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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	89884
Gene name	LIM homeobox 4
Gene symbol	LHX4
Synonyms (NCBI Gene)	CPHD4
Chromosome	1
Chromosome location	1q25.2
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 involved in the control of differentiation and development of the pituitary gland

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs587776662	->C	Pathogenic	Coding sequence variant, frameshift variant
rs886041420	A>-	Pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (56)

miRTarBase ID	miRNA	Experiments	Reference
MIRT023725	hsa-miR-1-3p	Microarray	18668037
MIRT702277	hsa-miR-548as-3p	HITS-CLIP	23313552
MIRT702276	hsa-miR-3614-5p	HITS-CLIP	23313552
MIRT702275	hsa-miR-6500-3p	HITS-CLIP	23313552
MIRT702274	hsa-miR-4768-3p	HITS-CLIP	23313552
MIRT702273	hsa-miR-4459	HITS-CLIP	23313552
MIRT702272	hsa-miR-4433a-3p	HITS-CLIP	23313552
MIRT702271	hsa-miR-6849-3p	HITS-CLIP	23313552
MIRT702270	hsa-miR-3190-5p	HITS-CLIP	23313552
MIRT702269	hsa-miR-4786-5p	HITS-CLIP	23313552
MIRT702268	hsa-miR-4470	HITS-CLIP	23313552
MIRT702267	hsa-miR-3926	HITS-CLIP	23313552
MIRT702266	hsa-miR-3688-5p	HITS-CLIP	23313552
MIRT702265	hsa-miR-548s	HITS-CLIP	23313552
MIRT623391	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT623390	hsa-miR-3605-5p	HITS-CLIP	23824327
MIRT623389	hsa-miR-4313	HITS-CLIP	23824327
MIRT656745	hsa-miR-6894-5p	HITS-CLIP	23824327
MIRT623391	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT623390	hsa-miR-3605-5p	HITS-CLIP	23824327
MIRT656745	hsa-miR-6894-5p	HITS-CLIP	23824327
MIRT623391	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT623390	hsa-miR-3605-5p	HITS-CLIP	23824327
MIRT623389	hsa-miR-4313	HITS-CLIP	23824327
MIRT576487	hsa-miR-548as-3p	HITS-CLIP	23313552
MIRT702276	hsa-miR-3614-5p	HITS-CLIP	23313552
MIRT702275	hsa-miR-6500-3p	HITS-CLIP	23313552
MIRT576486	hsa-miR-4768-3p	HITS-CLIP	23313552
MIRT576485	hsa-miR-4459	HITS-CLIP	23313552
MIRT576484	hsa-miR-4433a-3p	HITS-CLIP	23313552
MIRT576483	hsa-miR-6849-3p	HITS-CLIP	23313552
MIRT576482	hsa-miR-3190-5p	HITS-CLIP	23313552
MIRT576481	hsa-miR-4786-5p	HITS-CLIP	23313552
MIRT576480	hsa-miR-4470	HITS-CLIP	23313552
MIRT576479	hsa-miR-3926	HITS-CLIP	23313552
MIRT576478	hsa-miR-3688-5p	HITS-CLIP	23313552
MIRT576477	hsa-miR-548s	HITS-CLIP	23313552
MIRT623391	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT623390	hsa-miR-3605-5p	HITS-CLIP	23824327
MIRT623389	hsa-miR-4313	HITS-CLIP	23824327
MIRT656745	hsa-miR-6894-5p	HITS-CLIP	23824327
MIRT623391	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT623390	hsa-miR-3605-5p	HITS-CLIP	23824327
MIRT656745	hsa-miR-6894-5p	HITS-CLIP	23824327
MIRT623391	hsa-miR-6832-3p	HITS-CLIP	23824327
MIRT623390	hsa-miR-3605-5p	HITS-CLIP	23824327
MIRT623389	hsa-miR-4313	HITS-CLIP	23824327
MIRT2453014	hsa-miR-1294	CLIP-seq
MIRT2453015	hsa-miR-4316	CLIP-seq
MIRT2453016	hsa-miR-4446-3p	CLIP-seq
MIRT2453017	hsa-miR-4675	CLIP-seq
MIRT2453018	hsa-miR-4677-3p	CLIP-seq
MIRT2453019	hsa-miR-4741	CLIP-seq
MIRT2453020	hsa-miR-4753-5p	CLIP-seq
MIRT2453021	hsa-miR-4757-5p	CLIP-seq
MIRT2453022	hsa-miR-888	CLIP-seq

Show/Hide all (27)

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:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	15998782
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	20211142, 25416956, 25910212, 26871637, 27820671, 28514442, 31515488, 32296183, 33961781, 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:0006915	Process	Apoptotic process	IEA
GO:0008045	Process	Motor neuron axon guidance	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008327	Function	Methyl-CpG binding	IDA	28473536
GO:0009887	Process	Animal organ morphogenesis	IEA
GO:0021526	Process	Medial motor column neuron differentiation	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0043565	Function	Sequence-specific DNA binding	IDA	28473536
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	15998782
GO:0046872	Function	Metal ion binding	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

MIM	HGNC	e!Ensembl
602146	21734	ENSG00000121454

Q969G2

Protein name

LIM/homeobox protein Lhx4 (LIM homeobox protein 4)

Protein function

May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung. Binds preferentially to methylated DNA (PubMed:28473536).

PDB

5HOD

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00412	LIM	30 → 85	LIM domain	Domain
PF00412	LIM	89 → 148	LIM domain	Domain
PF00046	Homeodomain	158 → 214	Homeodomain	Domain

Sequence

MMQSATVPAEGAVKGLPEMLGVPMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADC
QMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIIC
NRQLATGDEFYLMEDGRLVCKEDYETAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSP
KPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRHRWGQFYKSVKRSRGSSKQ
EKESSAEDCGVSDSELSFREDQILSELGHTNRIYGNVGDVTGGQLMNGSFSMDGTGQSYQ
DLRDGSPYGIPQSPSSISSLPSHAPLLNGLDYTVDSNLGIIAHAGQGVSQTLRAMAGGPT
SDISTGSSVGYPDFPTSPGSWLDEMDHPPF

Sequence length

390

Interactions

View interactions

104

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
See cases	Likely pathogenic	rs2149256470	RCV001420326
Short stature-pituitary and cerebellar defects-small sella turcica syndrome	Pathogenic	rs786204780, rs748268631, rs121912641, rs121912643, rs121912644, rs587776662	RCV000169664 RCV000007935 RCV000007936 RCV000007938 RCV000007939 RCV000007940

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Combined pituitary hormone deficiencies, genetic form	Benign; Likely benign	rs771109452	RCV005414275
Combined Pituitary Hormone Deficiency, Dominant	Uncertain significance; Conflicting classifications of pathogenicity	rs145933198, rs150931176	RCV000374954 RCV000362800
LHX4-related disorder	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	rs375441662, rs367664877, rs762313842, rs1664150962, rs139155359, rs748004117, rs994001572, rs767622575, rs143798020, rs150875319, rs375216188, rs147491286, rs751665904, rs373879455	RCV003958759 RCV003980979 RCV003948958 RCV003901864 RCV003909597 RCV003934117 RCV003946998 RCV003966873 RCV003948288 RCV003912882 RCV003411927 RCV003906190 RCV003973065 RCV003928695
Pituitary hormone deficiency, combined, 1	Uncertain significance	rs1553282666, rs766381404	RCV000584396 RCV000582035

Show/Hide Text Mining Associations (24)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
ACTH Deficiency Isolated	Associate	17527005, 25955177
Arnold Chiari Malformation	Associate	17527005
Cerebellar Diseases	Associate	11567216
Chromosome Aberrations	Associate	34124982
Colorectal Neoplasms	Stimulate	25034524
Combined Pituitary Hormone Deficiency	Associate	17527005, 25871839, 25955177, 32796691
Cryptorchidism	Associate	25871839
Death	Associate	25871839
Developmental Defects of Enamel	Associate	11567216
Empty Sella Syndrome	Associate	11567216, 17527005
Growth Disorders	Associate	11567216
Hemochromatosis	Associate	23761422, 25955177
Hereditary renal agenesis	Associate	25871839
Hypoglycemia	Associate	17527005
Hypopituitarism	Associate	25871839, 25955177, 34124982
Hypothyroidism	Associate	25955177
Neoplasms	Associate	25034524
Pituitary Diseases	Associate	11567216, 17527005, 25871839, 34124982
Pituitary Hormone Deficiency Combined 2	Associate	25871839
Pituitary Neoplasms	Associate	31745224
Pregnancy Ectopic	Associate	17527005
Respiratory Tract Diseases	Associate	17527005
Turner Syndrome	Associate	23761422
Wyburn Mason's syndrome	Associate	25871839

LHX4 (LIM homeobox 4)