LHX6 LIM homeobox 6 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
LHX6 promoter hypermethylation in oncological pediatric patients conceived by IVF.
Title: LHX6 promoter hypermethylation in oncological pediatric patients conceived by IVF.
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.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH36482 (e-PCR)
- UniSTS:76578

LHX6_2099 (e-PCR)
- UniSTS:280823

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

NG_029683.1 RefSeqGene

Range

4856..31231

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

122202582..122228957 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423224.1 → XP_047279180.1 LIM/homeobox protein Lhx6 isoform X2
XM_047423223.1 → XP_047279179.1 LIM/homeobox protein Lhx6 isoform X1

UniProtKB/TrEMBL

Q3SY65
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

NC_060933.1 Alternate T2T-CHM13v2.0

Range

134400069..134426451 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054362728.1 → XP_054218703.1 LIM/homeobox protein Lhx6 isoform X2
XM_054362727.1 → XP_054218702.1 LIM/homeobox protein Lhx6 isoform X1

UniProtKB/TrEMBL

Q3SY65
XM_054362729.1 → XP_054218704.1 LIM/homeobox protein Lhx6 isoform X3