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	4009
Gene name	LIM homeobox transcription factor 1 alpha
Gene symbol	LMX1A
Synonyms (NCBI Gene)	DFNA7LMX1LMX1.1
Chromosome	1
Chromosome location	1q23.3
Summary	This gene encodes a homeodomain and LIM-domain containing protein. The encoded protein is a transcription factor that acts as a positive regulator of insulin gene transcription. This gene also plays a role in the development of dopamine producing neurons

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SNP ID	Visualize variation	Clinical significance	Consequence
rs1571177726	C>G	Pathogenic	Coding sequence variant, missense variant

125

Show/Hide all (125)

miRTarBase ID	miRNA	Experiments	Reference
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT630429	hsa-miR-329-3p	HITS-CLIP	23824327
MIRT630428	hsa-miR-362-3p	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT630427	hsa-miR-3941	HITS-CLIP	23824327
MIRT630426	hsa-miR-4672	HITS-CLIP	23824327
MIRT630425	hsa-miR-466	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT630429	hsa-miR-329-3p	HITS-CLIP	23824327
MIRT630428	hsa-miR-362-3p	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT630427	hsa-miR-3941	HITS-CLIP	23824327
MIRT630426	hsa-miR-4672	HITS-CLIP	23824327
MIRT630425	hsa-miR-466	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT616968	hsa-miR-1237-3p	HITS-CLIP	23824327
MIRT616967	hsa-miR-1248	HITS-CLIP	23824327
MIRT616966	hsa-miR-3120-5p	HITS-CLIP	23824327
MIRT616965	hsa-miR-3182	HITS-CLIP	23824327
MIRT616964	hsa-miR-6868-3p	HITS-CLIP	23824327
MIRT616963	hsa-miR-6888-3p	HITS-CLIP	23824327
MIRT616962	hsa-miR-4743-3p	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT630429	hsa-miR-329-3p	HITS-CLIP	23824327
MIRT630428	hsa-miR-362-3p	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT630427	hsa-miR-3941	HITS-CLIP	23824327
MIRT630426	hsa-miR-4672	HITS-CLIP	23824327
MIRT630425	hsa-miR-466	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT630429	hsa-miR-329-3p	HITS-CLIP	23824327
MIRT630428	hsa-miR-362-3p	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT630427	hsa-miR-3941	HITS-CLIP	23824327
MIRT630426	hsa-miR-4672	HITS-CLIP	23824327
MIRT630425	hsa-miR-466	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT616968	hsa-miR-1237-3p	HITS-CLIP	23824327
MIRT616967	hsa-miR-1248	HITS-CLIP	23824327
MIRT616966	hsa-miR-3120-5p	HITS-CLIP	23824327
MIRT616965	hsa-miR-3182	HITS-CLIP	23824327
MIRT616964	hsa-miR-6868-3p	HITS-CLIP	23824327
MIRT616963	hsa-miR-6888-3p	HITS-CLIP	23824327
MIRT616962	hsa-miR-4743-3p	HITS-CLIP	23824327
MIRT612813	hsa-miR-377-3p	HITS-CLIP	23824327
MIRT612812	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT612811	hsa-miR-8485	HITS-CLIP	23824327
MIRT612810	hsa-miR-603	HITS-CLIP	23824327
MIRT1112211	hsa-miR-3160-3p	CLIP-seq
MIRT1112212	hsa-miR-3173-5p	CLIP-seq
MIRT1112213	hsa-miR-3194-3p	CLIP-seq
MIRT1112214	hsa-miR-3545-3p	CLIP-seq
MIRT1112215	hsa-miR-3607-5p	CLIP-seq
MIRT1112216	hsa-miR-3657	CLIP-seq
MIRT1112217	hsa-miR-3921	CLIP-seq
MIRT1112218	hsa-miR-4290	CLIP-seq
MIRT1112219	hsa-miR-4303	CLIP-seq
MIRT1112220	hsa-miR-4474-5p	CLIP-seq
MIRT1112221	hsa-miR-4487	CLIP-seq
MIRT1112222	hsa-miR-4539	CLIP-seq
MIRT1112223	hsa-miR-4653-5p	CLIP-seq
MIRT1112224	hsa-miR-4667-3p	CLIP-seq
MIRT1112225	hsa-miR-4669	CLIP-seq
MIRT1112226	hsa-miR-4690-3p	CLIP-seq
MIRT1112227	hsa-miR-4733-3p	CLIP-seq
MIRT1112228	hsa-miR-4775	CLIP-seq
MIRT1112229	hsa-miR-558	CLIP-seq
MIRT1112230	hsa-miR-642a	CLIP-seq
MIRT1112231	hsa-miR-767-3p	CLIP-seq
MIRT1112218	hsa-miR-4290	CLIP-seq
MIRT1112224	hsa-miR-4667-3p	CLIP-seq
MIRT1112227	hsa-miR-4733-3p	CLIP-seq
MIRT1112218	hsa-miR-4290	CLIP-seq
MIRT1112224	hsa-miR-4667-3p	CLIP-seq
MIRT1112227	hsa-miR-4733-3p	CLIP-seq

Show/Hide all (41)

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:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISS
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:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	ISS
GO:0001558	Process	Regulation of cell growth	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	25814554, 32814053
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:0007411	Process	Axon guidance	IEA
GO:0007417	Process	Central nervous system development	IEA
GO:0007613	Process	Memory	IEA
GO:0007626	Process	Locomotory behavior	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0021542	Process	Dentate gyrus development	IEA
GO:0021549	Process	Cerebellum development	IEA
GO:0021766	Process	Hippocampus development	IEA
GO:0021953	Process	Central nervous system neuron differentiation	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0030901	Process	Midbrain development	IEA
GO:0042048	Process	Olfactory behavior	IEA
GO:0045665	Process	Negative regulation of neuron differentiation	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0050808	Process	Synapse organization	IEA
GO:0071542	Process	Dopaminergic neuron differentiation	IEA
GO:0071542	Process	Dopaminergic neuron differentiation	IEA
GO:0071542	Process	Dopaminergic neuron differentiation	TAS	24431302
GO:1904948	Process	Midbrain dopaminergic neuron differentiation	IEA
GO:1904948	Process	Midbrain dopaminergic neuron differentiation	ISS
GO:1904948	Process	Midbrain dopaminergic neuron differentiation	TAS	25640183
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

MIM	HGNC	e!Ensembl
600298	6653	ENSG00000162761

Q8TE12

Protein name

LIM homeobox transcription factor 1-alpha (LIM/homeobox protein 1.1) (LMX-1.1) (LIM/homeobox protein LMX1A)

Protein function

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing ver

PDB

8IK5 , 8IKE , 8ILW

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00412	LIM	35 → 90	LIM domain	Domain
PF00412	LIM	94 → 152	LIM domain	Domain
PF00046	Homeodomain	196 → 252	Homeodomain	Domain

Tissue specificity

TISSUE SPECIFICITY: Isoform 1 is expressed in many tissues. Not found in heart, liver, spleen and testis. Relatively highly expressed in fetal brain. Isoform LMX1A-4AB is expressed in testis. {ECO:0000269|PubMed:12062816}.

Sequence

MLDGLKMEENFQSAIDTSASFSSLLGRAVSPKSVCEGCQRVILDRFLLRLNDSFWHEQCV
QCASCKEPLETTCFYRDKKLYCKYDYEKLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCF
CCCVCERQLQKGDEFVLKEGQLLCKGDYEKERELLSLVSPAASDSGKSDDEESLCKSAHG
AGKGTAEEGKDHKRPKRPRTILTTQQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQ
VWFQNQRAKMKKLARRQQQQQQDQQNTQRLSSAQTNGGGSAGMEGIMNPYTALPTPQQLL
AIEQSVYSSDPFRQGLTPPQMPGDHMHPYGAEPLFHDLDSDDTSLSNLGDCFLATSEAGP
LQSRVGNPIDHLYSMQNSYFTS

Sequence length

382

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 Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal dominant nonsyndromic hearing loss 7	Likely pathogenic; Pathogenic	rs2102637875, rs2526238512, rs1396081975, rs776905403, rs1571147567, rs1571177726	RCV002251019 RCV002283656 RCV002306278 RCV003230243 RCV001003345 RCV001003346	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (28)

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.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANGIOEDEMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATYPICAL FEMORAL FRACTURE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL DOMINANT ISOLATED SENSORINEURAL DEAFNESS TYPE DFNA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL DOMINANT NONSYNDROMIC HEARING LOSS	—	ClinGen, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal-Recessive Hereditary Hearing Impairment	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL DOMINANT 7	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEARING IMPAIRMENT	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEARING LOSS	—	CTD, GWAS catalog CTD, GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEARING LOSS, AUTOSOMAL RECESSIVE	—	GenCC	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE IDIOPATHIC ARTHRITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LMX1A-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOBIUS SYNDROME	—	Disgenet, GenCC Disgenet, GenCC	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBSTRUCTIVE SLEEP APNEA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SENSORINEURAL HEARING LOSS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sensorineural hearing loss disorder	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENSORINEURAL HEARING LOSS OF BILATERAL EARS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TREATMENT-RESISTANT HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VESTIBULAR NEURONITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (30)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma	Associate	24407576	★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Associate	37665736	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cakut	Associate	30910156	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Associate	24018208	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Inhibit	32751497	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Associate	32207384	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Associate	24407576	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	31547144	★★★★★ ★☆☆☆☆ Found in Text Mining only
Deafness	Associate	29754270	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Associate	19761607	★★★★★ ★☆☆☆☆ Found in Text Mining only
Fetal Growth Retardation	Associate	30910156	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Associate	29754270, 34847940	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Associate	29754270	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lesch Nyhan Syndrome	Associate	40710358	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Inhibit	32751497	★★★★★ ★☆☆☆☆ Found in Text Mining only
Mouth Diseases	Associate	20564139	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	24018208	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	21159062, 24508839, 32207384	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	31915311, 32751497	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Associate	29754270	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Associate	32751497	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pigmentation Disorders	Associate	29754270	★★★★★ ★☆☆☆☆ Found in Text Mining only
Prodromal Symptoms	Associate	31547144	★★★★★ ★☆☆☆☆ Found in Text Mining only
Reproductive Tract Infections	Associate	29754270	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Associate	21159062, 31915311, 32751497	★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Associate	22529986	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Dysplasia	Stimulate	24508839	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Inhibit	21159062	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Associate	24018208, 32751497	★★★★★ ★☆☆☆☆ Found in Text Mining only
Vestibular Diseases	Associate	29754270	★★★★★ ★☆☆☆☆ Found in Text Mining only

LMX1A (LIM homeobox transcription factor 1 alpha)