Details for: LMX1A

Gene ID: 4009

Symbol: LMX1A

Ensembl ID: ENSG00000162761

Description: LIM homeobox transcription factor 1 alpha

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: ciliated cell of the bronchus (CL0002332)
    Fold Change: 5.0799
    Cell Significance Index: -4.8500
  • Cell Name: neuronal brush cell (CL0000555)
    Fold Change: 4.4797
    Cell Significance Index: 48.6200
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: 4.1370
    Cell Significance Index: 253.6400
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: 1.8201
    Cell Significance Index: 58.3000
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: 1.0241
    Cell Significance Index: 25.6000
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 0.7114
    Cell Significance Index: 70.3700
  • Cell Name: fibro/adipogenic progenitor cell (CL0009099)
    Fold Change: 0.7088
    Cell Significance Index: 35.8200
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.6399
    Cell Significance Index: 577.7900
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: 0.6393
    Cell Significance Index: 13.6200
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.4446
    Cell Significance Index: 48.3600
  • Cell Name: cytotoxic T cell (CL0000910)
    Fold Change: 0.4268
    Cell Significance Index: 6.2200
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.3876
    Cell Significance Index: 63.0400
  • Cell Name: gut absorptive cell (CL0000677)
    Fold Change: 0.3858
    Cell Significance Index: 23.1600
  • Cell Name: preadipocyte (CL0002334)
    Fold Change: 0.3013
    Cell Significance Index: 5.8800
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 0.2463
    Cell Significance Index: 17.0300
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.2371
    Cell Significance Index: 45.1300
  • Cell Name: CD14-low, CD16-positive monocyte (CL0002396)
    Fold Change: 0.1276
    Cell Significance Index: 3.0900
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: 0.1104
    Cell Significance Index: 2.2900
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 0.0961
    Cell Significance Index: 2.7700
  • Cell Name: keratocyte (CL0002363)
    Fold Change: 0.0838
    Cell Significance Index: 1.3300
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: 0.0683
    Cell Significance Index: 50.5700
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.0532
    Cell Significance Index: 1.8700
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: 0.0427
    Cell Significance Index: 24.0700
  • Cell Name: hematopoietic stem cell (CL0000037)
    Fold Change: 0.0228
    Cell Significance Index: 0.3900
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: 0.0155
    Cell Significance Index: 3.0700
  • Cell Name: BEST4+ enteroycte (CL4030026)
    Fold Change: 0.0119
    Cell Significance Index: 0.1800
  • Cell Name: GABAergic interneuron (CL0011005)
    Fold Change: 0.0118
    Cell Significance Index: 8.1300
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.0042
    Cell Significance Index: 0.1900
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 0.0009
    Cell Significance Index: 0.0200
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: -0.0012
    Cell Significance Index: -2.2700
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: -0.0023
    Cell Significance Index: -4.2200
  • Cell Name: pancreatic D cell (CL0000173)
    Fold Change: -0.0028
    Cell Significance Index: -0.6000
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: -0.0032
    Cell Significance Index: -4.9500
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: -0.0039
    Cell Significance Index: -5.2400
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: -0.0042
    Cell Significance Index: -1.5200
  • Cell Name: medial ganglionic eminence derived interneuron (CL4023063)
    Fold Change: -0.0056
    Cell Significance Index: -0.0800
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: -0.0058
    Cell Significance Index: -1.6800
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: -0.0059
    Cell Significance Index: -3.2300
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: -0.0061
    Cell Significance Index: -3.8900
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: -0.0098
    Cell Significance Index: -4.4400
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: -0.0115
    Cell Significance Index: -2.3000
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: -0.0169
    Cell Significance Index: -2.4500
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: -0.0211
    Cell Significance Index: -3.6000
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: -0.0221
    Cell Significance Index: -3.9800
  • Cell Name: fibroblast of cardiac tissue (CL0002548)
    Fold Change: -0.0299
    Cell Significance Index: -0.4300
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: -0.0343
    Cell Significance Index: -3.5000
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.0347
    Cell Significance Index: -3.6100
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.0364
    Cell Significance Index: -4.1700
  • Cell Name: basal cell of urothelium (CL1000486)
    Fold Change: -0.0368
    Cell Significance Index: -4.5200
  • Cell Name: lactocyte (CL0002325)
    Fold Change: -0.0395
    Cell Significance Index: -5.1000
  • Cell Name: radial glial cell (CL0000681)
    Fold Change: -0.0455
    Cell Significance Index: -0.2700
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: -0.0539
    Cell Significance Index: -4.1400
  • Cell Name: progenitor cell (CL0011026)
    Fold Change: -0.0555
    Cell Significance Index: -0.5900
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: -0.0642
    Cell Significance Index: -3.6000
  • Cell Name: hippocampal granule cell (CL0001033)
    Fold Change: -0.0644
    Cell Significance Index: -4.3300
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: -0.0686
    Cell Significance Index: -5.1100
  • Cell Name: forebrain radial glial cell (CL0013000)
    Fold Change: -0.0715
    Cell Significance Index: -0.5200
  • Cell Name: pancreatic epsilon cell (CL0005019)
    Fold Change: -0.0809
    Cell Significance Index: -0.7500
  • Cell Name: skeletal muscle fiber (CL0008002)
    Fold Change: -0.0836
    Cell Significance Index: -2.1500
  • Cell Name: forebrain neuroblast (CL1000042)
    Fold Change: -0.0870
    Cell Significance Index: -5.3500
  • Cell Name: CD14-positive monocyte (CL0001054)
    Fold Change: -0.0872
    Cell Significance Index: -1.7100
  • Cell Name: indirect pathway medium spiny neuron (CL4023029)
    Fold Change: -0.0882
    Cell Significance Index: -3.9000
  • Cell Name: L5 extratelencephalic projecting glutamatergic cortical neuron (CL4023041)
    Fold Change: -0.0942
    Cell Significance Index: -3.3000
  • Cell Name: periportal region hepatocyte (CL0019026)
    Fold Change: -0.0976
    Cell Significance Index: -1.4400
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: -0.0996
    Cell Significance Index: -4.6800
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: -0.1038
    Cell Significance Index: -4.8400
  • Cell Name: direct pathway medium spiny neuron (CL4023026)
    Fold Change: -0.1080
    Cell Significance Index: -4.0900
  • Cell Name: basal epithelial cell of tracheobronchial tree (CL0002329)
    Fold Change: -0.1102
    Cell Significance Index: -3.0800
  • Cell Name: fibroblast of dermis (CL0002551)
    Fold Change: -0.1108
    Cell Significance Index: -2.3200
  • Cell Name: L6b glutamatergic cortical neuron (CL4023038)
    Fold Change: -0.1132
    Cell Significance Index: -3.7100
  • Cell Name: cerebellar granule cell (CL0001031)
    Fold Change: -0.1150
    Cell Significance Index: -1.9700
  • Cell Name: corticothalamic-projecting glutamatergic cortical neuron (CL4023013)
    Fold Change: -0.1177
    Cell Significance Index: -3.7500
  • Cell Name: cerebral cortex endothelial cell (CL1001602)
    Fold Change: -0.1194
    Cell Significance Index: -2.4300
  • Cell Name: erythrocyte (CL0000232)
    Fold Change: -0.1346
    Cell Significance Index: -3.4300
  • Cell Name: stratified epithelial cell (CL0000079)
    Fold Change: -0.1354
    Cell Significance Index: -4.9700
  • Cell Name: erythroid progenitor cell (CL0000038)
    Fold Change: -0.1415
    Cell Significance Index: -1.8500
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: -0.1423
    Cell Significance Index: -3.8000
  • Cell Name: near-projecting glutamatergic cortical neuron (CL4023012)
    Fold Change: -0.1455
    Cell Significance Index: -3.6300
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: -0.1513
    Cell Significance Index: -4.0600
  • Cell Name: hippocampal pyramidal neuron (CL1001571)
    Fold Change: -0.1528
    Cell Significance Index: -4.3600
  • Cell Name: megakaryocyte-erythroid progenitor cell (CL0000050)
    Fold Change: -0.1553
    Cell Significance Index: -2.1300
  • Cell Name: keratinocyte (CL0000312)
    Fold Change: -0.1594
    Cell Significance Index: -3.9800
  • Cell Name: neuroblast (sensu Vertebrata) (CL0000031)
    Fold Change: -0.1599
    Cell Significance Index: -1.0400
  • Cell Name: kidney epithelial cell (CL0002518)
    Fold Change: -0.1640
    Cell Significance Index: -4.8300
  • Cell Name: hepatocyte (CL0000182)
    Fold Change: -0.1648
    Cell Significance Index: -2.2900
  • Cell Name: lens fiber cell (CL0011004)
    Fold Change: -0.1679
    Cell Significance Index: -5.3100
  • Cell Name: hematopoietic multipotent progenitor cell (CL0000837)
    Fold Change: -0.1698
    Cell Significance Index: -2.0500
  • Cell Name: ependymal cell (CL0000065)
    Fold Change: -0.1706
    Cell Significance Index: -2.0100
  • Cell Name: fibroblast of mammary gland (CL0002555)
    Fold Change: -0.1723
    Cell Significance Index: -4.9400
  • Cell Name: granulosa cell (CL0000501)
    Fold Change: -0.1723
    Cell Significance Index: -4.5300
  • Cell Name: Purkinje cell (CL0000121)
    Fold Change: -0.1742
    Cell Significance Index: -3.8200
  • Cell Name: lamp5 GABAergic cortical interneuron (CL4023011)
    Fold Change: -0.1754
    Cell Significance Index: -3.7900
  • Cell Name: megakaryocyte (CL0000556)
    Fold Change: -0.1772
    Cell Significance Index: -2.8700
  • Cell Name: pvalb GABAergic cortical interneuron (CL4023018)
    Fold Change: -0.1772
    Cell Significance Index: -3.7600
  • Cell Name: obsolete epithelial cell of alveolus of lung (CL0010003)
    Fold Change: -0.1778
    Cell Significance Index: -4.4300
  • Cell Name: chandelier pvalb GABAergic cortical interneuron (CL4023036)
    Fold Change: -0.1787
    Cell Significance Index: -3.7300
  • Cell Name: fraction A pre-pro B cell (CL0002045)
    Fold Change: -0.1819
    Cell Significance Index: -2.1500
  • Cell Name: medium spiny neuron (CL1001474)
    Fold Change: -0.1867
    Cell Significance Index: -2.5200
  • Cell Name: VIP GABAergic cortical interneuron (CL4023016)
    Fold Change: -0.1888
    Cell Significance Index: -3.7900
  • Cell Name: sncg GABAergic cortical interneuron (CL4023015)
    Fold Change: -0.1915
    Cell Significance Index: -3.7700

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** LMX1A is a member of the LIM homeobox transcription factor family, characterized by its unique LIM domain and homeobox structure. This domain enables the protein to interact with other transcription factors and DNA sequences, thereby regulating gene expression. LMX1A is highly expressed in neuronal cells, including CNS interneurons, retinal cone cells, and blood vessel endothelial cells. Its expression is also observed in progenitor cells, suggesting a role in neural development and differentiation. **Pathways and Functions:** LMX1A is involved in multiple signaling pathways, including: 1. **Axon guidance:** LMX1A regulates axon guidance by interacting with other transcription factors, such as LMX1B, to modulate the expression of axon guidance genes. 2. **Central nervous system neuron differentiation:** LMX1A promotes the differentiation of neurons by regulating the expression of transcription factors and genes involved in neural development. 3. **Cerebellum development:** LMX1A is essential for the development of the cerebellum, a critical region for motor coordination and learning. 4. **Dopaminergic neuron differentiation:** LMX1A regulates the differentiation of dopaminergic neurons, which are involved in reward, motivation, and motor control. 5. **Synaptic organization:** LMX1A modulates synaptic organization by regulating the expression of synaptic genes and proteins. **Clinical Significance:** LMX1A has been implicated in various neurological disorders, including: 1. **Autism Spectrum Disorder (ASD):** LMX1A mutations have been associated with ASD, highlighting its role in neural development and social behavior. 2. **Cerebellar ataxia:** LMX1A mutations have been linked to cerebellar ataxia, a disorder characterized by coordination and balance problems. 3. **Dyslexia:** LMX1A has been implicated in dyslexia, a learning disorder characterized by difficulties with reading and writing. 4. **Neurodegenerative diseases:** LMX1A may play a role in neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, by regulating the expression of genes involved in neuronal survival and function. In conclusion, LMX1A is a critical transcription factor involved in regulating neural development, axon guidance, and synaptic organization. Its dysregulation has been implicated in various neurological disorders, highlighting the importance of further research into the mechanisms underlying LMX1A function and its role in human disease.

Genular Protein ID: 3826052226

Symbol: LMX1A_HUMAN

Name: LIM homeobox transcription factor 1-alpha

UniProtKB Accession Codes:

Q8TE12 B3KXP6 Q0VDB5 Q5VWG4 Q8TE11

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CDD 3 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 17 Ensembl 3 GO 22 Gene3D 2 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 6 KEGG 1 MANE-Select 1 MIM 3 MalaCards 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PROSITE 4 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 2 SIGNOR 1 SMART 2 SMR 1 STRING 1 SUPFAM 2 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 12062816

Title: Cloning, expression and genomic structure of human LMX1A, and variant screening in Pima Indians.

PubMed ID: 12062816

DOI: 10.1016/s0378-1119(02)00582-6

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 16710414

Title: The DNA sequence and biological annotation of human chromosome 1.

PubMed ID: 16710414

DOI: 10.1038/nature04727

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 29754270

Title: Heterozygous missense variants of LMX1A lead to nonsyndromic hearing impairment and vestibular dysfunction.

PubMed ID: 29754270

DOI: 10.1007/s00439-018-1880-5

PubMed ID: 29971487

Title: A variant in LMX1A causes autosomal recessive severe-to-profound hearing impairment.

PubMed ID: 29971487

DOI: 10.1007/s00439-018-1899-7

Sequence Information:

  • Length: 382
  • Mass: 42747
  • Checksum: 55424762757FF5FD
  • Sequence:
    • MLDGLKMEEN FQSAIDTSAS FSSLLGRAVS PKSVCEGCQR VILDRFLLRL NDSFWHEQCV 
QCASCKEPLE TTCFYRDKKL YCKYDYEKLF AVKCGGCFEA IAPNEFVMRA QKSVYHLSCF 
CCCVCERQLQ KGDEFVLKEG QLLCKGDYEK ERELLSLVSP AASDSGKSDD EESLCKSAHG 
AGKGTAEEGK DHKRPKRPRT ILTTQQRRAF KASFEVSSKP CRKVRETLAA ETGLSVRVVQ 
VWFQNQRAKM KKLARRQQQQ QQDQQNTQRL SSAQTNGGGS AGMEGIMNPY TALPTPQQLL 
AIEQSVYSSD PFRQGLTPPQ MPGDHMHPYG AEPLFHDLDS DDTSLSNLGD CFLATSEAGP 
LQSRVGNPID HLYSMQNSYF TS

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.