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    LMX1B LIM homeobox transcription factor 1 beta [ Homo sapiens (human) ]

    Gene ID: 4010, updated on 6-Sep-2017
    Official Symbol
    LMX1Bprovided by HGNC
    Official Full Name
    LIM homeobox transcription factor 1 betaprovided by HGNC
    Primary source
    HGNC:HGNC:6654
    See related
    Ensembl:ENSG00000136944 MIM:602575; Vega:OTTHUMG00000020692
    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
    NPS1; LMX1.2
    Summary
    This gene encodes a member of LIM-homeodomain family of proteins containing two N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. It functions as a transcription factor, and is essential for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Mutations in this gene are associated with nail-patella syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
    Orthologs
    Location:
    9q33.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (126614443..126701032)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (129376722..129463311)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376276 Neighboring gene uncharacterized LOC105376277 Neighboring gene uncharacterized LOC107987129 Neighboring gene zinc finger and BTB domain containing 43

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Nail-patella syndrome
    MedGen: C0027341 OMIM: 161200 GeneReviews: Nail-Patella Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-04-19)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-19)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    NHGRI GWA Catalog
    Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC138325, MGC142051

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA polymerase II regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription factor activity, RNA polymerase II core promoter sequence-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    dopaminergic neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    dorsal/ventral pattern formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    in utero embryonic development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    multicellular organism development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription from RNA polymerase II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
    PubMed 
    regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    LIM homeobox transcription factor 1-beta
    Names
    LIM/homeobox protein 1.2
    LMX-1.2

    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_017039.1 RefSeqGene

      Range
      5001..91590
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001174146.1NP_001167617.1  LIM homeobox transcription factor 1-beta isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate donor splice site at an internal coding exon compared to variant 1, resulting in a longer isoform (3) containing an additional 11 aa protein segment compared to isoform 1.
      Source sequence(s)
      AL161731, AL161908, BC143801, EL952935
      Consensus CDS
      CCDS55343.1
      UniProtKB/TrEMBL
      B7ZLH2
      Related
      ENSP00000347684.5, ENST00000355497.9
      Conserved Domains (3) summary
      cd09371
      Location:56108
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      cd09378
      Location:115169
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:222275
      Homeobox; Homeobox domain
    2. NM_001174147.1NP_001167618.1  LIM homeobox transcription factor 1-beta isoform 2

      See identical proteins and their annotated locations for NP_001167618.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate donor splice site at the penultimate coding exon compared to variant 1, resulting in a longer isoform (2) containing an additional 7 aa protein segment compared to isoform 1.
      Source sequence(s)
      AL161731, AL161908, BC069588, BC113491, EL952935
      Consensus CDS
      CCDS55342.1
      UniProtKB/Swiss-Prot
      O60663
      UniProtKB/TrEMBL
      Q6ISE0
      Related
      ENSP00000362573.3, OTTHUMP00000022154, ENST00000373474.8, OTTHUMT00000054123
      Conserved Domains (3) summary
      cd09371
      Location:56108
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      cd09378
      Location:115169
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:222275
      Homeobox; Homeobox domain
    3. NM_002316.3NP_002307.2  LIM homeobox transcription factor 1-beta isoform 1

      See identical proteins and their annotated locations for NP_002307.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
      Source sequence(s)
      AL161731, AL161908, BC113491, EL952935
      Consensus CDS
      CCDS6866.2
      UniProtKB/Swiss-Prot
      O60663
      Related
      ENSP00000436930.1, OTTHUMP00000022153, ENST00000526117.5, OTTHUMT00000054122
      Conserved Domains (3) summary
      cd09371
      Location:56108
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      cd09378
      Location:115169
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:222275
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      126614443..126701032
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      129527362..129614009
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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