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

    Gene ID: 4010, updated on 7-Sep-2023

    Summary

    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; AllianceGenome:HGNC:6654
    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; FSGS10; 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]
    Expression
    Biased expression in salivary gland (RPKM 1.8), kidney (RPKM 0.4) and 3 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LMX1B in Genome Data Viewer
    Location:
    9q33.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (126613928..126701032)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (138819355..138906454)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (129376207..129463311)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129350903-129351737 Neighboring gene uncharacterized LOC124902272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129372327-129373191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129375135-129376103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129376359-129376940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129376941-129377520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129378101-129378680 Neighboring gene LMX1B divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129387803-129388768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129392623-129393190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129393191-129393758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129398978-129399478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129414454-129415333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129416491-129416990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129424890-129425503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129425974-129426490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129426491-129427005 Neighboring gene Sharpr-MPRA regulatory region 8141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129436714-129437369 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:129438749-129439277 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:129439278-129439806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129445577-129446297 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:129450160-129451042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129456574-129457344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129458734-129459234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129464425-129465019 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr9:129467063-129467788 and GRCh37_chr9:129467789-129468514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129468515-129469238 Neighboring gene uncharacterized LOC107987129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129482087-129482586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:129567045-129567546 Neighboring gene zinc finger and BTB domain containing 43 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129594985-129595486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129595487-129595986

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Nail-patella syndrome
    MedGen: C0027341 OMIM: 161200 GeneReviews: Nail-Patella Syndrome
    Compare labs
    Nail-patella-like renal disease
    MedGen: C0403548 OMIM: 256020 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-11-10)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-11-10)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC138325, MGC142051

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in dopaminergic neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in dorsal/ventral pattern formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    LIM homeobox transcription factor 1-beta
    Names
    LIM/homeobox protein 1.2
    LMX-1.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      4486..91590
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1014

    mRNA and Protein(s)

    1. NM_001174146.2NP_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, ENST00000355497.10
      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_001174147.2NP_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
      F8W7W6, O60663, O75463, Q5JU95, Q6ISC9
      UniProtKB/TrEMBL
      Q6ISE0
      Related
      ENSP00000362573.3, ENST00000373474.9
      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:222276
      Homeobox; Homeobox domain
    3. NM_002316.4NP_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) encodes isoform 1.
      Source sequence(s)
      AL161731, AL161908, BC113491, EL952935
      Consensus CDS
      CCDS6866.2
      UniProtKB/Swiss-Prot
      O60663
      UniProtKB/TrEMBL
      Q6ISE0
      Related
      ENSP00000436930.1, ENST00000526117.6
      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:222276
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      126613928..126701032
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      138819355..138906454
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)