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

Gene ID: 4010, updated on 5-Mar-2024

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
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Genomic context

See LMX1B in Genome Data Viewer
Location:
9q33.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (126613928..126701032)
RS_2023_10 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 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

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
 
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
part_of 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

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/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_10

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)