GeneBe

NSF

N-ethylmaleimide sensitive factor, vesicle fusing ATPase, the group of AAA ATPases

Basic information

Region (hg38): 17:46590669-46757679

Links

ENSG00000073969 ∙ NCBI:4905 ∙ OMIM:601633 ∙ HGNC:8016 ∙ Uniprot:P46459 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • developmental and epileptic encephalopathy 96 (Limited), mode of inheritance: AD
  • developmental and epileptic encephalopathy 96 (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NSF gene.

  • not_provided (23 variants)
  • not_specified (21 variants)
  • Developmental_and_epileptic_encephalopathy_96 (8 variants)
  • Alstrom_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSF gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006178.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
 4
missense
1
clinvar
3
clinvar
37
clinvar
2
clinvar
 43
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 1 3 37 6 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NSFprotein_codingprotein_codingENST00000398238 21166796
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.01830.9811247800101247900.0000401
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.581072130.5020.00001124914
Missense in Polyphen2275.4770.291481668
Synonymous1.655775.20.7580.000004141376
Loss of Function2.93721.80.3210.00000121505

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.0002230.000223
Finnish0.000.00
European (Non-Finnish)0.00005360.0000530
Middle Eastern0.0002230.000223
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for vesicle-mediated transport. Catalyzes the fusion of transport vesicles within the Golgi cisternae. Is also required for transport from the endoplasmic reticulum to the Golgi stack. Seems to function as a fusion protein required for the delivery of cargo proteins to all compartments of the Golgi stack independent of vesicle origin. Interaction with AMPAR subunit GRIA2 leads to influence GRIA2 membrane cycling (By similarity). {ECO:0000250}.;
Pathway
Synaptic vesicle cycle - Homo sapiens (human);GABAergic synapse - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Synaptic Vesicle Pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Vesicle-mediated transport;gamma-aminobutyric acid receptor life cycle pathway;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Neuronal System;BDNF;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Trafficking of GluR2-containing AMPA receptors;Trafficking of AMPA receptors;Intra-Golgi traffic;Glutamate binding, activation of AMPA receptors and synaptic plasticity;COPI-mediated anterograde transport;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec
0.300

Haploinsufficiency Scores

pHI
0.544
hipred
Y
hipred_score
0.819
ghis
0.666

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.570

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nsf
Phenotype
homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype;

Zebrafish Information Network

Gene name
nsfb
Affected structure
pigment cell
Phenotype tag
abnormal
Phenotype quality
quality

Gene ontology

Biological process
positive regulation of receptor recycling;potassium ion transport;intracellular protein transport;exocytosis;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;vesicle-mediated transport;regulation of exocytosis;SNARE complex disassembly;Golgi to plasma membrane protein transport;plasma membrane fusion;positive regulation of protein catabolic process;COPII vesicle coating;Golgi vesicle docking
Cellular component
Golgi membrane;lysosomal membrane;Golgi stack;cytosol;plasma membrane;postsynaptic density;dendritic shaft;myelin sheath
Molecular function
SNARE binding;protein binding;ATP binding;ATPase activity;syntaxin-1 binding;Rab GTPase binding;protein kinase binding;PDZ domain binding;ionotropic glutamate receptor binding;ATPase activity, coupled;protein-containing complex binding;metal ion binding