NTNG2 (netrin G2)

Gene

• Entrez ID: 84628
• Gene name: Netrin G2
• Gene symbol: NTNG2
• Synonyms (NCBI Gene): LHLL9381, Lmnt2, NEDBASH, NTNG1, NetrinG2, bA479K20.1
• Chromosome: 9
• Chromosome location: 9q34.13

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1227245973	C>T	Likely-pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant
rs1589440982	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant
rs1589441229	T>G	Pathogenic, likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant
rs1589441428	->T	Pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1589441679	T>C	Pathogenic, likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant
rs1589568476	C>G	Pathogenic, likely-pathogenic	Coding sequence variant, genic downstream transcript variant, genic upstream transcript variant, missense variant
rs1589568530	C>G	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, genic upstream transcript variant, missense variant
rs1589576879	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT613990	hsa-miR-3613-5p	HITS-CLIP	23824327
MIRT613989	hsa-miR-2054	HITS-CLIP	23824327
MIRT613988	hsa-miR-6885-3p	HITS-CLIP	23824327
MIRT613987	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT613990	hsa-miR-3613-5p	HITS-CLIP	23824327
MIRT613989	hsa-miR-2054	HITS-CLIP	23824327
MIRT613988	hsa-miR-6885-3p	HITS-CLIP	23824327
MIRT613987	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT1196196	hsa-miR-1291	CLIP-seq
MIRT1196197	hsa-miR-1908	CLIP-seq
MIRT1196198	hsa-miR-2277-5p	CLIP-seq
MIRT1196199	hsa-miR-4311	CLIP-seq
MIRT1196200	hsa-miR-4466	CLIP-seq
MIRT1196201	hsa-miR-4706	CLIP-seq
MIRT1196202	hsa-miR-4749-5p	CLIP-seq
MIRT1196203	hsa-miR-663	CLIP-seq
MIRT1196204	hsa-miR-675	CLIP-seq
MIRT1196205	hsa-miR-744	CLIP-seq
MIRT1196206	hsa-miR-939	CLIP-seq
MIRT1196200	hsa-miR-4466	CLIP-seq
MIRT1196201	hsa-miR-4706	CLIP-seq
MIRT1196202	hsa-miR-4749-5p	CLIP-seq
MIRT1196204	hsa-miR-675	CLIP-seq
MIRT1196205	hsa-miR-744	CLIP-seq
MIRT1196206	hsa-miR-939	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21946559
GO:0005576	Component	Extracellular region	TAS
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	TAS
GO:0007399	Process	Nervous system development	IEA
GO:0007409	Process	Axonogenesis	IEA
GO:0007409	Process	Axonogenesis	ISS
GO:0010975	Process	Regulation of neuron projection development	IEA
GO:0010975	Process	Regulation of neuron projection development	ISS
GO:0016020	Component	Membrane	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0030424	Component	Axon	IEA
GO:0048787	Component	Presynaptic active zone membrane	IEA
GO:0050804	Process	Modulation of chemical synaptic transmission	IEA
GO:0098552	Component	Side of membrane	IEA
GO:0098685	Component	Schaffer collateral - CA1 synapse	IEA
GO:0098698	Process	Postsynaptic specialization assembly	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099560	Process	Synaptic membrane adhesion	IEA
GO:0150011	Process	Regulation of neuron projection arborization	IEA
GO:0150011	Process	Regulation of neuron projection arborization	ISS
GO:1905606	Process	Regulation of presynapse assembly	IEA
GO:2001222	Process	Regulation of neuron migration	IEA
GO:2001222	Process	Regulation of neuron migration	ISS

Other IDs

• MIM: 618689
• HGNC: 14288
• e!Ensembl: ENSG00000196358

Protein

• UniProt ID: Q96CW9
• Protein name: Netrin-G2 (Laminet-2)
• Protein function: Involved in controlling patterning and neuronal circuit formation at the laminar, cellular, subcellular and synaptic levels. Promotes neurite outgrowth of both axons and dendrites.
• PDB: 3TBD, 3ZYG, 3ZYI
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00055	Laminin_N	39 → 285	Laminin N-terminal (Domain VI)	Family
  PF00053	Laminin_EGF	287 → 344	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	353 → 406	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	409 → 456	Laminin EGF domain	Domain

• Sequence:

  MLHLLALFLHCLPLASGDYDICKSWVTTDEGPTWEFYACQPKVMRLKDYVKVKVEPSGIT
  CGDPPERFCSHENPYLCSNECDASNPDLAHPPRLMFDKEEEGLATYWQSITWSRYPSPLE
  ANITLSWNKTVELTDDVVMTFEYGRPTVMVLEKSLDNGRTWQPYQFYAEDCMEAFGMSAR
  RARDMSSSSAHRVLCTEEYSRWAGSKKEKHVRFEVRDRFAIFAGPDLRNMDNLYTRLESA
  KGLKEFFTLTDLRMRLLRPALGGTYVQRENLYKYFYAISNIEVIGRCKCNLHANLCSMRE
  GSLQCECEHNTTGPDCGKCKKNFRTRSWRAGSYLPLPHGSPNACATAGSFGNCECYGHSN
  RCSYIDFLNVVTCVSCKHNTRGQHCQHCRLGYYRNGSAELDDENVCIECNCNQIGSVHDR
  CNETGFCECREGAAGPKCDDCLPTHYWRQGCYPNVCDDDQLLCQNGGTCLQNQRCACPRG
  YTGVRCEQPRCDPADDDGGLDCDRAPGAAPRPATLLGCLLLLGLAARLGR

• Sequence length: 530

Pathways

KEGG:

Axon guidance
Cell adhesion molecules

Reactome:

Post-translational modification: synthesis of GPI-anchored proteins

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Abnormality of the nervous system	Likely pathogenic	rs2130728045	RCV001814439	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Areflexia	Pathogenic	rs1589441428	RCV000851301	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Generalized hypotonia	Pathogenic	rs1589441428	RCV000851301	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Pathogenic	rs1589441428	RCV000851301	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs1589440982, rs1589441229, rs1227245973, rs1589568476, rs1589576879	RCV000852334 RCV000852331 RCV000852336 RCV000852333 RCV000852330	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia	Pathogenic; Likely pathogenic	rs1589441428, rs1589440982, rs1589441229, rs1227245973, rs1589568476, rs1589576879	RCV000984633 RCV000984637 RCV000984635 RCV004768715 RCV000984636 RCV000984634	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Stereotypical hand wringing	Pathogenic	rs1589441428	RCV000851301	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BELL'S PALSY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR I DISORDER, MOST RECENT EPISODE MANIC	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL NEUROLOGIC ANOMALIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEPRESSION, BIPOLAR	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental and epileptic encephalopathy, 27	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual developmental disorder with macrocephaly, seizures, and speech delay	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
MIXED BIPOLAR I DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental disorder with hypotonia, seizures, and absent language	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anorexia Nervosa	Anorexia	BEFREE	27483138		★☆☆☆☆ Found in Text Mining only
Anorexia Nervosa	Anorexia nervosa	Pubtator	27483138	Associate	★☆☆☆☆ Found in Text Mining only
Atypical Rett syndrome	Rett Syndrome	Orphanet			★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	22495309	Associate	★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	22495309, 31668703	Associate	★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	22922712		★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	BEFREE	17507910		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	CTD_human_DG	17507910		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	PSYGENET_DG	17507910, 20079890		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar disorder	Pubtator	20079890	Stimulate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bladder Neoplasm	Bladder Neoplasm	BEFREE	15239131		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	28257124	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	33127842	Inhibit	★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	15239131		★☆☆☆☆ Found in Text Mining only
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	33246661	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	33127842	Associate	★☆☆☆☆ Found in Text Mining only
Celiac Disease	Celiac disease	Pubtator	27483138	Associate	★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebrovascular accident	Stroke	BEFREE	29487502		★☆☆☆☆ Found in Text Mining only
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	30656857	Associate	★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	19303019		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	12615722, 25529012		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	CTD_human_DG	21278247		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	CTD_human_DG	21278247		★☆☆☆☆ Found in Text Mining only
Depression, Bipolar	Bipolar Disorder	CTD_human_DG	17507910		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental Disabilities	Developmental disability	Pubtator	31668703	Associate	★☆☆☆☆ Found in Text Mining only
Developmental regression	Developmental regression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	31895808	Associate	★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	BEFREE	17903671		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	17903671		★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	31372774, 31668703		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Developmental Delay	GENOMICS_ENGLAND_DG	31668703		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glomerulonephritis Membranous	Membranous glomerulonephritis	Pubtator	35985817	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	22922712		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	31668703		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	31668703	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ischemic stroke	Ischemic Stroke	BEFREE	23769687		★☆☆☆☆ Found in Text Mining only
Macrostomia	Macrostomia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	15239131		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	19303019		★☆☆☆☆ Found in Text Mining only
Manic	Manic Disorder	CTD_human_DG	17507910		★☆☆☆☆ Found in Text Mining only
Manic Disorder	Manic Disorder	CTD_human_DG	17507910		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	GENOMICS_ENGLAND_DG	31668703		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mirror movements disorder	Mirror Movements	BEFREE	30666715		★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	15239131, 26755661, 27651158, 28257124		★☆☆☆☆ Found in Text Mining only
Nephrolithiasis	Nephrolithiasis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	22922712, 31668703		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neuroendocrine Tumors	Neuroendocrine Tumors	BEFREE	26447612		★☆☆☆☆ Found in Text Mining only
Neuropathy	Neuropathy	BEFREE	31392393		★☆☆☆☆ Found in Text Mining only
Non-specific syndromic intellectual disability	Syndromic Mental Retardation	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	39972314	Inhibit	★☆☆☆☆ Found in Text Mining only
Pancreatitis	Pancreatitis	Pubtator	33127842	Associate	★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	BEFREE	25590802		★☆☆☆☆ Found in Text Mining only
Polyneuropathy	Polyneuropathy	BEFREE	31392393		★☆☆☆☆ Found in Text Mining only
Profound Mental Retardation	Mental retardation	BEFREE	31668703		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	36045381	Associate	★☆☆☆☆ Found in Text Mining only
Psychomotor Disorders	Psychiatric disorders	Pubtator	19296131	Associate	★☆☆☆☆ Found in Text Mining only
Rett Syndrome	Rett Syndrome	BEFREE	15870826, 16502428, 22922712, 31692205		★☆☆☆☆ Found in Text Mining only
Rett Syndrome	Rett Syndrome	LHGDN	16502428		★☆☆☆☆ Found in Text Mining only
Rett Syndrome	Rett syndrome	Pubtator	16502428	Associate	★☆☆☆☆ Found in Text Mining only
Rett Syndrome, Atypical	Rett Syndrome	BEFREE	17903671		★☆☆☆☆ Found in Text Mining only
Rett Syndrome, Atypical	Rett Syndrome	ORPHANET_DG	17903671		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	LHGDN	15508520, 15705354		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	BEFREE	15705354, 17507910, 18384956, 20079890, 21641949, 25325217		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	CTD_human_DG	17507910		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seizures	Seizures	Pubtator	16502428	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	26755661		★☆☆☆☆ Found in Text Mining only