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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 Autosomal Recessive Limb-Girdle Muscular Dystrophy Type 2W and Autosomal Recessive Limb-Girdle Muscular Dystrophy. Among its related pathways are EphB-EphrinB Signaling and ERK 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.

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

Genomics for LIMS2 Gene

Regulatory Elements for LIMS2 Gene

Enhancers for LIMS2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F127618 0.4 FANTOM5 22.9 +63.3 63269 0.3 LIMS2 MYO7B ENSG00000236682 ENSG00000272789 LOC105373609
GH02F127619 0.2 Ensembl 21.7 +61.7 61685 0.6 POLR2A LIMS2 MYO7B ENSG00000272789 LOC105373609
GH02F127591 0.9 Ensembl ENCODE 12.3 +90.3 90286 0.6 ELF3 ARID4B ZNF48 ZNF2 RAD21 GLIS2 ZNF143 CREM THAP11 ZNF654 MYO7B GPR17 LIMS2 ERCC3 LOC105373609 ENSG00000272789
GH02F127705 0.5 ENCODE 12.1 -23.9 -23879 1.2 BHLHE40 ZBTB33 YY1 LIMS2 GPR17 PIR38126 PIR55015
GH02F127613 1.2 Ensembl ENCODE 11.9 +66.3 66299 3.2 BHLHE40 MNT ZIC2 GPR17 LIMS2 MYO7B ENSG00000236682 BIN1 ENSG00000272789 LOC105373609
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LIMS2 on UCSC Golden Path with GeneCards custom track

Genomic Location for LIMS2 Gene

Chromosome:
2
Start:
127,638,381 bp from pter
End:
127,681,786 bp from pter
Size:
43,406 bases
Orientation:
Minus strand

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

Protein Domains for LIMS2 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q7Z4I7

UniProtKB/Swiss-Prot:

LIMS2_HUMAN :
  • Contains 5 LIM zinc-binding domains.
Domain:
  • Contains 5 LIM zinc-binding domains.
genes like me logo Genes that share domains with LIMS2: view

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.

Gene Ontology (GO) - Molecular Function for LIMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008270 zinc ion binding IEA --
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

Animal Models for LIMS2 Gene

MGI Knock Outs for LIMS2:

Animal Model Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
Jensen Localization Image for LIMS2 Gene COMPARTMENTS Subcellular localization image for LIMS2 gene
Compartment Confidence
cytosol 5
nucleus 3
plasma membrane 3

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 21423176
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:0016337 single organismal cell-cell adhesion IEA --
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 --
genes like me logo Genes that share ontologies with LIMS2: view

No data available for SIGNOR curated interactions for LIMS2 Gene

Transcripts for LIMS2 Gene

Unigene Clusters for LIMS2 Gene

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

Flow Cytometry 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 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
genes like me logo Genes that share expression patterns with LIMS2: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt 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 34 35
  • 99.5 (n)
oppossum
(Monodelphis domestica)
Mammalia LIMS2 35
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LIMS2 34 35
  • 91.77 (n)
cow
(Bos Taurus)
Mammalia LIMS2 34 35
  • 91.57 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LIMS2 35
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lims2 34 16 35
  • 88.76 (n)
rat
(Rattus norvegicus)
Mammalia Lims2 34
  • 87.73 (n)
chicken
(Gallus gallus)
Aves LIMS2 34 35
  • 83.53 (n)
lizard
(Anolis carolinensis)
Reptilia LIMS2 35
  • 86 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta stck 35
  • 63 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea unc-97 35
  • 58 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11312 35
  • 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 Sequence Context AA Info Type
rs754385302 Pathogenic 127,654,507(+) TTGTT(C/G)TTCAT intron-variant, nc-transcript-variant, reference, missense
rs768056213 Pathogenic 127,654,493(+) AGCCC(A/G)GGTGC intron-variant, nc-transcript-variant, reference, missense
rs869025562 Pathogenic 127,639,339(-) GAAGC(C/T)GTCGG nc-transcript-variant, reference, missense
rs145123078 Likely benign 127,643,047(+) CTCAC(A/G)GTTGT nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs150714487 Likely benign 127,657,538(+) ACGGC(A/G)TTGGC intron-variant, nc-transcript-variant, reference, synonymous-codon

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)

Relevant External Links for LIMS2 Gene

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

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: ClinVar, GeneTests, and GeneCards

Disorder Aliases PubMed IDs
autosomal recessive limb-girdle muscular dystrophy type 2w
  • lgmd2w
autosomal recessive limb-girdle muscular dystrophy
  • limb-girdle muscular dystrophies, autosomal recessive
- 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.

Relevant External Links for LIMS2

Human Genome Epidemiology (HuGE) Navigator
LIMS2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (J. Biol. Chem. 2002) 2 3 4 64
  2. LIMS2 mutations are associated with a novel muscular dystrophy, severe cardiomyopathy and triangular tongues. (PMID: 25589244) Chardon J.W. … Dyment D.A. (Clin. Genet. 2015) 3 4 64
  3. Structural basis of competition between PINCH1 and PINCH2 for binding to the ankyrin repeat domain of integrin-linked kinase. (PMID: 19963065) Chiswell B.P. … Calderwood D.A. (J. Struct. Biol. 2010) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for LIMS2 Gene

Sources for LIMS2 Gene

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