LRRC4C (leucine rich repeat containing 4C)

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Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 57689
• Gene name: Leucine rich repeat containing 4C
• Gene symbol: LRRC4C
• Synonyms (NCBI Gene): NGL-1, NGL1
• Chromosome: 11
• Chromosome location: 11p12
• Summary: NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2033834	hsa-miR-129-5p	CLIP-seq

Gene ontology (GO) Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	14595443, 21946559, 28514442, 32296183, 33961781
GO:0005615	Component	Extracellular space	HDA	22664934
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0016020	Component	Membrane	IDA	14595443
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	14595443
GO:0045202	Component	Synapse	IEA
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0050770	Process	Regulation of axonogenesis	IBA
GO:0050770	Process	Regulation of axonogenesis	IDA	14595443
GO:0050804	Process	Modulation of chemical synaptic transmission	IBA
GO:0050804	Process	Modulation of chemical synaptic transmission	IEA
GO:0050839	Function	Cell adhesion molecule binding	IPI	23986473
GO:0098632	Function	Cell-cell adhesion mediator activity	IBA
GO:0098632	Function	Cell-cell adhesion mediator activity	IGI	23986473
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:0099560	Process	Synaptic membrane adhesion	IGI	23986473

Other IDs

• MIM: 608817
• HGNC: 29317
• e!Ensembl: ENSG00000148948

Protein

• UniProt ID: Q9HCJ2
• Protein name: Leucine-rich repeat-containing protein 4C (Netrin-G1 ligand) (NGL-1)
• Protein function: May promote neurite outgrowth of developing thalamic neurons.
• PDB: 3ZYJ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07679	I-set	354 → 443	Immunoglobulin I-set domain	Domain
  PF13306	LRR_5	76 → 216	BspA type Leucine rich repeat region (6 copies)	Repeat
  PF13855	LRR_8	244 → 302	Leucine rich repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in the cerebral cortex, including frontal, parietal and occipital lobes. Putamen, amygdala, hippocampus and medulla oblongata show moderate expression. Caudate nucleus and thalamus express small amounts, whereas other
• Sequence:

  MLNKMTLHPQQIMIGPRFNRALFDPLLVVLLALQLLVVAGLVRAQTCPSVCSCSNQFSKV
  ICVRKNLREVPDGISTNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAF
  NGLANLNTLELFDNRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLG
  ELKRLSYISEGAFEGLSNLRYLNLAMCNLREIPNLTPLIKLDELDLSGNHLSAIRPGSFQ
  GLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINLAHNNLTLLPHDLFTPLHHLERIHLHH
  NPWNCNCDILWLSWWIKDMAPSNTACCARCNTPPNLKGRYIGELDQNYFTCYAPVIVEPP
  ADLNVTEGMAAELKCRASTSLTSVSWITPNGTVMTHGAYKVRIAVLSDGTLNFTNVTVQD
  TGMYTCMVSNSVGNTTASATLNVTAATTTPFSYFSTVTVETMEPSQDEARTTDNNVGPTP
  VVDWETTNVTTSLTPQSTRSTEKTFTIPVTDINSGIPGIDEVMKTTKIIIGCFVAITLMA
  AVMLVIFYKMRKQHHRQNHHAPTRTVEIINVDDEITGDTPMESHLPMPAIEHEHLNHYNS
  YKSPFNHTTTVNTINSIHSSVHEPLLIRMNSKDNVQETQI

• Sequence length: 640

Pathways

KEGG Pathway

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 Show/Hide Unknown Diseases (17)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
ALZHEIMER DISEASE	—	GWAS catalog	35851147	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	34446935	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	33226468	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC FATIGUE SYNDROME	—	GWAS catalog	39024449	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	26586795	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIVERTICULITIS	—	GWAS catalog	37196047	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EYE DISEASE	—	GWAS catalog	35841873	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	35851147	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LRRC4C-related disorder	Uncertain significance; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MASTOCYTOSIS	—	GWAS catalog	33421400	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPOROSIS	—	GWAS catalog	20548944	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	38538606	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	38538606	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	30019117	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STROKE	—	GWAS catalog	38317187	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	34446935	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UPPER AERODIGESTIVE TRACT NEOPLASM	—	GWAS catalog	33667223	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (14)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anorexia Nervosa	Anorexia nervosa	Pubtator	30519816	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	23879678	Associate	★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	27759917		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	27759917	Associate	★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	BEFREE	31680855		★☆☆☆☆ Found in Text Mining only
Cyclic neutropenia	Cyclic Neutropenia	BEFREE	27759917		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	27759917	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	31680855		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	GWASCAT_DG	27182965		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	36395078	Associate	★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	GWASDB_DG	19629137		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	27759917		★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	33867855	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	33867855	Associate	★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

LRRC4 2 shared pathwaysAxon guidance, Cell adhesion molecules Related via 2 shared pathways including Axon guidance, Cell adhesion molecules. HOXC6 2 shared diseasesGastroesophageal reflux disease, Osteoporosis 2 shared evidence sourcesGWAS catalog (Gastroesophageal reflux disease), GWAS catalog (Osteoporosis) Related via 2 shared diseases including Gastroesophageal reflux disease, Osteoporosis — evidence mostly GWAS catalog. H2AC6 2 shared diseasesGastroesophageal reflux disease, Upper aerodigestive tract neoplasm 2 shared evidence sourcesGWAS catalog (Gastroesophageal reflux disease), GWAS catalog (Upper aerodigestive tract neoplasm) Related via 2 shared diseases including Gastroesophageal reflux disease, Upper aerodigestive tract neoplasm — evidence mostly GWAS catalog. BTN1A1 2 shared diseasesGastroesophageal reflux disease, Upper aerodigestive tract neoplasm 2 shared evidence sourcesGWAS catalog (Gastroesophageal reflux disease), GWAS catalog (Upper aerodigestive tract neoplasm) Related via 2 shared diseases including Gastroesophageal reflux disease, Upper aerodigestive tract neoplasm — evidence mostly GWAS catalog. SHISA6 2 shared diseasesEye disease, Gastroesophageal reflux disease 3 shared evidence sourcesGWAS catalog (Eye disease), GWAS catalog (Gastroesophageal reflux disease), GWAS catalog (Stroke) Related via 2 shared diseases including Eye disease, Gastroesophageal reflux disease — evidence mostly GWAS catalog.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
LRRC4	0	[]	2	["Axon guidance","Cell adhesion molecules"]	0	[]
HOXC6	2	["Gastroesophageal reflux disease","Osteoporosis"]	0	[]	2	["GWAS catalog (Gastroesophageal reflux disease)","GWAS catalog (Osteoporosis)"]
H2AC6	2	["Gastroesophageal reflux disease","Upper aerodigestive tract neoplasm"]	0	[]	2	["GWAS catalog (Gastroesophageal reflux disease)","GWAS catalog (Upper aerodigestive tract neoplasm)"]
BTN1A1	2	["Gastroesophageal reflux disease","Upper aerodigestive tract neoplasm"]	0	[]	2	["GWAS catalog (Gastroesophageal reflux disease)","GWAS catalog (Upper aerodigestive tract neoplasm)"]
SHISA6	2	["Eye disease","Gastroesophageal reflux disease"]	0	[]	3	["GWAS catalog (Eye disease)","GWAS catalog (Gastroesophageal reflux disease)","GWAS catalog (Stroke)"]

Diseases Linked via Similar Genes

Schizophrenia Linked via 3 of 5 related genesLRRC4, H2AC6, SHISA6 Obstructive pulmonary disease Linked via 2 of 5 related genesHOXC6, BTN1A1 Insomnia Linked via 2 of 5 related genesH2AC6, SHISA6 Squamous cell carcinoma Linked via 2 of 5 related genesH2AC6, SHISA6 Oligodendroglioma Linked via 1 of 5 related genesLRRC4

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Schizophrenia	3	["LRRC4","H2AC6","SHISA6"]
Obstructive pulmonary disease	2	["HOXC6","BTN1A1"]
Insomnia	2	["H2AC6","SHISA6"]
Squamous cell carcinoma	2	["H2AC6","SHISA6"]
Oligodendroglioma	1	["LRRC4"]