This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative... See more...

Aliases for LHX6 Gene

Aliases for LHX6 Gene

  • LIM Homeobox 6 2 3 5
  • LIM/Homeobox Protein Lhx6.1 3 4
  • LIM/Homeobox Protein Lhx6 3 4
  • LHX6.1 3 4
  • LIM Homeodomain Protein 6.1 3
  • LIM Homeobox Protein 6 4

External Ids for LHX6 Gene

Previous GeneCards Identifiers for LHX6 Gene

  • GC09M116069
  • GC09M116611
  • GC09M118418
  • GC09M120340
  • GC09M122044
  • GC09M124004
  • GC09M124964
  • GC09M094579

Summaries for LHX6 Gene

Entrez Gene Summary for LHX6 Gene

  • This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]

GeneCards Summary for LHX6 Gene

LHX6 (LIM Homeobox 6) is a Protein Coding gene. Diseases associated with LHX6 include Cleft Palate, Isolated and Tooth Agenesis. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is LHX8.

UniProtKB/Swiss-Prot Summary for LHX6 Gene

  • Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity).

Gene Wiki entry for LHX6 Gene

Additional gene information for LHX6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LHX6 Gene

Genomics for LHX6 Gene

GeneHancer (GH) Regulatory Elements for LHX6 Gene

Promoters and enhancers for LHX6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J122225 Promoter 1.3 EPDnew Ensembl 500.7 +1.3 1325 1.8 NRF1 FOS CTCF ZIC2 ZNF263 GABPA ZBTB26 ZNF740 CTBP1 EZH2 LHX6 L13304-039 L13715-031 RF00017-7863
GH09J122263 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.3 -35.1 -35136 3.4 EP300 ZBTB40 ZNF217 CTCF SIN3A NRF1 TCF12 MYC POLR2G USF1 RBM18 MRRF lnc-RBM18-1 LHX6
GH09J122178 Enhancer 1 Ensembl ENCODE 11.8 +49.6 49609 2.8 KDM6A REST USF2 TOE1 MYC CTBP1 TEAD1 RAD51 FOXA2 USF1 RF00017-7863 LHX6 TTLL11 MORN5 L13304-039 L13715-031
GH09J122325 Enhancer 0.8 Ensembl ENCODE 10.7 -95.5 -95492 1 EP300 FOXA2 SAP130 CEBPB PBX2 JUND RXRA RARA MAX HNF4A lnc-PTGS1-1 piR-39495 piR-49771 MRRF RBM18 LHX6 TTLL11 OR1K1
GH09J122131 Enhancer 0.7 ENCODE CraniofacialAtlas 10.4 +98.1 98104 0.8 EP300 TEAD4 RFX1 MXI1 SIN3A EZH2 RBBP5 TTLL11 LHX6 OR1K1 MIR4478 lnc-LHX6-1 L13304-039 L13715-031
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LHX6 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LHX6

Top Transcription factor binding sites by QIAGEN in the LHX6 gene promoter:
  • CUTL1
  • HNF-3beta
  • IRF-7A
  • NF-1
  • NF-1/L
  • Sox5
  • STAT1alpha
  • STAT2
  • STAT3

Genomic Locations for LHX6 Gene

Genomic Locations for LHX6 Gene
chr9:122,185,652-122,229,626
(GRCh38/hg38)
Size:
43,975 bases
Orientation:
Minus strand
chr9:124,964,856-124,991,905
(GRCh37/hg19)
Size:
27,050 bases
Orientation:
Minus strand

Genomic View for LHX6 Gene

Genes around LHX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX6 Gene

Proteins for LHX6 Gene

  • Protein details for LHX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPM6-LHX6_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx6
    Protein Accession:
    Q9UPM6
    Secondary Accessions:
    • A6PVQ1
    • A6PVQ2
    • A8K1B2
    • B7Z4D0
    • H0YN76
    • Q5T7S7
    • Q5T7S8
    • Q9NTK3
    • Q9UPM5

    Protein attributes for LHX6 Gene

    Size:
    363 amino acids
    Molecular mass:
    40045 Da
    Quaternary structure:
    • Interacts with LDB1 (via the LIM zinc-binding domains).
    SequenceCaution:
    • Sequence=AAI03937.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAI03938.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAB66505.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for LHX6 Gene

neXtProt entry for LHX6 Gene

Post-translational modifications for LHX6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LHX6 Gene

Domains & Families for LHX6 Gene

Gene Families for LHX6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for LHX6 Gene

Blocks:
  • Zn-binding protein, LIM
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LHX6 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ94426, Homo sapiens LIM homeobox 6 (LHX6), mRNA (A8K1B2_HUMAN)
  • cDNA FLJ55755, highly similar to LIM/homeobox protein Lhx6.1 (B7Z4D0_HUMAN)
  • LIM/homeobox protein Lhx6.1 (LHX6_HUMAN)
  • LIM homeobox 6 (Q3SY65_HUMAN)
genes like me logo Genes that share domains with LHX6: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LHX6 Gene

Function for LHX6 Gene

Molecular function for LHX6 Gene

UniProtKB/Swiss-Prot Function:
Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity).

Phenotypes From GWAS Catalog for LHX6 Gene

Gene Ontology (GO) - Molecular Function for LHX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity NAS 10393337
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LHX6: view
genes like me logo Genes that share phenotypes with LHX6: view

Animal Models for LHX6 Gene

MGI Knock Outs for LHX6:
  • Lhx6 Lhx6<tm2Vpa>
  • Lhx6 Lhx6<tm1b(KOMP)Wtsi>
  • Lhx6 Lhx6<tm1And>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX6

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LHX6 Gene

Localization for LHX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX6 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LHX6 gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (1)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LHX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IDA --
genes like me logo Genes that share ontologies with LHX6: view

Pathways & Interactions for LHX6 Gene

PathCards logo

SuperPathways for LHX6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LHX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0021799 cerebral cortex radially oriented cell migration ISS --
GO:0021800 cerebral cortex tangential migration ISS --
genes like me logo Genes that share ontologies with LHX6: view

No data available for Pathways by source and SIGNOR curated interactions for LHX6 Gene

Drugs & Compounds for LHX6 Gene

No Compound Related Data Available

Transcripts for LHX6 Gene

mRNA/cDNA for LHX6 Gene

6 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX6

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LHX6 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14a · 14b · 14c · 14d
SP1: - - - - - - -
SP2: - - - - - - - -
SP3: - - - -
SP4:
SP5:
SP6:
SP7: - - -
SP8: -
SP9: - -

Relevant External Links for LHX6 Gene

GeneLoc Exon Structure for
LHX6

Expression for LHX6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LHX6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LHX6 Gene

This gene is overexpressed in Heart (64.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LHX6 Gene



Protein tissue co-expression partners for LHX6 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LHX6

SOURCE GeneReport for Unigene cluster for LHX6 Gene:

Hs.103137

Evidence on tissue expression from TISSUES for LHX6 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with LHX6: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX6 Gene

Orthologs for LHX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LHX6 31 30
  • 99.83 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LHX6 31 30
  • 93.88 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LHX6 31 30
  • 93.54 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LHX6 31
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lhx6 30
  • 92.96 (n)
mouse
(Mus musculus)
Mammalia Lhx6 17 31 30
  • 92.35 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LHX6 31
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves LHX6 31 30
  • 73.67 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx6 30
  • 71.89 (n)
zebrafish
(Danio rerio)
Actinopterygii lhx6 31 30
  • 72.84 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12957 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006537 30
  • 59.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta Awh 31 32
  • 41 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lim-4 31 32
  • 32 (a)
OneToMany
Species where no ortholog for LHX6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LHX6 Gene

ENSEMBL:
Gene Tree for LHX6 (if available)
TreeFam:
Gene Tree for LHX6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LHX6: view image

Paralogs for LHX6 Gene

(14) SIMAP similar genes for LHX6 Gene using alignment to 5 proteins:

  • LHX6_HUMAN
  • H0YKH7_HUMAN
  • H0YMH3_HUMAN
  • H0YMY8_HUMAN
  • Q3SY65_HUMAN
genes like me logo Genes that share paralogs with LHX6: view

Variants for LHX6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LHX6 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
778380 Likely Benign: not provided 122,227,488(-) A/G FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for LHX6 Gene

Structural Variations from Database of Genomic Variants (DGV) for LHX6 Gene

Variant ID Type Subtype PubMed ID
nsv1145261 CNV deletion 24896259
nsv831715 CNV gain 17160897

Variation tolerance for LHX6 Gene

Residual Variation Intolerance Score: 30.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.41; 27.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LHX6 Gene

Human Gene Mutation Database (HGMD)
LHX6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX6 Gene

Disorders for LHX6 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LHX6 Gene - From: DISEASES

Disorder Aliases PubMed IDs
cleft palate, isolated
  • cpi
tooth agenesis
  • familial tooth agenesis
- elite association - COSMIC cancer census association via MalaCards
Search LHX6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LHX6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LHX6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LHX6 Gene

Publications for LHX6 Gene

  1. A brain region-specific gene product Lhx6.1 interacts with Ldb1 through tandem LIM-domains. (PMID: 10393337) Kimura N … Taga T (Journal of biochemistry 1999) 2 3 4 23 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  3. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PMID: 20201926) Joslyn G … White RL (Alcoholism, clinical and experimental research 2010) 3 41 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for LHX6 Gene

Sources for LHX6 Gene