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    LIM2 lens intrinsic membrane protein 2 [ Homo sapiens (human) ]

    Gene ID: 3982, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LIM2provided by HGNC
    Official Full Name
    lens intrinsic membrane protein 2provided by HGNC
    Primary source
    HGNC:HGNC:6610
    See related
    Ensembl:ENSG00000105370 MIM:154045; AllianceGenome:HGNC:6610
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MP17; MP19; CTRCT19
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
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    Genomic context

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    See LIM2 in Genome Data Viewer
    Location:
    19q13.41
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (51379909..51387974, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (54468540..54476605, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (51883163..51891228, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:51869249-51870208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:51871167-51872126 Neighboring gene claudin domain containing 2 Neighboring gene uncharacterized LOC124904752 Neighboring gene natural killer cell granule protein 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:51879781-51880038 Neighboring gene LIM2 and SIGLEC10 antisense RNA 1 Neighboring gene chromosome 19 open reading frame 84 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:51897116-51897712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15015 Neighboring gene NIFK pseudogene 6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A recurrent variant in LIM2 causes an isolated congenital sutural/lamellar cataract in a Japanese family. Berry V, et al. Ophthalmic Genet, 2022 Oct. PMID 35736209, Free PMC Article
    2. Assignment of the lens intrinsic membrane protein MP19 structural gene to human chromosome 19. Church RL, et al. Curr Eye Res, 1992 May. PMID 1606837
    3. Assignment of the human lens fiber cell MP19 gene (LIM2) to chromosome 19q13.4, and adjacent to ETFB. Lieuallen K, et al. Somat Cell Mol Genet, 1994 Jan. PMID 8197479
    4. Identification of a lens-specific cis-acting element within the basal promoter of the human lens intrinsic membrane protein MP19 gene (LIM2). Hsu H, et al. Sheng Wu Gong Cheng Xue Bao, 2004 Jul. PMID 15968979
    5. A missense mutation in LIM2 causes autosomal recessive congenital cataract. Ponnam SP, et al. Mol Vis, 2008 Jun 23. PMID 18596884, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel and known variants in GJA3 and LIM2 in congenital cataract families from North India.
      Title: Novel and known variants in GJA3 and LIM2 in congenital cataract families from North India.
    2. A recurrent variant in LIM2 causes an isolated congenital sutural/lamellar cataract in a Japanese family.
      Title: A recurrent variant in LIM2 causes an isolated congenital sutural/lamellar cataract in a Japanese family.
    3. A novel missense mutation in LIM2 causing isolated autosomal dominant congenital cataract.
      Title: A novel missense mutation in LIM2 causing isolated autosomal dominant congenital cataract.
    4. A novel missense mutation in LIM2 is responsible for autosomal recessive congenital cataracts.
      Title: Mutation in LIM2 Is Responsible for Autosomal Recessive Congenital Cataracts.
    5. we report the absence of mutations in all studied genes in four families with phenotypes associating cataract, mental retardation and microcephaly.
      Title: Absence of mutations in four genes encoding for congenital cataract and expressed in the human brain in Tunisian families with cataract and mental retardation.
    6. The genetic mutation in GJA3, GJA8, and LIM2 may slightly contribute to the development of age-related cataracts.
      Title: Genetic variations in GJA3, GJA8, LIM2, and age-related cataract in the Chinese population: a mutation screening study.
    7. Since the LIM2 gene promoter does not contain a classic TATA box, the Hsu element may serve as the site for binding the RNA polymerase complex.
      Title: Identification of a lens-specific cis-acting element within the basal promoter of the human lens intrinsic membrane protein MP19 gene (LIM2).
    8. This study shows the involvement of LIM2 in human congenital cataract.
      Title: A missense mutation in LIM2 causes autosomal recessive congenital cataract.
    9. A missense mutation in the LIM2 gene is associated with autosomal recessive presenile cataract in an inbred Iraqi Jewish family
      Title: A missense mutation in the LIM2 gene is associated with autosomal recessive presenile cataract in an inbred Iraqi Jewish family.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Cataract 19 multiple types
    MedGen: C3809004 OMIM: 615277 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables structural constituent of eye lens IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-cell junction assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in lens development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell junction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lens fiber membrane intrinsic protein
    Names
    MP18
    MP20
    lens intrinsic membrane protein 2, 19kDa

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012924.1 RefSeqGene

      Range
      4983..13048
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001161748.2 → NP_001155220.1  lens fiber membrane intrinsic protein isoform 2

      See identical proteins and their annotated locations for NP_001155220.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate, in-frame donor splice site at the 5' coding exon compared to variant 1. This results in a shorter isoform (2) missing a 42 aa protein segment compared to isoform 1.
      Source sequence(s)
      AC008750, AF340020, BU734982, CD675859
      Consensus CDS
      CCDS59415.1
      UniProtKB/Swiss-Prot
      P55344, Q6B083, Q9BXD0, Q9HAR5
      Related
      ENSP00000472090.2, ENST00000596399.2
      Conserved Domains (1) summary
      cl21598
      Location:1 → 157
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    2. NM_030657.4 → NP_085915.2  lens fiber membrane intrinsic protein isoform 1

      See identical proteins and their annotated locations for NP_085915.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC008750, AF340019, BU734982, CD675859
      Consensus CDS
      CCDS12831.1
      UniProtKB/Swiss-Prot
      P55344
      Related
      ENSP00000221973.2, ENST00000221973.7
      Conserved Domains (1) summary
      cl21598
      Location:1 → 199
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      51379909..51387974 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      54468540..54476605 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P55344.2 GenPept UniProtKB/Swiss-Prot:P55344

    Gene LinkOut

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