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

    Gene ID: 4010, updated on 28-Oct-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See LMX1B in Genome Data Viewer
    Location:
    9q33.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (126613928..126701032)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (138819355..138906454)
    RS_2024_09 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 ReSE screen-validated silencer GRCh37_chr9:129370112-129370312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129372327-129373191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20289 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 ATAC-STARR-seq lymphoblastoid active region 29018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20290 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20291 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106693 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20292 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:129567045-129567546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29021 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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. LMX1B 17-bp deletion and A3243G mtDNA transition in a previously described patient. Finsterer J, et al. Eur Neurol, 2003. PMID 12646768
    2. Restricted distribution of loss-of-function mutations within the LMX1B genes of nail-patella syndrome patients. Clough MV, et al. Hum Mutat, 1999. PMID 10571942
    3. Deletion of a branch-point consensus sequence in the LMX1B gene causes exon skipping in a family with nail patella syndrome. Hamlington JD, et al. Eur J Hum Genet, 2000 Apr. PMID 10854116
    4. A familial case of nail patella syndrome with a heterozygous in-frame indel mutation in the LIM domain of LMX1B. Mukai M, et al. J Dermatol Sci, 2018 Apr. PMID 29290531
    5. Twenty-two novel LMX1B mutations identified in nail patella syndrome (NPS) patients. Hamlington JD, et al. Hum Mutat, 2001 Nov. PMID 11668639

    See all (96) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic polymorphisms of LMX1B and MLXIP are associated with hip osteoarthritis in the Chinese population.
      Title: Genetic polymorphisms of LMX1B and MLXIP are associated with hip osteoarthritis in the Chinese population.
    2. De novo enhancer deletion of LMX1B produces a mild nail-patella clinical phenotype.
      Title: De novo enhancer deletion of LMX1B produces a mild nail-patella clinical phenotype.
    3. ATG8-dependent LMX1B-autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience.
      Title: ATG8-dependent LMX1B-autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience.
    4. Knockdown of LMX1B Suppressed Cell Apoptosis and Inflammatory Response in IL-1beta-Induced Human Osteoarthritis Chondrocytes through NF-kappaB and NLRP3 Signal Pathway.
      Title: Knockdown of LMX1B Suppressed Cell Apoptosis and Inflammatory Response in IL-1β-Induced Human Osteoarthritis Chondrocytes through NF-κB and NLRP3 Signal Pathway.
    5. Association analysis of variants rs35934224 in TXNRD2 and rs6478746 in LMX1B in primary angle-closure and pseudoexfoliation glaucoma.
      Title: Association analysis of variants rs35934224 in TXNRD2 and rs6478746 in LMX1B in primary angle-closure and pseudoexfoliation glaucoma.
    6. LMX1B Activated Circular RNA GFRA1 Modulates the Tumorigenic Properties and Immune Escape of Prostate Cancer.
      Title: LMX1B Activated Circular RNA GFRA1 Modulates the Tumorigenic Properties and Immune Escape of Prostate Cancer.
    7. hsa-miR-206b Involves in the Development of Papillary Thyroid Carcinoma via Targeting LMX1B.
      Title: hsa-miR-206b Involves in the Development of Papillary Thyroid Carcinoma via Targeting LMX1B.
    8. Long noncoding RNA SNHG3 promotes glioma tumorigenesis by sponging miR-485-5p to upregulate LMX1B expression.
      Title: Long noncoding RNA SNHG3 promotes glioma tumorigenesis by sponging miR-485-5p to upregulate LMX1B expression.
    9. LMX1B Locus Associated with Low-Risk Baseline Glaucomatous Features in the POAAGG Study.
      Title: LMX1B Locus Associated with Low-Risk Baseline Glaucomatous Features in the POAAGG Study.
    10. Whole-Exome Sequencing Solved over 2-Decade Kidney Disease Enigma.
      Title: Whole-Exome Sequencing Solved over 2-Decade Kidney Disease Enigma.
    Submit: New GeneRIF Correction See all GeneRIFs (55)

    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
    Nail-patella syndrome
    MedGen: C0027341 OMIM: 161200 GeneReviews: Nail-Patella Syndrome
    		not available
    Nail-patella-like renal disease
    MedGen: C0403548 OMIM: 256020 GeneReviews: Not available
    		not available

    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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC138325, MGC142051

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    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
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    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_001174146.2 → NP_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:56 → 108
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      cd09378
      Location:115 → 169
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:222 → 275
      Homeobox; Homeobox domain

    2. NM_001174147.2 → NP_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:56 → 108
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      cd09378
      Location:115 → 169
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:222 → 276
      Homeobox; Homeobox domain

    3. NM_002316.4 → NP_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/TrEMBL
      Q6ISE0
      Related
      ENSP00000436930.1, ENST00000526117.6
      Conserved Domains (3) summary
      cd09371
      Location:56 → 108
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      cd09378
      Location:115 → 169
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:222 → 276
      Homeobox; Homeobox domain

    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_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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60663.3 GenPept UniProtKB/Swiss-Prot:O60663

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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