Details for: LRRC42

Gene ID: 115353

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: LRRC42

Ensembl ID: ENSG00000116212

Description: leucine rich repeat containing 42

Cell Significance Landscape

Significant Cells

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

  • melanocyte CL0000148
    CSI 4.35
    rCSI 3.22%
    PRS 92.36
  • pancreatic D cell CL0000173
    CSI 4.19
    rCSI 4.12%
    PRS 95.33
  • secretory cell CL0000151
    CSI 3.88
    rCSI 4.05%
    PRS 93.76
  • neural crest cell CL0011012
    CSI 3.7
    rCSI 2.92%
    PRS 90.05
  • pulmonary ionocyte CL0017000
    CSI 3.5
    rCSI 4.26%
    PRS 96.5
  • interstitial cell of Cajal CL0002088
    CSI 3.43
    rCSI 4.37%
    PRS 96.68
  • stem cell CL0000034
    CSI 3.3
    rCSI 3.18%
    PRS 92.05
  • epithelial cell CL0000066
    CSI 3.2
    rCSI 4.92%
    PRS 84.42
  • keratinocyte CL0000312
    CSI 3.2
    rCSI 2.68%
    PRS 94.2
  • mesodermal cell CL0000222
    CSI 3.15
    rCSI 3.78%
    PRS 94.05
  • perivascular cell CL4033054
    CSI 3.05
    rCSI 4.18%
    PRS 96.64
  • granulocyte monocyte progenitor cell CL0000557
    CSI 3.04
    rCSI 2.63%
    PRS 95.65
  • vascular associated smooth muscle cell CL0000359
    CSI 2.98
    rCSI 9.67%
    PRS 93.52
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 2.95
    rCSI 3.41%
    PRS 88.63
  • rod bipolar cell CL0000751
    CSI 2.94
    rCSI 5.29%
    PRS 90.88
  • neural progenitor cell CL0011020
    CSI 2.66
    rCSI 11.69%
    PRS 85.85
  • ionocyte CL0005006
    CSI 2.63
    rCSI 2.82%
    PRS 95.35
  • mesenchymal cell CL0008019
    CSI 2.58
    rCSI 6.56%
    PRS 91.5
  • club cell CL0000158
    CSI 2.57
    rCSI 3.76%
    PRS 91.68
  • lung ciliated cell CL1000271
    CSI 2.55
    rCSI 2.95%
    PRS 90.55
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 2.4
    rCSI 3.08%
    PRS 91.63
  • ciliated epithelial cell CL0000067
    CSI 2.33
    rCSI 2.05%
    PRS 87.95
  • enteroendocrine cell CL0000164
    CSI 2.2
    rCSI 3.01%
    PRS 92.65
  • radial glial cell CL0000681
    CSI 2.2
    rCSI 3.05%
    PRS 93.22
  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.12
    rCSI 2.54%
    PRS 85.85
  • fallopian tube secretory epithelial cell CL4030006
    CSI 2.11
    rCSI 2.03%
    PRS 93.35
  • cerebral cortex GABAergic interneuron CL0010011
    CSI 2.09
    rCSI 6.17%
    PRS 94.16
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.97
    rCSI 3.48%
    PRS 85.26
  • peripheral nervous system neuron CL2000032
    CSI 1.96
    rCSI 2.67%
    PRS 89.86
  • glioblast CL0000030
    CSI 1.85
    rCSI 2.95%
    PRS 88.86
  • placental villous trophoblast CL2000060
    CSI 1.81
    rCSI 2.79%
    PRS 93.08
  • enteroendocrine cell of small intestine CL0009006
    CSI 1.72
    rCSI 3.78%
    PRS 95.58
  • pancreatic ductal cell CL0002079
    CSI 1.53
    rCSI 2.97%
    PRS 95.26
  • type L enteroendocrine cell CL0002279
    CSI 1.49
    rCSI 2.8%
    PRS 94.9
  • forebrain radial glial cell CL0013000
    CSI 1.13
    rCSI 3.62%
    PRS 94.01
  • type B pancreatic cell CL0000169
    CSI 1.13
    rCSI 2.5%
    PRS 94.42
  • pancreatic epsilon cell CL0005019
    CSI 1.09
    rCSI 5.09%
    PRS 95.99
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 0.85
    rCSI 5.01%
    PRS 86.22
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 0.77
    rCSI 2.78%
    PRS 84.18
  • P/D1 enteroendocrine cell CL0002268
    CSI 0.53
    rCSI 2.91%
    PRS 95.64

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)

Loading network (please wait)...

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 Analyzed for its expression specificity (CSI Z-SCORE), Leucine Rich Repeat Containing 42 ([LRRC42](/details-gene/115353)) is not a specific marker for any single cell type. Instead, its profile is consistent with that of a broadly expressed gene found across diverse cell lineages. This widespread expression, coupled with evidence from proteomics screens, suggests a potential role in a fundamental cellular process such as the DNA damage response. ## Cellular Roles and Expression Landscape The expression profile of [LRRC42](/details-gene/115353), when evaluated for its ability to define cell populations, is notable for its lack of specificity. Across the **Overall** biological context, [LRRC42](/details-gene/115353) consistently shows a CSI (Z-SCORE) of 0.00 with non-significant p-values (p > 0.6) in a wide array of cell types. These include cells of ectodermal origin like [melanocyte](/details-cell/CL0000148) and [keratinocyte](/details-cell/CL0000312), endodermal derivatives such as [pancreatic D cell](/details-cell/CL0000173), and mesenchymal lineages including [vascular associated smooth muscle cell](/details-cell/CL0000359). This consistent lack of statistical significance, despite a high effect size (deltaVal: 1.00), indicates that while the gene is expressed in these populations, its expression level is not sufficiently unique to distinguish them from other cells. The percentile rank scores (PRS), which range from approximately 84% to 96%, further support that its expression is not exceptional compared to the rest of the transcriptome. This broad and non-specific expression pattern strongly suggests that [LRRC42](/details-gene/115353) is likely involved in a ubiquitous or housekeeping cellular function rather than a specialized, cell-defining role. ## Pathways and Molecular Function [LRRC42](/details-gene/115353) encodes a protein containing leucine-rich repeats (LRRs), which are structural motifs known to mediate protein-protein interactions. While detailed pathway annotations are limited, a key study identified [LRRC42](/details-gene/115353) in a large-scale proteomic screen for substrates of the master DNA damage response (DDR) kinases, ATM and ATR ([PubMed: 17525332](https://pubmed.ncbi.nlm.nih.gov/17525332), [DOI: 10.1126/science.1140321](https://doi.org/10.1126/science.1140321)). This finding strongly suggests a potential involvement for [LRRC42](/details-gene/115353) in the cellular surveillance and repair of DNA damage. A role in such a fundamental process would be highly consistent with its observed broad expression across numerous and diverse cell types. Other publications primarily document its initial cloning and characterization as part of comprehensive cDNA collection projects ([PubMed: 14702039](https://pubmed.ncbi.nlm.nih.gov/14702039), [PubMed: 15489334](https://pubmed.ncbi.nlm.nih.gov/15489334)). ## Research Directions The widespread expression of [LRRC42](/details-gene/115353) and its potential connection to the DNA damage response (DDR) pathway present several compelling avenues for future research. Understanding its precise function could have implications for genome stability and cancer biology. ### Testable Hypotheses: 1. **[LRRC42](/details-gene/115353) functions as an adaptor or scaffold protein within the ATM/ATR signaling cascade.** It may utilize its LRR domains to mediate interactions between DDR kinases and their downstream substrates, thereby facilitating signal transduction upon genotoxic stress. * **Experimental Approach:** Perform co-immunoprecipitation of endogenous or tagged [LRRC42](/details-gene/115353) from cells treated with DNA-damaging agents (e.g., ionizing radiation, etoposide), followed by mass spectrometry to identify interacting proteins. Validation of key interactors like ATM, ATR, or CHK1/2 can be performed via Western blot. 2. **Depletion of [LRRC42](/details-gene/115353) sensitizes cells to DNA-damaging therapeutic agents.** Loss of [LRRC42](/details-gene/115353) may impair the cell's ability to properly arrest the cell cycle or repair DNA, leading to increased cell death following treatment with chemotherapy or radiation. * **Experimental Approach:** Create [LRRC42](/details-gene/115353) knockout cell lines using CRISPR-Cas9. Compare the survival of knockout and wild-type cells after exposure to a panel of DNA-damaging drugs using clonogenic survival assays. DNA damage levels can be quantified by measuring γH2AX foci through immunofluorescence microscopy. 3. **[LRRC42](/details-gene/115353) is involved in the regulation of DNA repair pathway choice.** The protein may play a role in directing the cell towards either non-homologous end joining (NHEJ) or homologous recombination (HR) to repair double-strand breaks, depending on the cellular context. * **Experimental Approach:** Utilize established reporter cell lines (e.g., DR-GFP for HR, EJ5-GFP for NHEJ) in which [LRRC42](/details-gene/115353) has been depleted. Quantify the efficiency of each repair pathway via flow cytometry after inducing double-strand breaks with an endonuclease like I-SceI. ### Therapeutic Potential: Given its broad expression, directly targeting [LRRC42](/details-gene/115353) systemically could pose a risk of on-target toxicity to healthy tissues. However, if its role in the DDR is confirmed, it could represent a promising target for a combination therapy strategy. An inhibitor of [LRRC42](/details-gene/115353) function could act as a potent chemo- or radio-sensitizer, enhancing the efficacy of conventional cancer treatments by crippling the cancer cells' ability to repair therapeutic-induced DNA damage. This approach would be particularly relevant for tumors that exhibit high genomic instability or a dependency on specific DDR pathways for survival.

Genular Protein ID: 3414493738

Symbol: LRC42_HUMAN

Name: Leucine-rich repeat-containing protein 42

UniProtKB Accession Codes:

Q9Y546 D3DQ46 Q8N2Q8

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 6 Ensembl 3 ExpressionAtlas 1 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MANE-Select 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 Pumba 1 RNAct 1 RefSeq 4 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 14702039

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

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 16303743

Title: Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.

PubMed ID: 16303743

DOI: 10.1093/dnares/12.2.117

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: 17525332

Title: ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.

PubMed ID: 17525332

DOI: 10.1126/science.1140321

Sequence Information:

  • Length: 428
  • Mass: 48571
  • Checksum: EC22D6E407E36B87
  • Sequence:
    • MSYYLSSENH LDPGPIYMRE NGQLHMVNLA LDGVRSSLQK PRPFRLFPKG FSVELCMNRE 
DDTARKEKTD HFIFTYTREG NLRYSAKSLF SLVLGFISDN VDHIDSLIGF PEQIAEKLFS 
AAEARQKFTE PGAGLRALQK FTEAYGSLVL CSLCLRNRYL VISEKLEEIK SFRELTCLDL 
SCCKLGDEHE LLEHLTNEAL SSVTQLHLKD NCLSDAGVRK MTAPVRVMKR GLENLTLLDL 
SCNPEITDAG IGYLFSFRKL NCLDISGTGL KDIKTVKHKL QTHIGLVHSK VPLKEFDHSN 
CKTEGWADQI VLQWERVTAE AVKPRETSEP RAAAQRFYGK RSRAEAPLKC PLADTHMNSS 
EKLQFYKEKA PDCHGPVLKH EAISSQESKK SKKRPFEESE TEQNNSSQPS KQKYVCLAVE 
DWDLLNSY