C 5_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LIMS2 Gene

Variant ID Type Subtype PubMed ID
dgv4068n100 CNV gain 25217958
dgv4069n100 CNV gain 25217958
esv3893304 CNV loss 25118596
nsv1072974 CNV deletion 25765185
nsv1143958 CNV deletion 24896259
nsv470482 CNV loss 18288195
nsv508864 CNV insertion 20534489
nsv517532 CNV loss 19592680
nsv518085 CNV loss 19592680
nsv583037 CNV loss 21841781
nsv583038 CNV loss 21841781
nsv953155 CNV deletion 24416366

Variation tolerance for LIMS2 Gene

Residual Variation Intolerance Score: 43.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.47; 28.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIMS2 Gene

Human Gene Mutation Database (HGMD)
LIMS2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIMS2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIMS2 Gene

Disorders for LIMS2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LIMS2 Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
muscular dystrophy, limb-girdle, type 2w
  • lgmd2w
muscular dystrophy
  • muscular dystrophies
- elite association - COSMIC cancer census association via MalaCards
Search LIMS2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LIMS2_HUMAN
  • Limb-girdle muscular dystrophy 2W (LGMD2W) [MIM:616827]: A form of autosomal recessive limb-girdle muscular dystrophy, a degenerative myopathy characterized by slowly progressive wasting and weakness of the proximal muscles of arms and legs around the pelvic or shoulder girdles, elevated creatine kinase levels and dystrophic features on muscle biopsy. LGMD2W is characterized by childhood-onset of weakness progressing to a severe quadriparesis. Additionally, patients have biventricular cardiac dysfunction due to dilated cardiomyopathy. {ECO:0000269 PubMed:25589244}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LIMS2

genes like me logo Genes that share disorders with LIMS2: view

No data available for Genatlas for LIMS2 Gene

Publications for LIMS2 Gene

  1. Characterization of PINCH-2, a new focal adhesion protein that regulates the PINCH-1-ILK interaction, cell spreading, and migration. (PMID: 12167643) Zhang Y … Wu C (The Journal of biological chemistry 2002) 2 3 4 58
  2. LIMS2 mutations are associated with a novel muscular dystrophy, severe cardiomyopathy and triangular tongues. (PMID: 25589244) Chardon JW … Dyment DA (Clinical genetics 2015) 3 4 58
  3. Structural basis of competition between PINCH1 and PINCH2 for binding to the ankyrin repeat domain of integrin-linked kinase. (PMID: 19963065) Chiswell BP … Calderwood DA (Journal of structural biology 2010) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for LIMS2 Gene

Sources for LIMS2 Gene

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