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

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	8022
Gene name Gene Name - the full gene name approved by the HGNC.	LIM homeobox 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	LHX3
Synonyms (NCBI Gene) Gene synonyms aliases	CPHD3, LIM3, M2-LHX3
Chromosome Chromosome number	9
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	9q34.3
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutat

Show/Hide all(8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894117	T>C	Pathogenic	Coding sequence variant, missense variant
rs137854503	G>A	Pathogenic	Coding sequence variant, missense variant
rs137854504	GC>AGGA	Pathogenic	Coding sequence variant, frameshift variant
rs137854505	C>T	Pathogenic	Coding sequence variant, stop gained
rs137854506	T>A	Pathogenic	Coding sequence variant, stop gained
rs190916587	G>A,C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs587776711	GTCGTCCCCTCGGCTGACCTCGC>-	Pathogenic	Splice donor variant, coding sequence variant, intron variant
rs587776712	A>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all(60)

miRTarBase ID	miRNA	Experiments
MIRT1108993	hsa-miR-4761-5p	CLIP-seq
MIRT1108994	hsa-miR-545	CLIP-seq
MIRT1108995	hsa-miR-1207-5p	CLIP-seq
MIRT1108996	hsa-miR-125a-5p	CLIP-seq
MIRT1108997	hsa-miR-125b	CLIP-seq
MIRT1108998	hsa-miR-1271	CLIP-seq
MIRT1108999	hsa-miR-1321	CLIP-seq
MIRT1109000	hsa-miR-15a	CLIP-seq
MIRT1109001	hsa-miR-15b	CLIP-seq
MIRT1109002	hsa-miR-16	CLIP-seq
MIRT1109003	hsa-miR-182	CLIP-seq
MIRT1109004	hsa-miR-195	CLIP-seq
MIRT1109005	hsa-miR-302a	CLIP-seq
MIRT1109006	hsa-miR-302b	CLIP-seq
MIRT1109007	hsa-miR-302c	CLIP-seq
MIRT1109008	hsa-miR-302d	CLIP-seq
MIRT1109009	hsa-miR-302e	CLIP-seq
MIRT1109010	hsa-miR-3150b-3p	CLIP-seq
MIRT1109011	hsa-miR-342-5p	CLIP-seq
MIRT1109012	hsa-miR-3616-3p	CLIP-seq
MIRT1109013	hsa-miR-372	CLIP-seq
MIRT1109014	hsa-miR-373	CLIP-seq
MIRT1109015	hsa-miR-424	CLIP-seq
MIRT1109016	hsa-miR-4270	CLIP-seq
MIRT1109017	hsa-miR-4319	CLIP-seq
MIRT1109018	hsa-miR-4436b-3p	CLIP-seq
MIRT1109019	hsa-miR-4441	CLIP-seq
MIRT1109020	hsa-miR-4524	CLIP-seq
MIRT1109021	hsa-miR-4651	CLIP-seq
MIRT1109022	hsa-miR-4664-5p	CLIP-seq
MIRT1109023	hsa-miR-4687-3p	CLIP-seq
MIRT1109024	hsa-miR-4689	CLIP-seq
MIRT1109025	hsa-miR-4710	CLIP-seq
MIRT1109026	hsa-miR-4725-5p	CLIP-seq
MIRT1109027	hsa-miR-4728-5p	CLIP-seq
MIRT1109028	hsa-miR-4739	CLIP-seq
MIRT1109029	hsa-miR-4756-5p	CLIP-seq
MIRT1109030	hsa-miR-4763-3p	CLIP-seq
MIRT1109031	hsa-miR-4784	CLIP-seq
MIRT1109032	hsa-miR-497	CLIP-seq
MIRT1109033	hsa-miR-503	CLIP-seq
MIRT1109034	hsa-miR-504	CLIP-seq
MIRT1109035	hsa-miR-520a-3p	CLIP-seq
MIRT1109036	hsa-miR-520b	CLIP-seq
MIRT1109037	hsa-miR-520c-3p	CLIP-seq
MIRT1109038	hsa-miR-520d-3p	CLIP-seq
MIRT1109039	hsa-miR-520e	CLIP-seq
MIRT1109040	hsa-miR-544b	CLIP-seq
MIRT1109041	hsa-miR-608	CLIP-seq
MIRT1109042	hsa-miR-646	CLIP-seq
MIRT1109043	hsa-miR-765	CLIP-seq
MIRT1109044	hsa-miR-96	CLIP-seq
MIRT1108998	hsa-miR-1271	CLIP-seq
MIRT1109003	hsa-miR-182	CLIP-seq
MIRT1109023	hsa-miR-4687-3p	CLIP-seq
MIRT2030143	hsa-miR-543	CLIP-seq
MIRT1109044	hsa-miR-96	CLIP-seq
MIRT2261025	hsa-miR-4492	CLIP-seq
MIRT2261026	hsa-miR-4498	CLIP-seq
MIRT2261027	hsa-miR-762	CLIP-seq

Transcription factors

Show/Hide all(1)

Transcription factor	Regulation	Reference
SOX2	Activation	18407919

Show/Hide all(47)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription cis-regulatory region binding	IEA
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:0001221	Function	Transcription coregulator binding	IEA
GO:0001223	Function	Transcription coactivator binding	IEA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	15271874
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001890	Process	Placenta development	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	10598593
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:0006915	Process	Apoptotic process	IEA
GO:0008045	Process	Motor neuron axon guidance	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0009887	Process	Animal organ morphogenesis	TAS	10598593
GO:0009953	Process	Dorsal/ventral pattern formation	IEA
GO:0021520	Process	Spinal cord motor neuron cell fate specification	IEA
GO:0021521	Process	Ventral spinal cord interneuron specification	IEA
GO:0021526	Process	Medial motor column neuron differentiation	IEA
GO:0021527	Process	Spinal cord association neuron differentiation	IEA
GO:0021983	Process	Pituitary gland development	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0030324	Process	Lung development	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0043565	Function	Sequence-specific DNA binding	IDA	15271874
GO:0043565	Function	Sequence-specific DNA binding	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	IDA	15271874
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048839	Process	Inner ear development	IEP	18407919
GO:0060126	Process	Somatotropin secreting cell differentiation	IEA
GO:0060127	Process	Prolactin secreting cell differentiation	IEA
GO:0060129	Process	Thyroid-stimulating hormone-secreting cell differentiation	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IPI	26612202

MIM	HGNC	e!Ensembl
600577	6595	ENSG00000107187

Protein

UniProt ID

Q9UBR4

Protein name

LIM/homeobox protein Lhx3 (LIM homeobox protein 3)

Protein function

Transcription factor. Recognizes and binds to the consensus sequence motif 5'-AATTAATTA-3' in the regulatory elements of target genes, such as glycoprotein hormones alpha chain CGA and visual system homeobox CHX10, positively modulating transcri

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00412	LIM	31 → 86	LIM domain	Domain
PF00412	LIM	90 → 149	LIM domain	Domain
PF00046	Homeodomain	158 → 214	Homeodomain	Domain

Sequence

MLLETGLERDRARPGAAAVCTLGGTREIPLCAGCDQHILDRFILKALDRHWHSKCLKCSD
CHTPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVV
CKRQLATGDEFYLMEDSRLVCKADYETAKQREAEATAKRPRTTITAKQLETLKSAYNTSP
KPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRQRWGQYFRNMKRSRGGSKS
DKDSVQEGQDSDAEVSFPDEPSLAEMGPANGLYGSLGEPTQALGRPSGALGNFSLEHGGL
AGPEQYRELRPGSPYGVPPSPAAPQSLPGPQPLLSSLVYPDTSLGLVPSGAPGGPPPMRV
LAGNGPSSDLSTGSSGGYPDFPASPASWLDEVDHAQF

Sequence length

397

Interactions

View interactions

Show/Hide Unknown Diseases (6)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Atrial Fibrillation	Atrial fibrillation	N/A	N/A	GWAS
Diabetes	Diabetic kidney disease in type 2 diabetes (ESRD vs. no ESRD)	N/A	N/A	GWAS
Hypothyroidism	hypothyroidism due to deficient transcription factors involved in pituitary development or function	N/A	N/A	GenCC
Lung adenocarcinoma	Familial lung adenocarcinoma	N/A	N/A	GWAS
Non-acquired combined pituitary hormone deficiency-sensorineural hearing loss-spine abnormalities syndrome	non-acquired combined pituitary hormone deficiency with spine abnormalities	N/A	N/A	GenCC
Pituitary Hormone Deficiency	pituitary hormone deficiency, combined, 1	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (21)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma	Associate	28731174
Adenocarcinoma of Lung	Associate	28731174
Breast Neoplasms	Associate	19153192
Carcinoma Hepatocellular	Associate	31306102
Carcinoma Non Small Cell Lung	Associate	28731174
Cervical Vertebral Dysplasia	Stimulate	28302169
Chromosome Aberrations	Associate	34124982
Combined Pituitary Hormone Deficiency	Associate	22286346, 28302169, 29261175
Combined Pituitary Hormone Deficiency	Inhibit	28302169
Developmental Disabilities	Associate	22286346
Dwarfism Pituitary	Associate	34589056
Endometrial Neoplasms	Associate	35832124
Glioma	Associate	22983390
Head and Neck Neoplasms	Associate	22286346, 28302169
Hearing Loss Sensorineural	Associate	28302169
Hypopituitarism	Associate	34124982
Lung Diseases	Associate	26635082
Neoplasm Metastasis	Associate	31306102
Neoplasms	Stimulate	28731174, 31306102
Pituitary Diseases	Associate	18728160, 34124982
Uterine Cervicitis	Associate	28302169

LHX3 (LIM homeobox 3)