LRRC4 (leucine rich repeat containing 4)

Gene

• Entrez ID: 64101
• Gene name: Leucine rich repeat containing 4
• Gene symbol: LRRC4
• Synonyms (NCBI Gene): NAG14, NGL-2
• Chromosome: 7
• Chromosome location: 7q32.1
• Summary: This gene is significantly downregulated in primary brain tumors. The exact function of the protein encoded by this gene is unknown. [provided by RefSeq, Jul 2008]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016733	hsa-miR-335-5p	Microarray	18185580
MIRT022116	hsa-miR-124-3p	Microarray	18668037
MIRT437991	hsa-miR-182-5p	qRT-PCR, Immunohistochemistry, Luciferase reporter assay	24404152
MIRT437991	hsa-miR-182-5p	qRT-PCR, Immunohistochemistry, Luciferase reporter assay	24404152
MIRT437991	hsa-miR-182-5p	qRT-PCR, Immunohistochemistry, Luciferase reporter assay	24404152
MIRT437991	hsa-miR-182-5p	qRT-PCR, Immunohistochemistry, Luciferase reporter assay	24404152
MIRT719827	hsa-miR-6832-3p	HITS-CLIP	19536157
MIRT719825	hsa-miR-4469	HITS-CLIP	19536157
MIRT719826	hsa-miR-7113-3p	HITS-CLIP	19536157
MIRT719824	hsa-miR-4287	HITS-CLIP	19536157
MIRT719823	hsa-miR-4685-3p	HITS-CLIP	19536157
MIRT719822	hsa-miR-6845-3p	HITS-CLIP	19536157
MIRT719821	hsa-miR-627-3p	HITS-CLIP	19536157
MIRT719820	hsa-miR-6895-3p	HITS-CLIP	19536157
MIRT719819	hsa-miR-204-5p	HITS-CLIP	19536157
MIRT719818	hsa-miR-211-5p	HITS-CLIP	19536157
MIRT719817	hsa-miR-6867-3p	HITS-CLIP	19536157
MIRT656617	hsa-miR-495-3p	HITS-CLIP	23824327
MIRT656616	hsa-miR-5688	HITS-CLIP	23824327
MIRT656615	hsa-miR-8063	HITS-CLIP	23824327
MIRT719827	hsa-miR-6832-3p	HITS-CLIP	19536157
MIRT719825	hsa-miR-4469	HITS-CLIP	19536157
MIRT719826	hsa-miR-7113-3p	HITS-CLIP	19536157
MIRT719824	hsa-miR-4287	HITS-CLIP	19536157
MIRT719823	hsa-miR-4685-3p	HITS-CLIP	19536157
MIRT719822	hsa-miR-6845-3p	HITS-CLIP	19536157
MIRT719821	hsa-miR-627-3p	HITS-CLIP	19536157
MIRT719820	hsa-miR-6895-3p	HITS-CLIP	19536157
MIRT719819	hsa-miR-204-5p	HITS-CLIP	19536157
MIRT719818	hsa-miR-211-5p	HITS-CLIP	19536157
MIRT719817	hsa-miR-6867-3p	HITS-CLIP	19536157
MIRT656617	hsa-miR-495-3p	HITS-CLIP	23824327
MIRT656616	hsa-miR-5688	HITS-CLIP	23824327
MIRT656615	hsa-miR-8063	HITS-CLIP	23824327
MIRT1119619	hsa-miR-1237	CLIP-seq
MIRT1119620	hsa-miR-1247	CLIP-seq
MIRT1119621	hsa-miR-1248	CLIP-seq
MIRT1119622	hsa-miR-1283	CLIP-seq
MIRT1119623	hsa-miR-1343	CLIP-seq
MIRT1119624	hsa-miR-183	CLIP-seq
MIRT1119625	hsa-miR-2861	CLIP-seq
MIRT1119626	hsa-miR-3138	CLIP-seq
MIRT1119627	hsa-miR-3140-5p	CLIP-seq
MIRT1119628	hsa-miR-3153	CLIP-seq
MIRT1119629	hsa-miR-3184	CLIP-seq
MIRT1119630	hsa-miR-3192	CLIP-seq
MIRT1119631	hsa-miR-3607-5p	CLIP-seq
MIRT1119632	hsa-miR-3618	CLIP-seq
MIRT1119633	hsa-miR-423-5p	CLIP-seq
MIRT1119634	hsa-miR-4267	CLIP-seq
MIRT1119635	hsa-miR-4289	CLIP-seq
MIRT1119636	hsa-miR-4427	CLIP-seq
MIRT1119637	hsa-miR-4643	CLIP-seq
MIRT1119638	hsa-miR-4646-5p	CLIP-seq
MIRT1119639	hsa-miR-4668-5p	CLIP-seq
MIRT1119640	hsa-miR-4735-5p	CLIP-seq
MIRT1119641	hsa-miR-4757-5p	CLIP-seq
MIRT1119642	hsa-miR-552	CLIP-seq
MIRT1119643	hsa-miR-592	CLIP-seq
MIRT1119644	hsa-miR-597	CLIP-seq
MIRT1119645	hsa-miR-642b	CLIP-seq
MIRT1119646	hsa-miR-661	CLIP-seq
MIRT1119647	hsa-miR-759	CLIP-seq
MIRT1119648	hsa-miR-767-3p	CLIP-seq
MIRT1119649	hsa-miR-934	CLIP-seq
MIRT1119650	hsa-miR-942	CLIP-seq
MIRT1119629	hsa-miR-3184	CLIP-seq
MIRT1119633	hsa-miR-423-5p	CLIP-seq
MIRT2033809	hsa-miR-544b	CLIP-seq
MIRT2033810	hsa-miR-605	CLIP-seq
MIRT1119644	hsa-miR-597	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21946559
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0043197	Component	Dendritic spine	IEA
GO:0044309	Component	Neuron spine	IEA
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0050804	Process	Modulation of chemical synaptic transmission	IBA
GO:0050804	Process	Modulation of chemical synaptic transmission	IEA
GO:0050808	Process	Synapse organization	IEA
GO:0060076	Component	Excitatory synapse	IEA
GO:0097119	Process	Postsynaptic density protein 95 clustering	IBA
GO:0097119	Process	Postsynaptic density protein 95 clustering	IEA
GO:0098632	Function	Cell-cell adhesion mediator activity	IBA
GO:0098685	Component	Schaffer collateral - CA1 synapse	IEA
GO:0098839	Component	Postsynaptic density membrane	IBA
GO:0098839	Component	Postsynaptic density membrane	IEA
GO:0098978	Component	Glutamatergic synapse	IBA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099560	Process	Synaptic membrane adhesion	IBA
GO:0099560	Process	Synaptic membrane adhesion	IEA
GO:1904861	Process	Excitatory synapse assembly	IBA
GO:1904861	Process	Excitatory synapse assembly	IEA

Other IDs

• MIM: 610486
• HGNC: 15586
• e!Ensembl: ENSG00000128594

Protein

• UniProt ID: Q9HBW1
• Protein name: Leucine-rich repeat-containing protein 4 (Brain tumor-associated protein BAG) (Nasopharyngeal carcinoma-associated gene 14 protein) (Netrin-G2 ligand) (NGL-2)
• Protein function: Synaptic adhesion protein. Regulates the formation of exitatory synapses through the recruitment of pre-and-postsynaptic proteins. Organize the lamina/pathway-specific differentiation of dendrites. Plays an important role for auditory synaptic r
• PDB: 2DL9, 3ZYI
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13855	LRR_8	75 → 135	Leucine rich repeat	Repeat
  PF13855	LRR_8	109 → 159	Leucine rich repeat	Repeat
  PF13855	LRR_8	242 → 301	Leucine rich repeat	Repeat
  PF07679	I-set	353 → 441	Immunoglobulin I-set domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Specifically expressed in brain. {ECO:0000269|PubMed:15967442}.
• Sequence:

  MKLLWQVTVHHHTWNAILLPFVYLTAQVWILCAAIAAAASAGPQNCPSVCSCSNQFSKVV
  CTRRGLSEVPQGIPSNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFN
  GLASLNTLELFDNWLTVIPSGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGE
  LKKLEYISEGAFEGLFNLKYLNLGMCNIKDMPNLTPLVGLEELEMSGNHFPEIRPGSFHG
  LSSLKKLWVMNSQVSLIERNAFDGLASLVELNLAHNNLSSLPHDLFTPLRYLVELHLHHN
  PWNCDCDILWLAWWLREYIPTNSTCCGRCHAPMHMRGRYLVEVDQASFQCSAPFIMDAPR
  DLNISEGRMAELKCRTPPMSSVKWLLPNGTVLSHASRHPRISVLNDGTLNFSHVLLSDTG
  VYTCMVTNVAGNSNASAYLNVSTAELNTSNYSFFTTVTVETTEISPEDTTRKYKPVPTTS
  TGYQPAYTTSTTVLIQTTRVPKQVAVPATDTTDKMQTSLDEVMKTTKIIIGCFVAVTLLA
  AAMLIVFYKLRKRHQQRSTVTAARTVEIIQVDEDIPAATSAAATAAPSGVSGEGAVVLPT
  IHDHINYNTYKPAHGAHWTENSLGNSLHPTVTTISEPYIIQTHTKDKVQETQI

• Sequence length: 653

Pathways

KEGG:

Axon guidance
Cell adhesion molecules

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autism Spectrum Disorder	Autism	Pubtator	31332282	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	29949768, 31372774		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	15967442, 16077900		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain neoplasms	Pubtator	16215635	Inhibit	★☆☆☆☆ Found in Text Mining only
Brain Tumor, Primary	Brain Neoplasms	BEFREE	16077900		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	12902980, 15065599, 28510570		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	16215635	Inhibit	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	17503439		★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	33593879	Associate	★☆☆☆☆ Found in Text Mining only
Cerebrovascular accident	Stroke	BEFREE	30803829		★☆☆☆☆ Found in Text Mining only
Colitis	Colitis	BEFREE	24876225		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	37728516	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms Hereditary Nonpolyposis	Lynch syndrome	Pubtator	37728516	Associate	★☆☆☆☆ Found in Text Mining only
Cystic Fibrosis	Cystic Fibrosis	BEFREE	29986884		★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	37728516	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	LHGDN	16215635, 17541939		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	16215635, 27884160	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	17541939, 17549698, 29312296		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	17541939, 17549698, 29312296		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	16077900, 16723503, 17541939, 17549698, 18976507, 21435336, 22834685, 24404152, 24563334, 25526788		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	LHGDN	16215635, 16941076		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	16215635, 27884160	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	16723503, 18976507	Inhibit	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	32751923	Associate	★☆☆☆☆ Found in Text Mining only
Lipoma	Lipoma	BEFREE	30790560		★☆☆☆☆ Found in Text Mining only
Lipomatosis, Multiple	Lipomatosis	BEFREE	30790560		★☆☆☆☆ Found in Text Mining only
Liposarcoma	Liposarcoma	Pubtator	30790560	Associate	★☆☆☆☆ Found in Text Mining only
Liposarcoma, Dedifferentiated	liposarcoma	BEFREE	30790560		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	12902980, 15065599, 28510570		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of kidney	Kidney Cancer	BEFREE	19681889		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	17503439		★☆☆☆☆ Found in Text Mining only
Meningioma	Meningioma	BEFREE	24563334		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	26662436		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	26662436	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16723503, 17503439, 21435336, 22834685, 24404152, 25526788, 26271008, 29312296, 9721087		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	28523530		★☆☆☆☆ Found in Text Mining only
Osteomyelitis	Osteomyelitis	BEFREE	28050878		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	27612424		★☆☆☆☆ Found in Text Mining only
Pervasive Development Disorder	Autism spectrum disorder	BEFREE	31372774		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	17503439		★☆☆☆☆ Found in Text Mining only
Renal carcinoma	Renal Carcinoma	BEFREE	19681889		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	29949768		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sleep Apnea Syndromes	Sleep Apnea	BEFREE	30246243		★☆☆☆☆ Found in Text Mining only
Transient Ischemic Attack	Transient Ischemic Attack	BEFREE	30803829		★☆☆☆☆ Found in Text Mining only
Young onset Parkinson disease	Parkinson disease	BEFREE	15603737		★☆☆☆☆ Found in Text Mining only