LHX1 LIM homeobox 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LHX1provided by HGNC
Official Full Name: LIM homeobox 1provided by HGNC
Primary source: HGNC:HGNC:6593
See related: Ensembl:ENSG00000273706 MIM:601999; AllianceGenome:HGNC:6593
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: LIM1; LIM-1
Summary: This gene encodes a member of a large protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor important for the development of the renal and urogenital systems. This gene is a candidate for Mayer-Rokitansky-Kuster-Hauser syndrome, a disorder characterized by anomalies in the female genital tract. [provided by RefSeq, Dec 2010]
Expression: Restricted expression toward kidney (RPKM 4.6) See more
Orthologs: mouse all
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Genomic context

Location:: 17q12

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (36936785..36944612)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (37923784..37931669)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (35294772..35301912)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The potential pro-metastatic role of Lim1 in advanced clear cell renal cell carcinoma in vitro, ex vivo, and in vivo in a nude mouse model. Lim1 was found constitutively expressed in all metastatic tissues. Lim1 silencing decreased pulmonary metastasis in the in vivo model. Lim1 is involved in the expression of various proteins regulating cell movements and EMT, and induced clonogenicity in CCC cells.
Title: The Lim1 oncogene as a new therapeutic target for metastatic human renal cell carcinoma.
Report novel missense mutation in LHX1 in congenital absence of the uterus and vagina which could change the transcriptional activity of LHX1 and its effect on the regulation of the downstream target gene GSC.
Title: Identification and functional analysis of a novel LHX1 mutation associated with congenital absence of the uterus and vagina.
Our MRKH families included 43 quads, 26 trios, and 30 duos. Of our MRKH probands, 87/147 (59%) had MRKH type 1 and 60/147 (41%) had type 2 with additional anomalies. CONCLUSION(S): Although the prevalence of WNT4, HNF1B, and LHX1 point mutations is low in people with MRKH, the prevalence of CNVs was approximately 19%.
Title: Genetic analysis of Mayer-Rokitansky-Kuster-Hauser syndrome in a large cohort of families.
Data have identified TBX6 as a new gene associated with Mullerian aplasia. The results also support the relevance of LHX1 and CNVs in the development of this congenital malformation.
Title: TBX6, LHX1 and copy number variations in the complex genetics of Müllerian aplasia.
study concludes that heterozygous mutations of LHX1 might be one cause of the Mayer-Rokitansky-Kuster-Hauser syndrome in a subgroup of patients
Title: Frame shift mutation of LHX1 is associated with Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome.
Data indicate that expression of ERAS, LHX1, and CCRK is increased in aggressive subgroups of medulloblastomas.
Title: Functional genomics identifies drivers of medulloblastoma dissemination.
Lim1/LIM1 expression in neonatal, adult mouse and human endometrium suggesting Lim1/LIM1 may have a role in endometrial development and remodelling
Title: Lim1/LIM1 is expressed in developing and adult mouse and human endometrium.
Mutations in the coding regions of LHX1 may not be a common genetic etiologic factor involved in Han Chinese patients with mullerian duct abnormalities.
Title: LHX1 mutation screening in 96 patients with müllerian duct abnormalities.
Eleven dysplastic kidneys showed no expression of LIM1. In contrast, 12 of 32 nephroblastomas showed nuclear positivity.
Title: Lim1, an embryonal transcription factor, is absent in multicystic renal dysplasia, but reactivated in nephroblastomas.
findings establish that the developmental marker Lim1 acts as an oncogene in cancer cells and targeting Lim1 may constitute an innovative therapeutic intervention in human lear cell carcinoma
Title: LIM-class homeobox gene Lim1, a novel oncogene in human renal cell carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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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

RH71201 (e-PCR)
- UniSTS:55795

NoName (e-PCR)
- UniSTS:484349

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
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 cis-regulatory region sequence-specific DNA 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
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in S-shaped body morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in anatomical structure formation involved in morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in anatomical structure morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in animal organ morphogenesis	TAS Traceable Author Statement more info
involved_in anterior/posterior axis specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in anterior/posterior pattern specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in branching involved in ureteric bud morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cell-cell signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to fibroblast growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cerebellar Purkinje cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cerebellar Purkinje cell-granule cell precursor cell signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in cerebellum development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cervix development	ISS Inferred from Sequence or Structural Similarity more info
involved_in comma-shaped body morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in dorsal spinal cord interneuron posterior axon guidance	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 ectoderm formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic pattern specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic retina morphogenesis in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic viscerocranium morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoderm formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in forebrain regionalization	ISS Inferred from Sequence or Structural Similarity more info
involved_in gastrulation with mouth forming second	ISS Inferred from Sequence or Structural Similarity more info
involved_in head development	ISS Inferred from Sequence or Structural Similarity more info
involved_in kidney development	ISS Inferred from Sequence or Structural Similarity more info
involved_in lateral motor column neuron migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesendoderm development	IEA Inferred from Electronic Annotation more info
involved_in mesonephric duct development	IEA Inferred from Electronic Annotation more info
involved_in metanephric S-shaped body morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in metanephric comma-shaped body morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in metanephric glomerulus development	IEA Inferred from Electronic Annotation more info
involved_in metanephric part of ureteric bud development	IEA Inferred from Electronic Annotation more info
involved_in metanephric renal vesicle morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in motor neuron axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in nephric duct elongation	IEA Inferred from Electronic Annotation more info
involved_in nephric duct morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in oviduct development	ISS Inferred from Sequence or Structural Similarity more info
involved_in oviduct epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in paramesonephric duct development	ISS Inferred from Sequence or Structural Similarity more info
involved_in pattern specification process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of anterior head development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of branching involved in ureteric bud morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gastrulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of nephron tubule epithelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in post-embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in primitive streak formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in pronephros development	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in renal vesicle morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in retina layer formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in somite rostral/caudal axis specification	IEA Inferred from Electronic Annotation more info
involved_in spinal cord association neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in telencephalon development	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in ureter morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in ureteric bud development	ISS Inferred from Sequence or Structural Similarity more info
involved_in urogenital system development	ISS Inferred from Sequence or Structural Similarity more info
involved_in uterine epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in uterus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in vagina development	ISS Inferred from Sequence or Structural Similarity more info
involved_in ventral spinal cord development	IEA Inferred from Electronic Annotation 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	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM/homeobox protein Lhx1

Names: LIM homeobox protein 1; homeobox protein Lim-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.

mRNA and Protein(s)

NM_005568.5 → NP_005559.2 LIM/homeobox protein Lhx1

See identical proteins and their annotated locations for NP_005559.2

Status: REVIEWED

Source sequence(s)

AC243773, BC020470, BC101674

Consensus CDS

CCDS11316.1

UniProtKB/Swiss-Prot

P48742, Q3MIW0

Related

ENSP00000477829.1, ENST00000614239.1

Conserved Domains (4) summary

cd09367
Location:4 → 55

LIM1_Lhx1_Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

cd09375
Location:63 → 118

LIM2_Lhx1_Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

cl14561
Location:291 → 382

An_peroxidase_like; Animal heme peroxidases and related proteins

pfam00046
Location:183 → 236

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_000017.11 Reference GRCh38.p14 Primary Assembly

Range

36936785..36944612

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047435966.1 → XP_047291922.1 LIM/homeobox protein Lhx1 isoform X1

UniProtKB/Swiss-Prot

P48742, Q3MIW0
XM_047435967.1 → XP_047291923.1 LIM/homeobox protein Lhx1 isoform X1

UniProtKB/Swiss-Prot

P48742, Q3MIW0

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

1173092..1180977

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329298.1 → XP_054185273.1 LIM/homeobox protein Lhx1 isoform X1

UniProtKB/Swiss-Prot

P48742, Q3MIW0
XM_054329299.1 → XP_054185274.1 LIM/homeobox protein Lhx1 isoform X1

UniProtKB/Swiss-Prot

P48742, Q3MIW0

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

37923784..37931669

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054316049.1 → XP_054172024.1 LIM/homeobox protein Lhx1 isoform X1

UniProtKB/Swiss-Prot

P48742, Q3MIW0
XM_054316050.1 → XP_054172025.1 LIM/homeobox protein Lhx1 isoform X1

UniProtKB/Swiss-Prot

P48742, Q3MIW0