NTNG1

gene
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Also known as KIAA0976Lmnt1NetG1NetrinG1

Summary

NTNG1 (netrin G1, HGNC:23319) is a protein-coding gene on chromosome 1p13.3, encoding Netrin-G1 (Q9Y2I2). Involved in controlling patterning and neuronal circuit formation at the laminar, cellular, subcellular and synaptic levels.

This gene encodes a preproprotein that is processed into a secreted protein containing eukaroytic growth factor (EGF)-like domains. This protein acts to guide axon growth during neuronal development. Polymorphisms in this gene may be associated with schizophrenia. Alternative splicing results in multiple transcript variants encoding distinct isoforms.

Source: NCBI Gene 22854 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): atypical Rett syndrome (Supportive, GenCC) — +2 more curated relationships
  • Clinical variants (ClinVar): 85 total
  • MANE Select transcript: NM_001113226

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23319
Approved symbolNTNG1
Namenetrin G1
Location1p13.3
Locus typegene with protein product
StatusApproved
AliasesKIAA0976, Lmnt1, NetG1, NetrinG1
Ensembl geneENSG00000162631
Ensembl biotypeprotein_coding
OMIM608818
Entrez22854

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000294649, ENST00000370065, ENST00000370066, ENST00000370067, ENST00000370068, ENST00000370073, ENST00000370074, ENST00000370076, ENST00000462149, ENST00000477948, ENST00000901085, ENST00000945945

RefSeq mRNA: 11 — MANE Select: NM_001113226 NM_001113226, NM_001113228, NM_001312688, NM_001330665, NM_001372166, NM_001372167, NM_001372168, NM_001372169, NM_001372170, NM_001372171, NM_014917

CCDS: CCDS30785, CCDS44179, CCDS44180, CCDS81354

Canonical transcript exons

ENST00000370068 — 8 exons

ExonStartEnd
ENSE00001451652107141039107141140
ENSE00001451655107480611107484923
ENSE00001451660107436665107436799
ENSE00001451661107430750107430917
ENSE00001451666107407682107407708
ENSE00003471810107324282107324922
ENSE00003594347107148069107148839
ENSE00003599329107395154107395326

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 96.63.

FANTOM5 (CAGE): breadth broad, TPM avg 5.0538 / max 373.1940, expressed in 797 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
43162.9347663
43170.9556327
43240.7606392
43220.6288248
43180.2932118
2016000.2545145
43200.252061
2015990.2406105
43210.177999
43190.163947

Top tissues by expression

287 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lateral nuclear group of thalamusUBERON:000273696.63gold quality
buccal mucosa cellCL:000233689.10gold quality
Brodmann (1909) area 23UBERON:001355487.56gold quality
middle temporal gyrusUBERON:000277187.27gold quality
primary visual cortexUBERON:000243686.51gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.01gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.62gold quality
germinal epithelium of ovaryUBERON:000130482.43gold quality
occipital lobeUBERON:000202181.46gold quality
entorhinal cortexUBERON:000272880.79gold quality
dorsal plus ventral thalamusUBERON:000189780.56gold quality
superior frontal gyrusUBERON:000266178.02gold quality
ventricular zoneUBERON:000305377.86gold quality
prefrontal cortexUBERON:000045177.70gold quality
dorsolateral prefrontal cortexUBERON:000983477.43gold quality
parietal pleuraUBERON:000240077.27gold quality
right frontal lobeUBERON:000281076.98gold quality
frontal cortexUBERON:000187076.84gold quality
hypothalamusUBERON:000189876.71gold quality
neocortexUBERON:000195076.55gold quality
postcentral gyrusUBERON:000258176.32gold quality
ganglionic eminenceUBERON:000402375.96gold quality
endothelial cellCL:000011575.80silver quality
Brodmann (1909) area 9UBERON:001354075.74gold quality
cerebral cortexUBERON:000095675.39gold quality
cingulate cortexUBERON:000302775.32gold quality
anterior cingulate cortexUBERON:000983575.08gold quality
parietal lobeUBERON:000187274.84gold quality
temporal lobeUBERON:000187174.35gold quality
sural nerveUBERON:001548873.71gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-HCAD-35yes56.43
E-CURD-119yes33.78
E-ANND-3yes6.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

197 targeting NTNG1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-9-5P100.0072.282361
HSA-MIR-4455100.0065.481587
HSA-MIR-574-5P100.0066.01989
HSA-MIR-118499.9968.191458
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-806899.9873.852376
HSA-MIR-548N99.9871.944170
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-569699.9872.364487
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-590-3P99.9674.346478
HSA-MIR-185-3P99.9567.011743
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-335-3P99.9373.364958
HSA-MIR-311999.9271.342390
HSA-MIR-7-1-3P99.9171.534384

Literature-anchored findings (GeneRIF, showing 17)

  • Netrin-G1 is an important part of the NGL-1 receptor and functions to promote the outgrowth of dorsal thalamic axons. (PMID:14595443)
  • findings suggest that netrin G1 or a nearby gene may contribute to overall genetic risk for schizophrenia (PMID:15508520)
  • Specific haplotypes encompassing alternatively spliced exons of NTNG1 were associated with schizophrenia, and concordantly, messenger ribonucleic acid isoform expression was significantly different between schizophrenic and control brains. (PMID:15705354)
  • Sequence analysis of the cloned junction fragment indicated that on chromosome 1 the predominantly brain-expressed Netrin G1 (NTNG1) gene is disrupted, whereas on chromosome 7 there was no indication for a truncated gene (PMID:15870826)
  • NTNG1 may use alternative splicing to diversify its function in a developmentally and tissue-specific manner. (PMID:15901489)
  • Mutations in the NTNG1 gene appear to be a rare cause of Rett syndrome but NTNG1 function demands further investigation in relation to the central nervous system pathophysiology of the disorder. (PMID:16502428)
  • The data of this stusty implicate NTNG1 in the pathophysiology of schizophrenia and bipolar disorder, but do not support the hypothesis that altered mRNA expression is the mechanism by which genetic variation of NTNG1 may confer disease susceptibility. (PMID:17507910)
  • Netrin G1 is not involved in atypical Rett syndrome or in unexplained encephalopathy with epilepsy, but in specific forms to be delineated better in the future. (PMID:17903671)
  • Genotype and allele frequencies of single nucleotide polymorphisms on NTNG1 are significantly associated with schizophrenia. (PMID:22227940)
  • Our finding nominates the minor G allele of the NTNG1 rs628117 single nucleotide polymorphism as a risk factor for ischemic stroke at least in Armenian population. (PMID:23769687)
  • Interaction between the tripartite NGL-1, netrin-G1 and LAR adhesion complex promotes development of excitatory synapses. (PMID:23986473)
  • examined the hypothesis that NTNG1 allelic variation contributes to the risk for schizophrenia (PMID:25325217)
  • Significant genetic family-based associations were detected between NTNG1 polymorphisms and cocaine dependence. NTNG1 expression in BA10, BA46 and the cerebellum, however, were not significantly associated with any allele or haplotype of this gene. (PMID:28074533)
  • A 117-base pair SARS-CoV-2 orf1b sequence matched a sequence in the human genome with 94.6% identity. The sequence was in chromosome 1p within an intronic region of the netrin G1 (NTNG1) gene, implicated in schizophrenia. (PMID:32503821)
  • A Genetic Study of Cerebral Atherosclerosis Reveals Novel Associations with NTNG1 and CNOT3. (PMID:34073619)
  • CircNTNG1 inhibits renal cell carcinoma progression via HOXA5-mediated epigenetic silencing of Slug. (PMID:36536414)
  • Comprehensive analysis of the role of Netrin G1 (NTNG1) in hepatocellular carcinoma cells. (PMID:38101695)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriontng1aENSDARG00000014973
danio_reriontng1bENSDARG00000073713
mus_musculusNtng1ENSMUSG00000059857
rattus_norvegicusNtng1ENSRNOG00000031136

Paralogs (27): USH2A (ENSG00000042781), LAMC3 (ENSG00000050555), LAMA3 (ENSG00000053747), LAMC2 (ENSG00000058085), NTN1 (ENSG00000065320), NTN4 (ENSG00000074527), ATRN (ENSG00000088812), LAMB4 (ENSG00000091128), LAMB1 (ENSG00000091136), LAMA1 (ENSG00000101680), MEGF8 (ENSG00000105429), MEGF9 (ENSG00000106780), ATRNL1 (ENSG00000107518), LAMA4 (ENSG00000112769), LAMA5 (ENSG00000130702), LAMC1 (ENSG00000135862), NTN5 (ENSG00000142233), HSPG2 (ENSG00000142798), TMEFF2 (ENSG00000144339), NTN3 (ENSG00000162068), EGFLAM (ENSG00000164318), LAMB2 (ENSG00000172037), AGRN (ENSG00000188157), NTNG2 (ENSG00000196358), LAMA2 (ENSG00000196569), LAMB3 (ENSG00000196878), TMEFF1 (ENSG00000241697)

Protein

Protein identifiers

Netrin-G1Q9Y2I2 (reviewed: Q9Y2I2)

Alternative names: Laminet-1

All UniProt accessions (2): Q9Y2I2, X5DNW2

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Interacts with NGL1.

Subcellular location. Cell membrane.

Tissue specificity. Highly expressed in the thalamus, with very low expression, if any, in other tissues.

Post-translational modifications. N-glycosylated.

Domain organisation. The laminin N-terminal domain mediates 1:1 binding to NGL ligand with sub-micromolar affinity. Three NGL-binding loops mediate discrimination for LRRC4C/NGL1 among other NGLs by binding specifically to its LRR repeats. This specificity drives the sorting of a mixed population of molecules into discrete cell surface subdomains.

Miscellaneous. Mostly expressed in adult brain. Hi expression in Expressed in brain and. Mostly expressed in kidney, also expressed in adult and fetal brain. Some expression in fetal brain.

Isoforms (6)

UniProt IDNamesCanonical?
Q9Y2I2-33, 1Ayes
Q9Y2I2-22, 1F
Q9Y2I2-11, 1C
Q9Y2I2-44, 1D
Q9Y2I2-55, 1E
Q9Y2I2-66, 1G

RefSeq proteins (11): NP_001106697, NP_001106699, NP_001299617, NP_001317594, NP_001359095, NP_001359096, NP_001359097, NP_001359098, NP_001359099, NP_001359100, NP_055732 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000742EGFDomain
IPR002049LE_domDomain
IPR008211Laminin_NDomain
IPR050440Laminin/Netrin_ECMFamily
IPR056863LMN_ATRN_NET-like_EGFDomain

Pfam: PF00053, PF00055, PF24973

UniProt features (79 total): strand 20, disulfide bond 19, splice variant 9, helix 9, glycosylation site 4, domain 4, sequence conflict 4, turn 3, region of interest 3, signal peptide 1, chain 1, lipid moiety-binding region 1, propeptide 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3ZYJX-RAY DIFFRACTION3.25

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y2I2-F184.130.59

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 510

Disulfide bonds (19): 33–50, 72–92, 80–88, 182–206, 297–306, 299–315, 317–326, 329–354, 364–373, 366–384, 387–396, 399–417, 420–432, 422–438, 440–449, 452–462, 467–480, 474–486, 488–497

Glycosylation sites (4): 133, 320, 406, 433

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-163125Post-translational modification: synthesis of GPI-anchored proteins

MSigDB gene sets: 293 (showing top): GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_NEUROGENESIS, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_CELL_ADHESION, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CELL_JUNCTION_ORGANIZATION, MODULE_379, GOBP_REGULATION_OF_NEURON_MIGRATION, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_NEURON_MIGRATION, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOBP_SYNAPTIC_SIGNALING, MODULE_88, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT

GO Biological Process (8): axonogenesis (GO:0007409), regulation of neuron projection development (GO:0010975), modulation of chemical synaptic transmission (GO:0050804), synaptic membrane adhesion (GO:0099560), regulation of neuron projection arborization (GO:0150011), regulation of neuron migration (GO:2001222), nervous system development (GO:0007399), cell differentiation (GO:0030154)

GO Molecular Function (3): cell adhesion molecule binding (GO:0050839), cell-cell adhesion mediator activity (GO:0098632), protein binding (GO:0005515)

GO Cellular Component (7): extracellular region (GO:0005576), plasma membrane (GO:0005886), presynaptic active zone membrane (GO:0048787), side of membrane (GO:0098552), Schaffer collateral - CA1 synapse (GO:0098685), glutamatergic synapse (GO:0098978), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cell-cell adhesion2
membrane2
synapse2
cell morphogenesis involved in neuron differentiation1
neuron projection morphogenesis1
axon development1
neuron projection development1
regulation of plasma membrane bounded cell projection organization1
chemical synaptic transmission1
regulation of trans-synaptic signaling1
synapse organization1
regulation of cell morphogenesis1
regulation of cell projection organization1
neuron projection arborization1
neuron migration1
regulation of cell migration1
system development1
cellular developmental process1
protein binding1
cell adhesion mediator activity1
binding1
cell periphery1
presynaptic membrane1
presynaptic active zone1
synaptic membrane1
leaflet of membrane bilayer1

Protein interactions and networks

STRING

2528 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NTNG1LRRC4CQ9HCJ2999
NTNG1CDKL5O76039844
NTNG1LRRC4Q9HBW1799
NTNG1LRRC4BQ9NT99751
NTNG1MECP2P51608673
NTNG1GLRA2P23416669
NTNG1GPM6BQ13491668
NTNG1GRPRP30550659
NTNG1GDI1P31150639
NTNG1GLUD2P49448638
NTNG1ROBO2Q9HCK4603
NTNG1HCCSP53701580
NTNG1UNC5CO95185566
NTNG1CDH8P55286531
NTNG1IL1RAPL1Q9NZN1531

IntAct

11 interactions, top by confidence:

ABTypeScore
NTNG1NUDT16L1psi-mi:“MI:0915”(physical association)0.620
NTNG1LRRC4Cpsi-mi:“MI:0407”(direct interaction)0.620
LRRC4CNTNG1psi-mi:“MI:0407”(direct interaction)0.620
NTNG1LRRC4psi-mi:“MI:0407”(direct interaction)0.440
LRRC4NTNG1psi-mi:“MI:0407”(direct interaction)0.440
NTNG1RPN1psi-mi:“MI:0915”(physical association)0.400
NTNG1AMY1Apsi-mi:“MI:0914”(association)0.350
NTNG1UBA6psi-mi:“MI:0914”(association)0.350
NTNG1SRPX2psi-mi:“MI:0914”(association)0.350

BioGRID (105): HSPA6 (Affinity Capture-MS), GAS6 (Affinity Capture-MS), LRRC4C (Affinity Capture-Western), LRRC4C (Reconstituted Complex), NTNG1 (Proximity Label-MS), LRRC4C (Co-crystal Structure), MUC5B (Affinity Capture-MS), NUDT16L1 (Affinity Capture-MS), AMY1C (Affinity Capture-MS), BPIFA1 (Affinity Capture-MS), PGA4 (Affinity Capture-MS), LIPF (Affinity Capture-MS), USO1 (Affinity Capture-MS), PPME1 (Affinity Capture-MS), HDLBP (Affinity Capture-MS)

ESM2 similar proteins: A0A6I8RMG7, A0JP86, A4D0S4, O54890, O70309, P02468, P02469, P05106, P0CY46, P11046, P11047, P13387, P13388, P15215, P15800, P18084, P18563, P18564, P19137, P24043, P25391, P35555, P55268, P80747, P98133, Q07441, Q18823, Q1LVF0, Q1RPR6, Q2KIT5, Q5RB89, Q60675, Q61220, Q61292, Q61526, Q61554, Q61555, Q62918, Q6AYF4, Q6UXH1

Diamond homologs: A0JP86, A2ASQ1, G5ECE3, O00468, O00634, O09118, O15230, O75445, O75882, O95631, P02468, P11047, P15215, P19137, P24043, P25304, P25391, P31696, P34710, P97927, Q00174, Q01635, Q13751, Q13753, Q16363, Q16787, Q18823, Q19981, Q1LVF0, Q24567, Q24568, Q27262, Q2HXW4, Q2QI47, Q5RB89, Q5VV63, Q60675, Q61001, Q61087, Q61092

SIGNOR signaling

1 interactions.

AEffectBMechanism
NTNG1“up-regulates activity”LRRC4Cbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

85 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance54
Likely benign5
Benign15

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

3547 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:107324309:T:AC92S1.000
1:107324310:G:CC92S1.000
1:107324387:T:AW118R1.000
1:107324387:T:CW118R1.000
1:107324389:G:CW118C1.000
1:107324389:G:TW118C1.000
1:107324551:G:CW172C1.000
1:107324551:G:TW172C1.000
1:107324581:C:GC182W1.000
1:107324652:G:AC206Y1.000
1:107324653:C:GC206W1.000
1:107324820:T:CL262P1.000
1:107430812:T:AC384S1.000
1:107430812:T:CC384R1.000
1:107430813:G:AC384Y1.000
1:107430813:G:CC384S1.000
1:107430814:C:GC384W1.000
1:107430821:T:AC387S1.000
1:107430822:G:AC387Y1.000
1:107430822:G:CC387S1.000
1:107430823:T:GC387W1.000
1:107430848:T:AC396S1.000
1:107430848:T:CC396R1.000
1:107430849:G:AC396Y1.000
1:107430849:G:CC396S1.000
1:107430849:G:TC396F1.000
1:107430850:T:GC396W1.000
1:107430857:T:AC399S1.000
1:107430858:G:CC399S1.000
1:107436727:T:AC440S1.000

dbSNP variants (sampled 300 via entrez): RS1000012192 (1:107222474 T>C), RS1000015331 (1:107474997 A>T), RS1000018353 (1:107240457 C>T), RS1000026575 (1:107283393 C>G,T), RS1000030157 (1:107333217 A>G), RS1000034719 (1:107313065 G>A), RS1000042553 (1:107409973 C>T), RS1000052186 (1:107431730 A>G), RS1000061495 (1:107162971 G>A,C), RS1000078443 (1:107161262 C>T), RS1000086770 (1:107312795 G>A), RS1000090177 (1:107270258 CTG>C), RS1000102655 (1:107388212 A>T), RS1000109017 (1:107270672 A>G), RS1000111799 (1:107155410 T>C)

Disease associations

OMIM: gene MIM:608818 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
atypical Rett syndromeSupportiveAutosomal dominant
syndromic intellectual disabilitySupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
complex neurodevelopmental disorderLimitedAD

Mondo (2): atypical Rett syndrome (MONDO:0017746), syndromic intellectual disability (MONDO:0000508)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs61816456Efficacy3allopurinol

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Estradiolincreases expression, decreases expression, affects cotreatment3
monomethylarsonous acidaffects expression, decreases expression2
aristolochic acid Idecreases expression1
sodium arseniteincreases expression1
tobacco tardecreases expression1
rutecarpinedecreases expression1
S-(1,2-dichlorovinyl)cysteinedecreases expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608increases reaction, affects binding1
2-palmitoylglycerolincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Zoledronic Aciddecreases expression1
Vorinostatdecreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Cytarabineincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Silicon Dioxidedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Valproic Aciddecreases expression1
Aflatoxin B1decreases methylation1
Thapsigarginincreases expression1
Copper Sulfateincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.