Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	3975
Gene name	LIM homeobox 1
Gene symbol	LHX1
Synonyms (NCBI Gene)	LIM-1LIM1
Chromosome	17
Chromosome location	17q12
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

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miRTarBase ID	miRNA	Experiments	Reference
MIRT614583	hsa-miR-141-3p	HITS-CLIP	23824327
MIRT614582	hsa-miR-200a-3p	HITS-CLIP	23824327
MIRT614581	hsa-miR-302c-5p	HITS-CLIP	23824327
MIRT614580	hsa-miR-552-5p	HITS-CLIP	23824327
MIRT614583	hsa-miR-141-3p	HITS-CLIP	23824327
MIRT614582	hsa-miR-200a-3p	HITS-CLIP	23824327
MIRT614581	hsa-miR-302c-5p	HITS-CLIP	23824327
MIRT614580	hsa-miR-552-5p	HITS-CLIP	23824327
MIRT614583	hsa-miR-141-3p	HITS-CLIP	23824327
MIRT614582	hsa-miR-200a-3p	HITS-CLIP	23824327
MIRT614581	hsa-miR-302c-5p	HITS-CLIP	23824327
MIRT614580	hsa-miR-552-5p	HITS-CLIP	23824327
MIRT614583	hsa-miR-141-3p	HITS-CLIP	23824327
MIRT614582	hsa-miR-200a-3p	HITS-CLIP	23824327
MIRT614581	hsa-miR-302c-5p	HITS-CLIP	23824327
MIRT614580	hsa-miR-552-5p	HITS-CLIP	23824327
MIRT1108954	hsa-miR-1271	CLIP-seq
MIRT1108955	hsa-miR-182	CLIP-seq
MIRT1108956	hsa-miR-219-1-3p	CLIP-seq
MIRT1108957	hsa-miR-30a	CLIP-seq
MIRT1108958	hsa-miR-30b	CLIP-seq
MIRT1108959	hsa-miR-30c	CLIP-seq
MIRT1108960	hsa-miR-30d	CLIP-seq
MIRT1108961	hsa-miR-30e	CLIP-seq
MIRT1108962	hsa-miR-3136-5p	CLIP-seq
MIRT1108963	hsa-miR-3140-5p	CLIP-seq
MIRT1108964	hsa-miR-3143	CLIP-seq
MIRT1108965	hsa-miR-3613-3p	CLIP-seq
MIRT1108966	hsa-miR-3927	CLIP-seq
MIRT1108967	hsa-miR-421	CLIP-seq
MIRT1108968	hsa-miR-4436a	CLIP-seq
MIRT1108969	hsa-miR-4439	CLIP-seq
MIRT1108970	hsa-miR-450a	CLIP-seq
MIRT1108971	hsa-miR-452	CLIP-seq
MIRT1108972	hsa-miR-4528	CLIP-seq
MIRT1108973	hsa-miR-4539	CLIP-seq
MIRT1108974	hsa-miR-4650-3p	CLIP-seq
MIRT1108975	hsa-miR-4676-3p	CLIP-seq
MIRT1108976	hsa-miR-4680-3p	CLIP-seq
MIRT1108977	hsa-miR-4680-5p	CLIP-seq
MIRT1108978	hsa-miR-4700-3p	CLIP-seq
MIRT1108979	hsa-miR-4709-5p	CLIP-seq
MIRT1108980	hsa-miR-4724-5p	CLIP-seq
MIRT1108981	hsa-miR-543	CLIP-seq
MIRT1108982	hsa-miR-943	CLIP-seq
MIRT1108983	hsa-miR-944	CLIP-seq
MIRT1108984	hsa-miR-96	CLIP-seq
MIRT2030128	hsa-miR-101	CLIP-seq
MIRT2030129	hsa-miR-1266	CLIP-seq
MIRT2030130	hsa-miR-138	CLIP-seq
MIRT2030131	hsa-miR-144	CLIP-seq
MIRT2030132	hsa-miR-2113	CLIP-seq
MIRT2030133	hsa-miR-218	CLIP-seq
MIRT1108962	hsa-miR-3136-5p	CLIP-seq
MIRT2030134	hsa-miR-3664-3p	CLIP-seq
MIRT1108966	hsa-miR-3927	CLIP-seq
MIRT2030135	hsa-miR-4269	CLIP-seq
MIRT1108969	hsa-miR-4439	CLIP-seq
MIRT1108970	hsa-miR-450a	CLIP-seq
MIRT2030136	hsa-miR-4518	CLIP-seq
MIRT1108971	hsa-miR-452	CLIP-seq
MIRT2030137	hsa-miR-4645-5p	CLIP-seq
MIRT1108974	hsa-miR-4650-3p	CLIP-seq
MIRT2030138	hsa-miR-4673	CLIP-seq
MIRT1108975	hsa-miR-4676-3p	CLIP-seq
MIRT2030139	hsa-miR-4703-3p	CLIP-seq
MIRT2030140	hsa-miR-4755-3p	CLIP-seq
MIRT2030141	hsa-miR-548q	CLIP-seq
MIRT2030142	hsa-miR-582-5p	CLIP-seq
MIRT1108982	hsa-miR-943	CLIP-seq
MIRT1108983	hsa-miR-944	CLIP-seq
MIRT2261022	hsa-miR-147	CLIP-seq
MIRT2030132	hsa-miR-2113	CLIP-seq
MIRT2261023	hsa-miR-3611	CLIP-seq
MIRT2261024	hsa-miR-599	CLIP-seq

149

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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: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:0000987	Function	Cis-regulatory region sequence-specific DNA binding	IEA
GO:0001655	Process	Urogenital system development	IEA
GO:0001655	Process	Urogenital system development	ISS
GO:0001656	Process	Metanephros development	IEA
GO:0001657	Process	Ureteric bud development	IEA
GO:0001657	Process	Ureteric bud development	ISS
GO:0001658	Process	Branching involved in ureteric bud morphogenesis	IEA
GO:0001702	Process	Gastrulation with mouth forming second	IEA
GO:0001702	Process	Gastrulation with mouth forming second	ISS
GO:0001705	Process	Ectoderm formation	IEA
GO:0001705	Process	Ectoderm formation	ISS
GO:0001706	Process	Endoderm formation	IEA
GO:0001706	Process	Endoderm formation	ISS
GO:0001822	Process	Kidney development	IEA
GO:0001822	Process	Kidney development	ISS
GO:0001823	Process	Mesonephros development	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003700	Function	DNA-binding transcription factor activity	ISS
GO:0003700	Function	DNA-binding transcription factor activity	NAS	9212161
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005667	Component	Transcription regulator complex	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006366	Process	Transcription by RNA polymerase II	IEA
GO:0006366	Process	Transcription by RNA polymerase II	ISS
GO:0007267	Process	Cell-cell signaling	IEA
GO:0007267	Process	Cell-cell signaling	ISS
GO:0007389	Process	Pattern specification process	IEA
GO:0007389	Process	Pattern specification process	ISS
GO:0007399	Process	Nervous system development	IEA
GO:0007399	Process	Nervous system development	TAS	9212161
GO:0007492	Process	Endoderm development	IEA
GO:0008045	Process	Motor neuron axon guidance	IEA
GO:0008045	Process	Motor neuron axon guidance	ISS
GO:0008270	Function	Zinc ion binding	IEA
GO:0009653	Process	Anatomical structure morphogenesis	IEA
GO:0009653	Process	Anatomical structure morphogenesis	IEA
GO:0009653	Process	Anatomical structure morphogenesis	ISS
GO:0009791	Process	Post-embryonic development	IEA
GO:0009791	Process	Post-embryonic development	ISS
GO:0009880	Process	Embryonic pattern specification	IEA
GO:0009880	Process	Embryonic pattern specification	ISS
GO:0009887	Process	Animal organ morphogenesis	TAS
GO:0009948	Process	Anterior/posterior axis specification	IEA
GO:0009948	Process	Anterior/posterior axis specification	ISS
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0009952	Process	Anterior/posterior pattern specification	ISS
GO:0009953	Process	Dorsal/ventral pattern formation	IEA
GO:0009953	Process	Dorsal/ventral pattern formation	ISS
GO:0010468	Process	Regulation of gene expression	IEA
GO:0010468	Process	Regulation of gene expression	ISS
GO:0010842	Process	Retina layer formation	IEA
GO:0010842	Process	Retina layer formation	ISS
GO:0021510	Process	Spinal cord development	IEA
GO:0021517	Process	Ventral spinal cord development	IEA
GO:0021527	Process	Spinal cord association neuron differentiation	IEA
GO:0021527	Process	Spinal cord association neuron differentiation	ISS
GO:0021537	Process	Telencephalon development	IEA
GO:0021549	Process	Cerebellum development	IEA
GO:0021549	Process	Cerebellum development	ISS
GO:0021702	Process	Cerebellar Purkinje cell differentiation	IEA
GO:0021702	Process	Cerebellar Purkinje cell differentiation	ISS
GO:0021871	Process	Forebrain regionalization	IEA
GO:0021871	Process	Forebrain regionalization	ISS
GO:0021937	Process	Cerebellar Purkinje cell-granule cell precursor cell signaling	IEA
GO:0021937	Process	Cerebellar Purkinje cell-granule cell precursor cell signaling	ISS
GO:0030154	Process	Cell differentiation	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0032525	Process	Somite rostral/caudal axis specification	IEA
GO:0032991	Component	Protein-containing complex	IEA
GO:0032991	Component	Protein-containing complex	ISS
GO:0035502	Process	Metanephric part of ureteric bud development	IEA
GO:0035846	Process	Oviduct epithelium development	IEA
GO:0035846	Process	Oviduct epithelium development	ISS
GO:0035847	Process	Uterine epithelium development	IEA
GO:0035847	Process	Uterine epithelium development	ISS
GO:0035849	Process	Nephric duct elongation	IEA
GO:0040019	Process	Positive regulation of embryonic development	IEA
GO:0040019	Process	Positive regulation of embryonic development	ISS
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0044344	Process	Cellular response to fibroblast growth factor stimulus	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	ISS
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0048382	Process	Mesendoderm development	IEA
GO:0048646	Process	Anatomical structure formation involved in morphogenesis	IEA
GO:0048646	Process	Anatomical structure formation involved in morphogenesis	ISS
GO:0048703	Process	Embryonic viscerocranium morphogenesis	IEA
GO:0048703	Process	Embryonic viscerocranium morphogenesis	ISS
GO:0048731	Process	System development	IEA
GO:0048793	Process	Pronephros development	IEA
GO:0060041	Process	Retina development in camera-type eye	IEA
GO:0060059	Process	Embryonic retina morphogenesis in camera-type eye	IEA
GO:0060059	Process	Embryonic retina morphogenesis in camera-type eye	ISS
GO:0060065	Process	Uterus development	IEA
GO:0060065	Process	Uterus development	ISS
GO:0060066	Process	Oviduct development	IEA
GO:0060066	Process	Oviduct development	ISS
GO:0060067	Process	Cervix development	IEA
GO:0060067	Process	Cervix development	ISS
GO:0060068	Process	Vagina development	IEA
GO:0060068	Process	Vagina development	ISS
GO:0060322	Process	Head development	IEA
GO:0060322	Process	Head development	ISS
GO:0060429	Process	Epithelium development	IEA
GO:0060429	Process	Epithelium development	ISS
GO:0061205	Process	Paramesonephric duct development	IEA
GO:0061205	Process	Paramesonephric duct development	ISS
GO:0072049	Process	Comma-shaped body morphogenesis	IEA
GO:0072049	Process	Comma-shaped body morphogenesis	ISS
GO:0072050	Process	S-shaped body morphogenesis	IEA
GO:0072050	Process	S-shaped body morphogenesis	ISS
GO:0072077	Process	Renal vesicle morphogenesis	IEA
GO:0072077	Process	Renal vesicle morphogenesis	ISS
GO:0072164	Process	Mesonephric tubule development	IEA
GO:0072177	Process	Mesonephric duct development	IEA
GO:0072178	Process	Nephric duct morphogenesis	IEA
GO:0072178	Process	Nephric duct morphogenesis	ISS
GO:0072197	Process	Ureter morphogenesis	IEA
GO:0072224	Process	Metanephric glomerulus development	IEA
GO:0072278	Process	Metanephric comma-shaped body morphogenesis	IEA
GO:0072283	Process	Metanephric renal vesicle morphogenesis	IEA
GO:0072284	Process	Metanephric S-shaped body morphogenesis	IEA
GO:0090009	Process	Primitive streak formation	IEA
GO:0090009	Process	Primitive streak formation	ISS
GO:0090190	Process	Positive regulation of branching involved in ureteric bud morphogenesis	IEA
GO:0090190	Process	Positive regulation of branching involved in ureteric bud morphogenesis	ISS
GO:0097379	Process	Dorsal spinal cord interneuron posterior axon guidance	ISS
GO:0097477	Process	Lateral motor column neuron migration	IEA
GO:0097477	Process	Lateral motor column neuron migration	ISS
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:2000543	Process	Positive regulation of gastrulation	IEA
GO:2000543	Process	Positive regulation of gastrulation	ISS
GO:2000744	Process	Positive regulation of anterior head development	IEA
GO:2000744	Process	Positive regulation of anterior head development	ISS
GO:2000768	Process	Positive regulation of nephron tubule epithelial cell differentiation	IEA
GO:2000768	Process	Positive regulation of nephron tubule epithelial cell differentiation	ISS

MIM	HGNC	e!Ensembl
601999	6593	ENSG00000273706

P48742

Protein name

LIM/homeobox protein Lhx1 (LIM homeobox protein 1) (Homeobox protein Lim-1) (hLim-1)

Protein function

Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00412	LIM	4 → 59	LIM domain	Domain
PF00412	LIM	63 → 122	LIM domain	Domain
PF00046	Homeodomain	181 → 237	Homeodomain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in the brain, thymus, and tonsils. Expressed in samples from patients with chronic myeloid leukemia (CML) and in 58% of acute myeloid leukemia (AML) cell lines. {ECO:0000269|PubMed:9212161}.

Sequence

MVHCAGCKRPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFRCFG
TKCAGCAQGISPSDLVRRARSKVFHLNCFTCMMCNKQLSTGEELYIIDENKFVCKEDYLS
NSSVAKENSLHSATTGSDPSLSPDSQDPSQDDAKDSESANVSDKEAGSNENDDQNLGAKR
RGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRMKQ
LSALGARRHAFFRSPRRMRPLVDRLEPGELIPNGPFSFYGDYQSEYYGPGGNYDFFPQGP
PSSQAQTPVDLPFVPSSGPSGTPLGGLEHPLPGHHPSSEAQRFTDILAHPPGDSPSPEPS
LPGPLHSMSAEVFGPSPPFSSLSVNGGASYGNHLSHPPEMNEAAVW

Sequence length

406

Interactions

View interactions

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)

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
17Q12 MICRODELETION SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FEMALE UROGENITAL DISEASES	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LHX1-related disorder	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (35)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
17q12 microdeletion syndrome	17q12 Deletion Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorder	Autism	Pubtator	36700567	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Abnormalities	Cardiovascular Abnormalities	BEFREE	25510704		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Abnormalities	Cardiovascular abnormalities	Pubtator	25510704	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
CHROMOSOME 17q12 DELETION SYNDROME	17q12 Deletion Syndrome	ORPHANET_DG	22740494		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	33111631	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	21132009, 30076415		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	36700567	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	36116266	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Female Urogenital Diseases	Female Urogenital Diseases	CTD_human_DG	16002989		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glioblastoma	Glioblastoma	Pubtator	38563293	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	22983390, 32857719, 35180817	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycosuria Renal	Renal glycosuria	Pubtator	22583611	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	38563293	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Language Disorders	Language Disorders	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	31526458	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	31856144	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	BEFREE	22875024		★★★★★ ★☆☆☆☆ Found in Text Mining only
Multicystic Dysplastic Kidney	Multicystic renal dysplasia	BEFREE	21778788		★★★★★ ★☆☆☆☆ Found in Text Mining only
Multicystic Dysplastic Kidney	Multicystic renal dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	21132009, 30076415		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephroblastoma	Nephroblastoma	BEFREE	21778788		★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	21132009, 21778788, 30076415		★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal dysplasia	Renal dysplasia	BEFREE	21778788		★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Insufficiency	Renal Insufficiency	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Subcortical cerebral atrophy	Subcortical cerebral atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ureterocele	Ureterocele	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Von Hippel-Lindau Syndrome	Von Hippel-Lindau Syndrome	BEFREE	30076415		★★★★★ ★☆☆☆☆ Found in Text Mining only

LHX1 (LIM homeobox 1)