Details for: LRTM1

Gene ID: 57408

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: LRTM1

Ensembl ID: ENSG00000144771

Description: leucine rich repeats and transmembrane domains 1

Cell Significance Landscape

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • OFF-bipolar cell CL0000750
    CSI 29.4
    rCSI 40.2%
    PRS 92.68
  • ON-bipolar cell CL0000749
    CSI 15.02
    rCSI 22.32%
    PRS 93.12
  • rod bipolar cell CL0000751
    CSI 7.26
    rCSI 13.05%
    PRS 90.94
  • retinal bipolar neuron CL0000748
    CSI 5.88
    rCSI 11%
    PRS 88.83
  • Mueller cell CL0000636
    CSI 5.77
    rCSI 13.17%
    PRS 90
  • VIP GABAergic cortical interneuron CL4023016
    CSI 4.33
    rCSI 5.17%
    PRS 86
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 4.18
    rCSI 7.39%
    PRS 85.35
  • interneuron CL0000099
    CSI 3.97
    rCSI 7.98%
    PRS 90.7
  • invaginating midget bipolar cell CL4033034
    CSI 3.69
    rCSI 21.82%
    PRS 87.11
  • inhibitory interneuron CL0000498
    CSI 3.6
    rCSI 8.32%
    PRS 88.16
  • neural progenitor cell CL0011020
    CSI 2.74
    rCSI 12.06%
    PRS 85.95
  • sst GABAergic cortical interneuron CL4023017
    CSI 2.55
    rCSI 3.29%
    PRS 86.87
  • glycinergic amacrine cell CL4030028
    CSI 2.33
    rCSI 6.06%
    PRS 89.76
  • regular ventricular cardiac myocyte CL0002131
    CSI 2.05
    rCSI 12.83%
    PRS 89.87
  • central nervous system neuron CL2000029
    CSI 2
    rCSI 14.71%
    PRS 89.2
  • cone retinal bipolar cell CL0000752
    CSI 1.99
    rCSI 26.03%
    PRS 90.96
  • L6b glutamatergic cortical neuron CL4023038
    CSI 1.94
    rCSI 6.07%
    PRS 86.9
  • retinal ganglion cell CL0000740
    CSI 1.94
    rCSI 4.28%
    PRS 87.18
  • glial cell CL0000125
    CSI 1.79
    rCSI 6.81%
    PRS 89.6
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.77
    rCSI 4.3%
    PRS 84.06
  • retinal pigment epithelial cell CL0002586
    CSI 1.71
    rCSI 3.4%
    PRS 92.12
  • sncg GABAergic cortical interneuron CL4023015
    CSI 1.69
    rCSI 2.71%
    PRS 86.81
  • diffuse bipolar 3b cell CL4033030
    CSI 1.68
    rCSI 11.12%
    PRS 89.34
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 1.66
    rCSI 5.96%
    PRS 84.32
  • placental villous trophoblast CL2000060
    CSI 1.64
    rCSI 2.54%
    PRS 93.11
  • amacrine cell CL0000561
    CSI 1.63
    rCSI 4.72%
    PRS 88.48
  • direct pathway medium spiny neuron CL4023026
    CSI 1.62
    rCSI 38.75%
    PRS 83.74
  • indirect pathway medium spiny neuron CL4023029
    CSI 1.61
    rCSI 38.83%
    PRS 83.63
  • diffuse bipolar 6 cell CL4033032
    CSI 1.28
    rCSI 6.74%
    PRS 86.25
  • diffuse bipolar 2 cell CL4033028
    CSI 1.01
    rCSI 7.82%
    PRS 88.19
  • flat midget bipolar cell CL4033033
    CSI 0.71
    rCSI 5.08%
    PRS 86.53
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 0.7
    rCSI 4.11%
    PRS 86.34
  • medium spiny neuron CL1001474
    CSI 0.58
    rCSI 4.96%
    PRS 88.84
  • ON midget ganglion cell CL4033046
    CSI 0.48
    rCSI 9.77%
    PRS 87.97
  • ON parasol ganglion cell CL4033052
    CSI 0.48
    rCSI 6.8%
    PRS 88.66
  • OFF midget ganglion cell CL4033047
    CSI 0.35
    rCSI 7.18%
    PRS 88.43

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.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [LRTM1](/details-gene/57408) is a protein-coding gene that encodes Leucine-rich repeat and transmembrane domain-containing protein 1, a member of the LRRTM protein family. **Overall**, expression data reveals a highly specific and significant role for [LRTM1](/details-gene/57408) within the central nervous system, particularly as a defining marker for neuronal subtypes in the retina. Its highest significance is observed in `[OFF-bipolar cell](/details-cell/CL0000750)` and `[ON-bipolar cell](/details-cell/CL0000749)`, suggesting a critical function in visual signal processing. Functional annotations link the gene to processes such as `[Axon guidance](/details-gene/GO:0007411)` and `[Roundabout binding](/details-gene/GO:0048495)`, which is consistent with its role in establishing precise neural circuitry. ## Cellular Roles and Expression Landscape The expression profile of [LRTM1](/details-gene/57408) demonstrates a strong and specific association with the nervous system, particularly in the retina. **Overall**, the gene shows its most profound significance in various subtypes of `[retinal bipolar neuron](/details-cell/CL0000748)`, including `[OFF-bipolar cell](/details-cell/CL0000750)` (CSI: 29.40), `[ON-bipolar cell](/details-cell/CL0000749)` (CSI: 15.02), and `[rod bipolar cell](/details-cell/CL0000751)` (CSI: 7.26). This indicates that [LRTM1](/details-gene/57408) is not just a general neuronal marker but is integral to the identity and function of these specific interneurons that transmit signals from photoreceptors to ganglion cells. Beyond bipolar cells, [LRTM1](/details-gene/57408) is also a significant marker for `[Mueller cell](/details-cell/CL0000636)` (CSI: 5.77), the principal glial cell of the retina, suggesting a potential role in retinal structural support or neuron-glia communication. The gene's significance extends to cortical `[interneuron](/details-cell/CL0000099)` populations, such as `[VIP GABAergic cortical interneuron](/details-cell/CL4023016)` and `[sst GABAergic cortical interneuron](/details-cell/CL4023017)`, highlighting a broader role in regulating cortical circuits. An unexpected but notable finding is its significance in `[regular ventricular cardiac myocyte](/details-cell/CL0002131)` (CSI: 2.05), which suggests a potential, yet unexplored, function outside of the nervous system. ## Pathways and Molecular Function Functional annotations provide a mechanistic basis for the observed expression pattern of [LRTM1](/details-gene/57408). As a `[Membrane](/details-gene/GO:0016020)` protein, it is positioned to interact with the extracellular environment. Its molecular function is annotated with `[Roundabout binding](/details-gene/GO:0048495)`, linking it directly to the Slit-Robo signaling pathway, a key regulator of neuronal development. This molecular function is highly consistent with its involvement in the biological process of `[Axon guidance](/details-gene/GO:0007411)`. This suggests that [LRTM1](/details-gene/57408) likely plays a crucial role in establishing the precise synaptic connections of retinal bipolar cells and cortical interneurons during development by mediating cell-cell recognition and adhesion. The gene was first identified as part of large-scale cDNA cloning efforts ([Link](https://doi.org/10.1073/pnas.160270997), [Link](https://doi.org/10.1101/gr.2596504)), which provided the foundational clones for subsequent functional studies. ## Research Directions The highly specific expression of [LRTM1](/details-gene/57408) in distinct neuronal subtypes, combined with its annotated role in axon guidance, presents several avenues for future research. ### Proposed Hypotheses 1. **[LRTM1](/details-gene/57408) is essential for the proper lamination and synaptic targeting of retinal bipolar cell subtypes.** Its high expression in both ON and OFF bipolar cells and its known interaction with the Roundabout guidance machinery suggest it may be a key molecule that directs the axons of these cells to the correct sublaminae of the inner plexiform layer, ensuring the segregation of ON and OFF visual pathways. 2. **[LRTM1](/details-gene/57408) has a non-canonical function in cardiac myocytes.** The unexpected expression in `[regular ventricular cardiac myocyte](/details-cell/CL0002131)` suggests a novel role in the heart, potentially related to the organization of the intercalated disc, regulation of ion channel localization, or cell-cell signaling, which may parallel its adhesive and organizing functions in the nervous system. ### Key Experimental Approach To test the hypothesis that [LRTM1](/details-gene/57408) is critical for retinal circuit formation, a conditional knockout mouse model could be generated. By crossing a mouse with a floxed `Lrtm1` allele to a line expressing Cre recombinase specifically in developing bipolar cells (e.g., Vsx2-Cre), one could achieve cell-type-specific deletion. The retinas of the resulting knockout mice could be analyzed using immunohistochemistry to visualize the axonal projections of ON and OFF bipolar cells. Disorganization of the inner plexiform layer or mis-targeting of bipolar cell axon terminals would provide strong evidence for the gene's essential role in retinal wiring. ### Therapeutic Potential Currently, the therapeutic potential of [LRTM1](/details-gene/57408) is speculative and largely confined to basic research. However, given its high specificity for certain retinal neurons, it could serve as a valuable diagnostic marker for congenital retinal disorders affecting bipolar cell function. If mutations in [LRTM1](/details-gene/57408) are linked to diseases like congenital stationary night blindness, it could become a target for gene replacement therapy. As a cell surface protein, it is theoretically targetable with biologics like antibodies, but a clear disease-modifying rationale (inhibition vs. activation) is not yet established.

Genular Protein ID: 3795190759

Symbol: LRTM1_HUMAN

Name: Leucine-rich repeat and transmembrane domain-containing protein 1

UniProtKB Accession Codes:

Q9HBL6 Q8IUU2

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CTD 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 2 GO 5 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyCosmos 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 5 KEGG 1 MANE-Select 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRINTS 1 PRO 1 PROSITE 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 2 RNAct 1 RefSeq 2 SMART 2 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 10931946

Title: Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning.

PubMed ID: 10931946

DOI: 10.1073/pnas.160270997

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

Sequence Information:

  • Length: 345
  • Mass: 38171
  • Checksum: 428C8754272D575D
  • Sequence:
    • MKGELLLFSS VIVLLQVVCS CPDKCYCQSS TNFVDCSQQG LAEIPSHLPP QTRTLHLQDN 
QIHHLPAFAF RSVPWLMTLN LSNNSLSNLA PGAFHGLQHL QVLNLTQNSL LSLESRLFHS 
LPQLRELDLS SNNISHLPTS LGETWENLTI LAVQQNQLQQ LDRALLESMP SVRLLLLKDN 
LWKCNCHLLG LKLWLEKFVY KGGLTDGIIC ESPDTWKGKD LLRIPHELYQ PCPLPAPDPV 
SSQAQWPGSA HGVVLRPPEN HNAGERELLE CELKPKPRPA NLRHAIATVI ITGVVCGIVC 
LMMLAAAIYG CTYAAITAQY HGGPLAQTND PGKVEEKERF DSSPA