LHX2 (LIM homeobox 2)

Gene

• Entrez ID: 9355
• Gene name: LIM homeobox 2
• Gene symbol: LHX2
• Synonyms (NCBI Gene): LH2, hLhx2
• Chromosome: 9
• Chromosome location: 9q33.3
• Summary: This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator. The protein can recapitulate or rescue phe

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022169	hsa-miR-124-3p	Microarray	18668037
MIRT042689	hsa-miR-196b-5p	CLASH	23622248
MIRT734416	hsa-miR-1238-3p	Immunohistochemistry (IHC), Luciferase reporter assay, Microarray, qRT-PCR, Western blotting	32526477
MIRT735618	hsa-miR-409-3p	Immunohistochemistry (IHC), qRT-PCR	32040954
MIRT735620	hsa-miR-409-5p	Immunohistochemistry (IHC), qRT-PCR	32040954
MIRT1108985	hsa-miR-185	CLIP-seq
MIRT1108986	hsa-miR-3919	CLIP-seq
MIRT1108987	hsa-miR-4306	CLIP-seq
MIRT1108988	hsa-miR-4419a	CLIP-seq
MIRT1108989	hsa-miR-4510	CLIP-seq
MIRT1108990	hsa-miR-4644	CLIP-seq
MIRT1108991	hsa-miR-4797-5p	CLIP-seq
MIRT1108992	hsa-miR-583	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001843	Process	Neural tube closure	IEA
GO:0001942	Process	Hair follicle development	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0005515	Function	Protein binding	IPI	20211142, 32296183, 35140242
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007399	Process	Nervous system development	IEA
GO:0007411	Process	Axon guidance	IEA
GO:0007420	Process	Brain development	IEA
GO:0007498	Process	Mesoderm development	IEA
GO:0009953	Process	Dorsal/ventral pattern formation	IEA
GO:0021537	Process	Telencephalon development	IEA
GO:0021772	Process	Olfactory bulb development	IEA
GO:0021978	Process	Telencephalon regionalization	IEA
GO:0021987	Process	Cerebral cortex development	IEA
GO:0022008	Process	Neurogenesis	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0030182	Process	Neuron differentiation	IEA
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0045199	Process	Maintenance of epithelial cell apical/basal polarity	IEA
GO:0045814	Process	Negative regulation of gene expression, epigenetic	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	ISS
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048646	Process	Anatomical structure formation involved in morphogenesis	IEA
GO:0048675	Process	Axon extension	IEA
GO:0050768	Process	Negative regulation of neurogenesis	IEA
GO:0060041	Process	Retina development in camera-type eye	IEA
GO:2000179	Process	Positive regulation of neural precursor cell proliferation	IEA

Other IDs

• MIM: 603759
• HGNC: 6594
• e!Ensembl: ENSG00000106689

Protein

• UniProt ID: P50458
• Protein name: LIM/homeobox protein Lhx2 (Homeobox protein LH-2) (LIM homeobox protein 2)
• Protein function: Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types (By similarity). {ECO:00
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00412	LIM	53 → 110	LIM domain	Domain
  PF00412	LIM	115 → 172	LIM domain	Domain
  PF00046	Homeodomain	267 → 323	Homeodomain	Domain

• Sequence:

  MLFHSLSGPEVHGVIDEMDRRAKSEAPAISSAIDRGDTETTMPSISSDRAALCAGCGGKI
  SDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDYYRRFSVQRCARCHL
  GISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDSLVYCRLHFEALLQGEYPAH
  FNHADVAAAAAAAAAAKSAGLGAAGANPLGLPYYNGVGTVQKGRPRKRKSPGPGADLAAY
  NAALSCNENDAEHLDRDQPYPSSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLA
  QKTGLTKRVLQVWFQNARAKFRRNLLRQENTGVDKSTDAALQTGTPSGPASELSNASLSP
  SSTPTTLTDLTSPTLPTVTSVLTSVPGNLEGHEPHSPSQTTLTNLF

• Sequence length: 406

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Variable neurodevelopmental disorder	Likely pathogenic	rs2540147394	RCV003314216	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ARTHRITIS, RHEUMATOID	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOIMMUNE DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LHX2-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYCYSTIC OVARY SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POST-TRAUMATIC STRESS DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHEUMATOID ARTHRITIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenoid Cystic Carcinoma	Adenocarcinoma	BEFREE	31128548		★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	BEFREE	22535646		★☆☆☆☆ Found in Text Mining only
Anophthalmos	Syndromic microphthalmia	BEFREE	21203406		★☆☆☆☆ Found in Text Mining only
Anophthalmos	Anophthalmia	Pubtator	21203406	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	23456299	Associate	★☆☆☆☆ Found in Text Mining only
Astrocytoma	Astrocytoma	Pubtator	26497896	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	37057675	Associate	★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	31708105		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	24423492		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	26510686	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	31724536	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	31128548		★☆☆☆☆ Found in Text Mining only
Cirrhosis	Cirrhosis	BEFREE	19815628		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	38092774	Associate	★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	17568789		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	36011368	Associate	★☆☆☆☆ Found in Text Mining only
Fibrosis, Liver	Liver Fibrosis	BEFREE	15536133		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Tumors	Gastrointestinal stromal tumor	Pubtator	24133624	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	38563293	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	32857719	Associate	★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	38563293	Inhibit	★☆☆☆☆ Found in Text Mining only
insulinoma	Insulinoma	BEFREE	24423492		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	37057675	Associate	★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis	Liver Cirrhosis	BEFREE	19815628		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	24423492		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	23864708, 25324171, 26510686, 31724536		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	37057675	Associate	★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	30791932		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	35300558, 35864158	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	22366991, 24423492		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	31708105		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	26189214, 28927097		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	31724536		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	31724536	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic Ductal Adenocarcinoma	Pancreatic adenocarcinoma	BEFREE	25324171		★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	BEFREE	25324171		★☆☆☆☆ Found in Text Mining only
Pituitary Diseases	Pituitary Diseases	BEFREE	22535646		★☆☆☆☆ Found in Text Mining only
Post-Traumatic Stress Disorder	Stress Disorder	GWASCAT_DG	25456346		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	Lymphoblastic Leukemia	BEFREE	29278703		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	17568789		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Rheumatoid Arthritis	Rheumatoid arthritis	CTD_human_DG	17568789		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	BEFREE	31708105		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	31173287	Associate	★☆☆☆☆ Found in Text Mining only
Teratoma	Teratoma	BEFREE	26339946		★☆☆☆☆ Found in Text Mining only