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LHX6 LIM homeobox 6 [ Homo sapiens (human) ]

Gene ID: 26468, updated on 2-Nov-2024

Summary

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Official Symbol
LHX6provided by HGNC
Official Full Name
LIM homeobox 6provided by HGNC
Primary source
HGNC:HGNC:21735
See related
Ensembl:ENSG00000106852 MIM:608215; AllianceGenome:HGNC:21735
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
hLHX6; LHX6.1
Summary
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]
Expression
Broad expression in fat (RPKM 1.9), brain (RPKM 1.8) and 20 other tissues See more
Orthologs
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Genomic context

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See LHX6 in Genome Data Viewer
Location:
9q33.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (122202582..122228957, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (134400069..134426451, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (124964861..124991236, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:124896063-124896602 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124896718-124897622 Neighboring gene NADH:ubiquinone oxidoreductase subunit A8 Neighboring gene Sharpr-MPRA regulatory region 3979 Neighboring gene MORN repeat containing 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:124962138-124962350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124988963-124989468 Neighboring gene MPRA-validated peak7328 silencer Neighboring gene RNA binding motif protein 18 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:125026651-125027850 Neighboring gene mitochondrial ribosome recycling factor

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. LHX6 promoter hypermethylation in oncological pediatric patients conceived by IVF. Dangoni GD, et al. J Dev Orig Health Dis, 2023 Feb. PMID 36154949
  2. LHX6 is a sensitive methylation marker in head and neck carcinomas. Estécio MR, et al. Oncogene, 2006 Aug 17. PMID 16732332
  3. The role of hLHX6-HMR as a methylation biomarker for early diagnosis of cervical cancer. Jung S, et al. Oncol Rep, 2010 Jun. PMID 20428825
  4. Epigenetic regulation of the potential tumor suppressor gene, hLHX6.1, in human cervical cancer. Jung S, et al. Int J Oncol, 2011 Mar. PMID 21240459
  5. LHX6 acts as a novel potential tumour suppressor with epigenetic inactivation in lung cancer. Liu WB, et al. Cell Death Dis, 2013 Oct 24. PMID 24157876, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Lhx6 deficiency causes human embryonic palatal mesenchymal cell mitophagy dysfunction in cleft palate.
    Title: Lhx6 deficiency causes human embryonic palatal mesenchymal cell mitophagy dysfunction in cleft palate.
  2. LHX6 promoter hypermethylation in oncological pediatric patients conceived by IVF.
    Title: LHX6 promoter hypermethylation in oncological pediatric patients conceived by IVF.
  3. The exon 12-containing LHX6 isoforms promote cervical cancer cell proliferation by regulating the MAPK signaling pathway.
    Title: The exon 12-containing LHX6 isoforms promote cervical cancer cell proliferation by regulating the MAPK signaling pathway.
  4. Tumor suppressor LHX6 upregulation contributes to the inhibitory effect of miR-346 knockdown on colorectal cancer cell growth.
    Title: Tumor suppressor LHX6 upregulation contributes to the inhibitory effect of miR-346 knockdown on colorectal cancer cell growth.
  5. LHX6 is essential for the migration of human pluripotent stem cell-derived GABAergic interneurons.
    Title: LHX6 is essential for the migration of human pluripotent stem cell-derived GABAergic interneurons.
  6. Methylation-mediated silencing of the LIM homeobox 6 (LHX6) gene promotes cell proliferation in human pancreatic cancer.
    Title: Methylation-mediated silencing of the LIM homeobox 6 (LHX6) gene promotes cell proliferation in human pancreatic cancer.
  7. LHX6 gene expression is regulated by DNA methylation and can inhibit the proliferation, invasion and migration through Wnt/beta-catenin and P53 signaling pathways during the Microcystin-LR-induced hepatocarcinogenesis.
    Title: Epigenetic inactivation of LHX6 mediated microcystin-LR induced hepatocarcinogenesis via the Wnt/β-catenin and P53 signaling pathways.
  8. The downregulation of LHX6 expression might be important in promoting cancer progression. [review]
    Title: Downregulation of tumor-suppressor gene LHX6 in cancer: a systematic review.
  9. The orthotopic implantation model showed that miR-1290 overexpression promoted tumor growth while LHX6 overexpression inhibited it. MiR-1290 could promote glioma cell propagation and metastasis by inhibiting LHX6.
    Title: MiR-1290 promotes proliferation, migration, and invasion of glioma cells by targeting LHX6.
  10. expression of the single transcription factor LHX6 under GABAergic interneurons differentiation condition is sufficient to robustly induce human parvalbumin and somatostatin subtypes.
    Title: Induction of human somatostatin and parvalbumin neurons by expressing a single transcription factor LIM homeobox 6.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC119542, MGC119544, MGC119545

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity NAS
Non-traceable Author Statement
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 RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
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 cell maturation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cerebral cortex GABAergic interneuron migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cerebral cortex radially oriented cell migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cerebral cortex tangential migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in forebrain neuron development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  

General protein information

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Preferred Names
LIM/homeobox protein Lhx6
Names
LIM homeodomain protein 6.1
LIM/homeobox protein Lhx6.1

NCBI Reference Sequences (RefSeq)

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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_029683.1 RefSeqGene

    Range
    4856..31231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242333.2 → NP_001229262.1  LIM/homeobox protein Lhx6 isoform 3

    See identical proteins and their annotated locations for NP_001229262.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks a segment in the coding region, which leads to a frameshift, compared to variant 1. The resulting isoform (3) has shorter and distinct N- and C- termini compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982, AK297175, AL162424, BC103936
    Consensus CDS
    CCDS56584.1
    UniProtKB/TrEMBL
    Q3SY65
    Related
    ENSP00000441464.2, ENST00000541397.2
    Conserved Domains (3) summary
    cd09380
    Location:88 → 141
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:149 → 203
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:241 → 293
    Homeobox; Homeobox domain

  2. NM_001242334.2 → NP_001229263.1  LIM/homeobox protein Lhx6 isoform 4

    See identical proteins and their annotated locations for NP_001229263.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982, AK289827, BC103936
    Consensus CDS
    CCDS56583.1
    UniProtKB/Swiss-Prot
    A6PVQ1, A6PVQ2, A8K1B2, B7Z4D0, H0YN76, Q5T7S7, Q5T7S8, Q9NTK3, Q9UPM5, Q9UPM6
    UniProtKB/TrEMBL
    Q3SY65
    Related
    ENSP00000362860.2, ENST00000373755.6
    Conserved Domains (3) summary
    cd09380
    Location:70 → 123
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:131 → 185
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:223 → 275
    Homeobox; Homeobox domain

  3. NM_001242335.2 → NP_001229264.1  LIM/homeobox protein Lhx6 isoform 5

    See identical proteins and their annotated locations for NP_001229264.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (5) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982
    Consensus CDS
    CCDS59144.1
    UniProtKB/Swiss-Prot
    Q9UPM6
    Related
    ENSP00000475927.1, ENST00000559895.5
    Conserved Domains (1) summary
    pfam00046
    Location:36 → 88
    Homeobox; Homeobox domain

  4. NM_001348190.2 → NP_001335119.1  LIM/homeobox protein Lhx6 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (6) is shorter at the N-terminus and a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AB031042, AI265821, AK126982, AK289827
    Consensus CDS
    CCDS87683.1
    UniProtKB/TrEMBL
    Q3SY65
    Related
    ENSP00000362859.2, ENST00000373754.6
    Conserved Domains (3) summary
    cd09380
    Location:70 → 123
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:131 → 185
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:223 → 275
    Homeobox; Homeobox domain

  5. NM_014368.5 → NP_055183.2  LIM/homeobox protein Lhx6 isoform 1

    See identical proteins and their annotated locations for NP_055183.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AI265821, AK126982, AK299709, AL162424
    Consensus CDS
    CCDS6838.2
    UniProtKB/TrEMBL
    Q3SY65
    Related
    ENSP00000377854.4, ENST00000394319.9
    Conserved Domains (3) summary
    cd09380
    Location:99 → 152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160 → 214
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:252 → 305
    Homeobox; Homeobox domain

  6. NM_199160.4 → NP_954629.2  LIM/homeobox protein Lhx6 isoform 2

    See identical proteins and their annotated locations for NP_954629.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a segment in the coding region, which leads to a frameshift, compared to variant 1. The resulting isoform (2) contains a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AI265821, AK126982, AK299709, AL162424, BC103936
    Consensus CDS
    CCDS6837.2
    UniProtKB/TrEMBL
    Q3SY65
    Related
    ENSP00000340137.3, ENST00000340587.7
    Conserved Domains (3) summary
    cd09380
    Location:99 → 152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cd09382
    Location:160 → 214
    LIM2_Lhx6; The second LIM domain of Lhx6
    pfam00046
    Location:252 → 305
    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
    122202582..122228957 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423224.1 → XP_047279180.1  LIM/homeobox protein Lhx6 isoform X2

  2. XM_047423223.1 → XP_047279179.1  LIM/homeobox protein Lhx6 isoform X1

  3. XM_005251916.4 → XP_005251973.1  LIM/homeobox protein Lhx6 isoform X3

    Conserved Domains (2) summary
    cd09380
    Location:99 → 152
    LIM1_Lhx6; The first LIM domain of Lhx6
    cl02475
    Location:160 → 214
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    134400069..134426451 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362728.1 → XP_054218703.1  LIM/homeobox protein Lhx6 isoform X2

  2. XM_054362727.1 → XP_054218702.1  LIM/homeobox protein Lhx6 isoform X1

  3. XM_054362729.1 → XP_054218704.1  LIM/homeobox protein Lhx6 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UPM6.2 GenPept UniProtKB/Swiss-Prot:Q9UPM6

Gene LinkOut

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