NSG1

gene
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Also known as P21D4S234ENEEP21

Summary

NSG1 (neuronal vesicle trafficking associated 1, HGNC:18790) is a protein-coding gene on chromosome 4p16.3, encoding Neuronal vesicle trafficking-associated protein 1 (P42857). Plays a role in the recycling mechanism in neurons of multiple receptors, including AMPAR, APP and L1CAM and acts at the level of early endosomes to promote sorting of receptors toward a recycling pathway.

Predicted to enable clathrin light chain binding activity. Involved in apoptotic process. Located in endoplasmic reticulum.

Source: NCBI Gene 27065 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 7 total
  • MANE Select transcript: NM_014392

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18790
Approved symbolNSG1
Nameneuronal vesicle trafficking associated 1
Location4p16.3
Locus typegene with protein product
StatusApproved
AliasesP21, D4S234E, NEEP21
Ensembl geneENSG00000168824
Ensembl biotypeprotein_coding
OMIM607645
Entrez27065

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000397958, ENST00000421177, ENST00000433139, ENST00000450293, ENST00000504171, ENST00000504347, ENST00000505246, ENST00000506380, ENST00000513555, ENST00000513829, ENST00000621129, ENST00000889808, ENST00000889809, ENST00000889810, ENST00000930399, ENST00000930400, ENST00000930401, ENST00000930402, ENST00000963790

RefSeq mRNA: 6 — MANE Select: NM_014392 NM_001040101, NM_001287763, NM_001287764, NM_001382227, NM_001382228, NM_014392

CCDS: CCDS3376, CCDS93472

Canonical transcript exons

ENST00000621129 — 5 exons

ExonStartEnd
ENSE0000116190444095734409683
ENSE0000116190943914754391591
ENSE0000116193043876044387758
ENSE0000170411244172354419058
ENSE0000393391043871024387173

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 99.52.

FANTOM5 (CAGE): breadth broad, TPM avg 14.8437 / max 445.2521, expressed in 766 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
467429.4468694
467353.3339475
467340.6123230
467370.4548196
467380.2999159
467400.2225117
467410.188099
467390.1840106
467360.101655

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.52gold quality
cortical plateUBERON:000534399.48gold quality
endothelial cellCL:000011599.30gold quality
middle temporal gyrusUBERON:000277199.22gold quality
ganglionic eminenceUBERON:000402398.69gold quality
Brodmann (1909) area 23UBERON:001355498.52gold quality
lateral nuclear group of thalamusUBERON:000273698.41gold quality
ponsUBERON:000098898.39gold quality
oocyteCL:000002397.92gold quality
pituitary glandUBERON:000000797.70gold quality
superior vestibular nucleusUBERON:000722797.29gold quality
adenohypophysisUBERON:000219696.95gold quality
right hemisphere of cerebellumUBERON:001489096.92gold quality
substantia nigra pars compactaUBERON:000196596.76gold quality
cerebellar cortexUBERON:000212996.29gold quality
cerebellar hemisphereUBERON:000224596.28gold quality
cerebellumUBERON:000203796.04gold quality
gingival epitheliumUBERON:000194995.70gold quality
skin of legUBERON:000151195.57gold quality
gingivaUBERON:000182895.57gold quality
germinal epithelium of ovaryUBERON:000130495.53gold quality
hypothalamusUBERON:000189895.49gold quality
skin of abdomenUBERON:000141695.39gold quality
primary visual cortexUBERON:000243695.36gold quality
nucleus accumbensUBERON:000188295.12gold quality
zone of skinUBERON:000001495.02gold quality
lateral globus pallidusUBERON:000247694.99gold quality
substantia nigra pars reticulataUBERON:000196694.83gold quality
embryoUBERON:000092294.51gold quality
right frontal lobeUBERON:000281094.37gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 9.

ExperimentMarker?Max mean expression
E-MTAB-9906yes734.23
E-ANND-5yes599.27
E-GEOD-93593yes590.04
E-HCAD-5yes48.48
E-MTAB-8142yes19.03
E-GEOD-137537yes15.04
E-HCAD-25yes11.93
E-MTAB-5061yes11.28
E-ANND-3yes10.98
E-MTAB-9154no1073.88
E-ENAD-20no579.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

129 targeting NSG1, 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-188-3P100.0068.761240
HSA-MIR-3646100.0073.565283
HSA-MIR-4262100.0073.263931
HSA-MIR-4283100.0066.422097
HSA-MIR-8485100.0077.574731
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-548P99.9872.253784
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-480399.9871.993117
HSA-MIR-25-3P99.9874.601817
HSA-MIR-32-5P99.9875.211964

Literature-anchored findings (GeneRIF, showing 5)

  • a novel p53-responsive gene D4S234E is accumulated in the ER and induces apoptosis in response to DNA damage. (PMID:20599942)
  • These results suggest that NEEP21 may play a critical role in apoptosis as a mediator of p53. (PMID:20878061)
  • NEEP21 profoundly affects the processing of beta-amyloid precursor proteins and Abeta peptide production. (PMID:21084623)
  • This review focuses on two closely related, neuron-enriched endosomal proteins: NEEP21 and Calcyon which perform distinct roles in regulating receptor endocytosis, recycling, and degradation–{REVIEW} (PMID:25376768)
  • miR-107 Targets NSG1 to Regulate Hypopharyngeal Squamous Cell Carcinoma Progression through ERK Pathway. (PMID:38892156)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusNsg1ENSMUSG00000029126
rattus_norvegicusNsg1ENSRNOG00000005700

Paralogs (2): CALY (ENSG00000130643), NSG2 (ENSG00000170091)

Protein

Protein identifiers

Neuronal vesicle trafficking-associated protein 1P42857 (reviewed: P42857)

Alternative names: Neuron-enriched endosomal protein of 21 kDa, Neuron-specific protein family member 1

All UniProt accessions (2): P42857, B2R5R8

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the recycling mechanism in neurons of multiple receptors, including AMPAR, APP and L1CAM and acts at the level of early endosomes to promote sorting of receptors toward a recycling pathway. Regulates sorting and recycling of GRIA2 through interaction with GRIP1 and then contributes to the regulation of synaptic transmission and plasticity by affecting the recycling and targeting of AMPA receptors to the synapse. Is required for faithful sorting of L1CAM to axons by facilitating trafficking from somatodendritic early endosome or the recycling endosome. In an other hand, induces apoptosis via the activation of CASP3 in response to DNA damage.

Subunit / interactions. Forms a complex with GRIP1, GRIA2 and STX12 through direct interaction with GRIP1; controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting. Interacts with STX12. Interacts with APP; could regulate APP processing. Interacts with FAM171A1.

Subcellular location. Membrane. Golgi apparatus. trans-Golgi network membrane. Endosome membrane. Cell projection. Dendrite. Early endosome membrane. Late endosome membrane. Lysosome lumen. Recycling endosome membrane. Cytoplasmic vesicle membrane. Golgi stack membrane. Endosome. Multivesicular body membrane. Endoplasmic reticulum membrane.

Induction. Up-regulated by TP53 after DNA damage. Up-regulated by genotoxic stress.

Similarity. Belongs to the NSG family.

Isoforms (2)

UniProt IDNamesCanonical?
P42857-11yes
P42857-22

RefSeq proteins (6): NP_001035190, NP_001274692, NP_001274693, NP_001369156, NP_001369157, NP_055207* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009431NSGFamily

Pfam: PF06387

UniProt features (6 total): topological domain 2, chain 1, transmembrane region 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P42857-F160.700.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 252 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_CLATHRIN_COAT_ASSEMBLY, GOBP_VESICLE_MEDIATED_TRANSPORT, BAKER_HEMATOPOESIS_STAT1_TARGETS, BAKER_HEMATOPOIESIS_STAT3_TARGETS, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP, GOBP_CELL_CELL_SIGNALING, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, GOCC_TRANS_GOLGI_NETWORK, GOBP_REGULATION_OF_SYNAPTIC_PLASTICITY, MODULE_379, BILD_E2F3_ONCOGENIC_SIGNATURE, HUPER_BREAST_BASAL_VS_LUMINAL_UP

GO Biological Process (12): receptor recycling (GO:0001881), positive regulation of receptor recycling (GO:0001921), apoptotic process (GO:0006915), endosomal transport (GO:0016197), amyloid precursor protein metabolic process (GO:0042982), clathrin coat assembly (GO:0048268), spontaneous synaptic transmission (GO:0098814), neurotransmitter receptor transport, endosome to postsynaptic membrane (GO:0098887), vesicle-mediated transport in synapse (GO:0099003), neurotransmitter receptor cycle (GO:0099627), postsynaptic neurotransmitter receptor cycle (GO:0099630), regulation of long-term synaptic potentiation (GO:1900271)

GO Molecular Function (4): clathrin light chain binding (GO:0032051), ionotropic glutamate receptor binding (GO:0035255), signaling receptor binding (GO:0005102), protein binding (GO:0005515)

GO Cellular Component (27): nucleus (GO:0005634), cytoplasm (GO:0005737), endosome (GO:0005768), late endosome (GO:0005770), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), lateral plasma membrane (GO:0016328), dendrite (GO:0030425), early endosome membrane (GO:0031901), Golgi cisterna membrane (GO:0032580), multivesicular body membrane (GO:0032585), trans-Golgi network membrane (GO:0032588), somatodendritic compartment (GO:0036477), lysosomal lumen (GO:0043202), postsynaptic membrane (GO:0045211), recycling endosome membrane (GO:0055038), postsynaptic endosome (GO:0098845), glutamatergic synapse (GO:0098978), lysosome (GO:0005764), early endosome (GO:0005769), Golgi apparatus (GO:0005794), endosome membrane (GO:0010008), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410), late endosome membrane (GO:0031902), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
postsynapse3
organelle membrane3
vesicle-mediated transport2
synapse2
intracellular membrane-bounded organelle2
endomembrane system2
endosome2
endosome membrane2
endocytosis1
receptor metabolic process1
receptor recycling1
regulation of receptor recycling1
positive regulation of macromolecule metabolic process1
positive regulation of signaling1
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
intracellular transport1
protein metabolic process1
protein-containing complex assembly1
chemical synaptic transmission1
spontaneous neurotransmitter secretion1
intercellular transport1
neurotransmitter receptor transport to postsynaptic membrane1
neurotransmitter receptor transport, endosome to plasma membrane1
neurotransmitter receptor transport1
establishment of localization in cell1
neurotransmitter receptor cycle1
regulation of synaptic plasticity1
long-term synaptic potentiation1
clathrin binding1
glutamate receptor binding1
protein binding1
binding1
intracellular anatomical structure1
cytoplasmic vesicle1
cytoplasm1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1

Protein interactions and networks

STRING

642 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NSG1STX18Q9P2W9806
NSG1GRIP1Q9Y3R0783
NSG1EVC2Q86UK5749
NSG1CRMP1Q14194717
NSG1EVCP57679639
NSG1GRIA2P42262621
NSG1GRIA1P42261571
NSG1MSX1P28360557
NSG1GRIPAP1Q4V328502
NSG1PICK1Q9NRD5495
NSG1OAZ1P54368442
NSG1STX12Q86Y82440
NSG1CENPHQ9H3R5419
NSG1SRSF5Q13243403
NSG1EEIG2Q5T8I3394
NSG1TMEM128Q5BJH2394

IntAct

120 interactions, top by confidence:

ABTypeScore
NSG1KASH5psi-mi:“MI:0915”(physical association)0.720
KASH5NSG1psi-mi:“MI:0915”(physical association)0.720
NSG1BSCL2psi-mi:“MI:0915”(physical association)0.560
BSCL2NSG1psi-mi:“MI:0915”(physical association)0.560
NSG1TMEM139psi-mi:“MI:0915”(physical association)0.560
OPRM1NSG1psi-mi:“MI:0915”(physical association)0.560
NSG1psi-mi:“MI:0915”(physical association)0.560
NSG1CREB3L1psi-mi:“MI:0915”(physical association)0.560
NSG1FNDC9psi-mi:“MI:0915”(physical association)0.560
NSG1SLC7A14psi-mi:“MI:0915”(physical association)0.560
SLC30A4NSG1psi-mi:“MI:0915”(physical association)0.560
NSG1SPACA1psi-mi:“MI:0915”(physical association)0.560
NSG1TMEM207psi-mi:“MI:0915”(physical association)0.560
NSG1TMEM52Bpsi-mi:“MI:0915”(physical association)0.560
ATP6AP2NSG1psi-mi:“MI:0915”(physical association)0.560
NSG1KIR2DL3psi-mi:“MI:0915”(physical association)0.560
NSG1PDZK1IP1psi-mi:“MI:0915”(physical association)0.560
EVI2BNSG1psi-mi:“MI:0915”(physical association)0.560
FFAR2NSG1psi-mi:“MI:0915”(physical association)0.560
FCGR2ANSG1psi-mi:“MI:0915”(physical association)0.560
NSG1RELL2psi-mi:“MI:0915”(physical association)0.560
NSG1TMX2psi-mi:“MI:0915”(physical association)0.560
MGST3NSG1psi-mi:“MI:0915”(physical association)0.560
NSG1BTN2A1psi-mi:“MI:0915”(physical association)0.560
GPR42NSG1psi-mi:“MI:0915”(physical association)0.560

BioGRID (43): NSG1 (Two-hybrid), CCDC155 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid), NSG1 (Two-hybrid)

ESM2 similar proteins: A4IG66, B2RUZ4, B3DHH5, F1NVK6, F1Q930, O70367, O76024, O77770, O95772, P02683, P0C8K7, P42857, P56695, P84889, Q0P4Z1, Q15053, Q1JPG0, Q28DG6, Q2TBG9, Q4QQM5, Q4R5Q3, Q56JY4, Q5BLE2, Q5M836, Q5RF46, Q5XJS0, Q5ZKK0, Q62092, Q6GR21, Q6IQA2, Q6NRB7, Q6P606, Q7L4E1, Q7Z3D4, Q8BG50, Q8BK03, Q8BXV2, Q8IUW5, Q8K2J7, Q8NAN2

Diamond homologs: P02683, P42857, P47759, P58821, Q0VCZ0, Q3KR51, Q4R5Q3, Q5RF46, Q62092, Q8QFP1, Q9DCA7, Q9NYX4, Q9Y328

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance5
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1935 predictions. Top by Δscore:

VariantEffectΔscore
4:4387759:G:GAdonor_loss1.0000
4:4387759:G:GGdonor_gain1.0000
4:4387760:T:Gdonor_loss1.0000
4:4391460:T:TAacceptor_gain1.0000
4:4391467:T:Aacceptor_gain1.0000
4:4391468:G:Aacceptor_gain1.0000
4:4391471:TAAG:Tacceptor_loss1.0000
4:4391472:A:AGacceptor_gain1.0000
4:4391472:AAG:Aacceptor_gain1.0000
4:4391472:AAGGT:Aacceptor_gain1.0000
4:4391473:A:Gacceptor_gain1.0000
4:4391473:AGGT:Aacceptor_gain1.0000
4:4391474:G:Aacceptor_gain1.0000
4:4391474:G:GCacceptor_loss1.0000
4:4391474:GGTG:Gacceptor_gain1.0000
4:4391586:TTTA:Tdonor_gain1.0000
4:4391589:AAG:Adonor_loss1.0000
4:4391592:GTG:Gdonor_loss1.0000
4:4391593:T:Gdonor_loss1.0000
4:4409567:CCACA:Cacceptor_loss1.0000
4:4409568:CACAG:Cacceptor_loss1.0000
4:4409570:CA:Cacceptor_loss1.0000
4:4409571:A:AGacceptor_gain1.0000
4:4409571:A:Cacceptor_loss1.0000
4:4409572:G:GTacceptor_gain1.0000
4:4409572:GGTCT:Gacceptor_gain1.0000
4:4409640:TGTAC:Tdonor_gain1.0000
4:4409681:AAG:Adonor_loss1.0000
4:4409684:GT:Gdonor_loss1.0000
4:4409685:T:Adonor_loss1.0000

AlphaMissense

1204 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:4409612:T:CC96R0.999
4:4409660:T:CC112R0.998
4:4417244:T:AC123S0.998
4:4417244:T:CC123R0.998
4:4417245:G:CC123S0.998
4:4387721:T:AL31H0.997
4:4409595:C:AA90D0.997
4:4409616:T:AV97D0.997
4:4409607:T:CL94P0.996
4:4409660:T:AC112S0.996
4:4409661:G:CC112S0.996
4:4387736:T:CL36P0.995
4:4409607:T:AL94H0.995
4:4409607:T:GL94R0.995
4:4409661:G:AC112Y0.995
4:4409662:C:GC112W0.995
4:4417246:C:GC123W0.995
4:4409586:T:AV87D0.994
4:4409625:T:CL100P0.994
4:4409628:T:AV101D0.994
4:4409672:T:CF116L0.994
4:4409674:C:AF116L0.994
4:4409674:C:GF116L0.994
4:4387693:T:CF22L0.993
4:4387695:C:AF22L0.993
4:4387695:C:GF22L0.993
4:4387721:T:CL31P0.993
4:4409598:T:CL91P0.993
4:4409598:T:GL91R0.993
4:4387709:T:CL27P0.992

dbSNP variants (sampled 300 via entrez): RS1000101417 (4:4416706 C>G), RS10002237 (4:4417884 C>T), RS1000245748 (4:4400245 C>T), RS1000310322 (4:4411054 C>T), RS1000457234 (4:4394648 A>T), RS1000506951 (4:4397652 G>A,C), RS1000527789 (4:4398947 T>A), RS1000580248 (4:4398726 G>A), RS1000676336 (4:4386701 G>A,T), RS1000810713 (4:4414633 C>A,T), RS1000839739 (4:4408324 T>A), RS10008550 (4:4384861 C>G,T), RS1000870988 (4:4408098 T>C), RS1000937479 (4:4386912 C>A,T), RS1001033624 (4:4409951 C>T)

Disease associations

OMIM: gene MIM:607645 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST005173_80Coronary artery calcified atherosclerotic plaque (130 HU threshold) in type 2 diabetes3.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004723coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression8
Benzo(a)pyreneaffects methylation, increases expression2
Diethylhexyl Phthalatedecreases methylation, increases abundance, decreases expression2
Doxorubicinincreases expression2
Estradiolaffects cotreatment, increases expression2
Aflatoxin B1decreases expression, increases methylation2
methylmercuric chloridedecreases expression1
triphenyl phosphatedecreases expression1
propionaldehydeincreases expression1
testosterone undecanoateaffects cotreatment, decreases expression1
trichostatin Aincreases expression1
mono-(2-ethylhexyl)phthalatedecreases methylation, increases abundance1
butyraldehydeincreases expression1
benzo(e)pyreneincreases methylation1
beta-methylcholineaffects expression1
pentanalincreases expression1
deguelindecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
nutlin 3affects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Air Pollutantsincreases abundance, increases expression1
Aldehydesincreases expression1
Camptothecinincreases expression1
Cisplatinaffects cotreatment, increases expression1
Dactinomycinaffects cotreatment, increases expression1
Formaldehydedecreases expression1
Methapyrileneincreases methylation1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.