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

Gene ID: 3982, updated on 5-Mar-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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Location:
19q13.41
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (51379909..51387974, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (54468540..54476605, complement)
105.20220307 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. A novel missense mutation in LIM2 causing isolated autosomal dominant congenital cataract. Berry V, et al. Ophthalmic Genet, 2020 Apr. PMID 32202185
  3. Mutation in LIM2 Is Responsible for Autosomal Recessive Congenital Cataracts. Irum B, et al. PLoS One, 2016. PMID 27814360, Free PMC Article
  4. A missense mutation in LIM2 causes autosomal recessive congenital cataract. Ponnam SP, et al. Mol Vis, 2008 Jun 23. PMID 18596884, Free PMC Article
  5. 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

See all (21) 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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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_2023_10

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

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