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Aliases for SZT2 Gene

Aliases for SZT2 Gene

  • SZT2, KICSTOR Complex Subunit 2 3 5
  • KIAA0467 2 3 4
  • Seizure Threshold 2 Protein Homolog 3 4
  • C1orf84 3 4
  • Seizure Threshold 2 Homolog A (Mouse) 2
  • Seizure Threshold 2 Homolog B (Mouse) 2
  • Seizure Threshold 2 Homolog (Mouse) 2
  • Chromosome 1 Open Reading Frame 84 2
  • KICSTOR Complex Protein SZT2 3
  • Seizure Threshold 2 Homolog 3
  • Protein SZT2 3
  • EIEE18 3
  • SZT2A 3
  • SZT2B 3

External Ids for SZT2 Gene

Previous HGNC Symbols for SZT2 Gene

  • C1orf84
  • KIAA0467

Previous GeneCards Identifiers for SZT2 Gene

  • GC01P043890

Summaries for SZT2 Gene

Entrez Gene Summary for SZT2 Gene

  • The protein encoded by this gene is expressed in the brain, predominantly in the parietal and frontal cortex as well as in dorsal root ganglia. It is localized to the peroxisome, and is implicated in resistance to oxidative stress. It likely functions by increasing superoxide dismutase (SOD) activity, but itself has no direct SOD activity. Studies in mice show that this gene confers low seizure threshold, and may also enhance epileptogenesis. [provided by RefSeq, Jun 2011]

GeneCards Summary for SZT2 Gene

SZT2 (SZT2, KICSTOR Complex Subunit) is a Protein Coding gene. Diseases associated with SZT2 include Epileptic Encephalopathy, Early Infantile, 18 and Early Infantile Epileptic Encephalopathy Without Suppression Burst.

UniProtKB/Swiss-Prot for SZT2 Gene

  • As part of the KICSTOR complex functions in the amino acid-sensing branch of the TORC1 signaling pathway. Recruits, in an amino acid-independent manner, the GATOR1 complex to the lysosomal membranes and allows its interaction with GATOR2 and the RAG GTPases. Functions upstream of the RAG GTPases and is required to negatively regulate mTORC1 signaling in absence of amino acids. In absence of the KICSTOR complex mTORC1 is constitutively localized to the lysosome and activated. The KICSTOR complex is also probably involved in the regulation of mTORC1 by glucose (PubMed:28199306, PubMed:28199315). May play a role in the cellular response to oxidative stress (By similarity).

Additional gene information for SZT2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SZT2 Gene

Genomics for SZT2 Gene

Regulatory Elements for SZT2 Gene

Enhancers for SZT2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H044212 1.2 ENCODE 134.6 +828.7 828653 2 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC SZT2 DMAP1 KDM4A-AS1 HYI ARTN LOC101929609 PTCH2 MED8 CCDC24 HECTD3
GH01H044325 2.3 Ensembl ENCODE 31 +943.1 943054 4 PKNOX1 FOXA2 SIN3A FEZF1 ZNF2 YY1 ZNF121 GLIS2 FOS TSHZ1 SZT2 ZSWIM5 LOC101929609 DMAP1 ERI3 HYI ERI3-IT1 PTCH2 ARTN GC01P044305
GH01H043522 1.9 FANTOM5 Ensembl ENCODE dbSUPER 29.1 +139.2 139205 3 HDGF PKNOX1 FOXA2 ARNT YBX1 ZNF766 FOS SP3 SP5 REST MED8 SZT2 P3H1 PPIH KDM4A-AS1 DMAP1 KDM4A HYI PTPRF GC01M043545
GH01H042923 1.6 Ensembl ENCODE dbSUPER 33.2 -460.1 -460078 3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 FOXJ3 SZT2 HYI MKRN8P HNRNPFP1 PPIH P3H1 RNU6-880P CCDC30 ZNF691
GH01H043705 1.1 ENCODE 45.5 +322.8 322765 3 HDGF FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 SZT2 DMAP1 KDM4A P3H1 HYI MED8 ARTN ZNF691 KDM4A-AS1 SZT2-AS1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SZT2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SZT2 Gene

Chromosome:
1
Start:
43,384,830 bp from pter
End:
43,454,247 bp from pter
Size:
69,418 bases
Orientation:
Plus strand

Genomic View for SZT2 Gene

Genes around SZT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SZT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SZT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SZT2 Gene

Proteins for SZT2 Gene

  • Protein details for SZT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5T011-SZT2_HUMAN
    Recommended name:
    KICSTOR complex protein SZT2
    Protein Accession:
    Q5T011
    Secondary Accessions:
    • A0PJK5
    • A7E2X4
    • O75055
    • Q5JUY7
    • Q5T012
    • Q5XKC7
    • Q6ZNI8
    • Q6ZT24
    • Q7Z636
    • Q8NAY9
    • Q9H5H7
    • Q9UFQ8

    Protein attributes for SZT2 Gene

    Size:
    3432 amino acids
    Molecular mass:
    378029 Da
    Quaternary structure:
    • Part of the KICSTOR complex composed of KPTN, ITFG2, C12orf66 and SZT2. SZT2 probably serves as a link between the other three proteins in the KICSTOR complex and mediates the direct interaction with the GATOR1 complex.
    SequenceCaution:
    • Sequence=AAH52802.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI51233.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15649.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC03755.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=BAC86771.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=BF926328; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=BF926328; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305}; Sequence=BU101724; Type=Frameshift; Positions=287; Evidence={ECO:0000305}; Sequence=CAI14886.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI23384.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for SZT2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SZT2 Gene

Post-translational modifications for SZT2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SZT2 Gene

Domains & Families for SZT2 Gene

Gene Families for SZT2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SZT2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SZT2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SZT2: view

No data available for UniProtKB/Swiss-Prot for SZT2 Gene

Function for SZT2 Gene

Molecular function for SZT2 Gene

UniProtKB/Swiss-Prot Function:
As part of the KICSTOR complex functions in the amino acid-sensing branch of the TORC1 signaling pathway. Recruits, in an amino acid-independent manner, the GATOR1 complex to the lysosomal membranes and allows its interaction with GATOR2 and the RAG GTPases. Functions upstream of the RAG GTPases and is required to negatively regulate mTORC1 signaling in absence of amino acids. In absence of the KICSTOR complex mTORC1 is constitutively localized to the lysosome and activated. The KICSTOR complex is also probably involved in the regulation of mTORC1 by glucose (PubMed:28199306, PubMed:28199315). May play a role in the cellular response to oxidative stress (By similarity).

Phenotypes From GWAS Catalog for SZT2 Gene

Gene Ontology (GO) - Molecular Function for SZT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with SZT2: view
genes like me logo Genes that share phenotypes with SZT2: view

Human Phenotype Ontology for SZT2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SZT2
  • Applied Biological Materials Clones for SZT2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SZT2 Gene

Localization for SZT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SZT2 Gene

Lysosome membrane. Peroxisome. Note=Localization to lysosomes is amino acid-independent. {ECO:0000269 PubMed:28199306, ECO:0000269 PubMed:28199315}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SZT2 gene
Compartment Confidence
extracellular 5
lysosome 5
peroxisome 4
nucleus 4
cytoskeleton 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SZT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA,IDA 28199315
GO:0005777 peroxisome IEA,ISS 20045724
GO:0016020 membrane IEA --
GO:0061700 colocalizes_with GATOR2 complex IDA 28199306
genes like me logo Genes that share ontologies with SZT2: view

Pathways & Interactions for SZT2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SZT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007417 central nervous system development ISS,IEA --
GO:0009791 post-embryonic development ISS,IEA --
GO:0021540 corpus callosum morphogenesis IMP 23932106
GO:0031667 response to nutrient levels IEA --
GO:0034198 cellular response to amino acid starvation IMP 28199306
genes like me logo Genes that share ontologies with SZT2: view

No data available for Pathways by source and SIGNOR curated interactions for SZT2 Gene

Drugs & Compounds for SZT2 Gene

No Compound Related Data Available

Transcripts for SZT2 Gene

Unigene Clusters for SZT2 Gene

Seizure threshold 2 homolog (mouse):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SZT2
  • Applied Biological Materials Clones for SZT2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SZT2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b · 14c ^ 15a · 15b · 15c ^ 16 ^ 17 ^ 18 ^ 19a ·
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: - -
SP7: - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:

ExUns: 19b ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24a · 24b · 24c ^ 25a · 25b ^ 26a · 26b ^ 27a · 27b ^ 28a · 28b ^ 29 ^ 30a · 30b ^ 31a · 31b · 31c ^ 32a ·
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:

ExUns: 32b ^ 33a · 33b ^ 34a · 34b ^ 35 ^ 36 ^ 37
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:

Relevant External Links for SZT2 Gene

GeneLoc Exon Structure for
SZT2
ECgene alternative splicing isoforms for
SZT2

Expression for SZT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SZT2 Gene

Protein differential expression in normal tissues from HIPED for SZT2 Gene

This gene is overexpressed in Blymphocyte (13.1), Peripheral blood mononuclear cells (12.7), Placenta (12.1), Ovary (9.3), Pancreas (6.5), and CD8 Tcells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SZT2 Gene



Protein tissue co-expression partners for SZT2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SZT2 Gene:

SZT2

SOURCE GeneReport for Unigene cluster for SZT2 Gene:

Hs.643560

mRNA Expression by UniProt/SwissProt for SZT2 Gene:

Q5T011-SZT2_HUMAN
Tissue specificity: Expressed in the brain, predominantly in the parietal and frontal cortex, as well as in dorsal root ganglia. Expressed in peripheral white blood cells.

Evidence on tissue expression from TISSUES for SZT2 Gene

  • Nervous system(4.7)
  • Lung(4.2)
  • Spleen(4.2)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SZT2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • forehead
  • head
  • skull
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with SZT2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for SZT2 Gene

Orthologs for SZT2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SZT2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 34
  • 100 (a)
OneToMany
-- 34
  • 93 (a)
OneToMany
dog
(Canis familiaris)
Mammalia SZT2 33 34
  • 89.84 (n)
cow
(Bos Taurus)
Mammalia SZT2 33 34
  • 89.19 (n)
mouse
(Mus musculus)
Mammalia Szt2 33 16 34
  • 87.46 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 85 (a)
OneToMany
-- 34
  • 85 (a)
OneToMany
-- 34
  • 76 (a)
OneToMany
-- 34
  • 66 (a)
OneToMany
-- 34
  • 64 (a)
OneToMany
-- 34
  • 48 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia SZT2 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SZT2 33 34
  • 67.01 (n)
lizard
(Anolis carolinensis)
Reptilia SZT2 34
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia szt2 33
  • 61.59 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC571986 33
  • 60.91 (n)
SZT2 34
  • 55 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F54B3.1 34
  • 16 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
OneToMany
-- 34
  • 33 (a)
OneToMany
Species where no ortholog for SZT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SZT2 Gene

ENSEMBL:
Gene Tree for SZT2 (if available)
TreeFam:
Gene Tree for SZT2 (if available)

Paralogs for SZT2 Gene

No data available for Paralogs for SZT2 Gene

Variants for SZT2 Gene

Sequence variations from dbSNP and Humsavar for SZT2 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
VAR_078574 Epileptic encephalopathy, early infantile, 18 (EIEE18) [MIM:615476]
rs397515489 Pathogenic 43,403,222(+) ATTAT(C/T)GAATC nc-transcript-variant, upstream-variant-2KB, reference, stop-gained
rs397515490 Pathogenic 43,423,153(+) GGGTA(C/T)AAAGC nc-transcript-variant, reference, stop-gained
rs766090540 Pathogenic 43,430,098(+) GCAGG(A/C/T)GAGAA nc-transcript-variant, reference, synonymous-codon, stop-gained
rs886041034 Pathogenic 43,420,983(+) GCAGA(G/T)GTCAG nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SZT2 Gene

Variant ID Type Subtype PubMed ID
esv2400702 CNV deletion 18987734
esv2560782 CNV deletion 19546169
esv2747586 CNV deletion 23290073
esv2747597 CNV deletion 23290073
esv3099 CNV loss 18987735
esv3561382 CNV deletion 23714750
esv5810 CNV loss 19470904
nsv1077802 CNV deletion 25765185
nsv1137755 CNV deletion 24896259
nsv1149353 CNV deletion 26484159
nsv159253 CNV deletion 16902084
nsv438377 CNV loss 16468122
nsv527798 CNV loss 19592680
nsv546128 CNV loss 21841781
nsv950701 CNV deletion 24416366
nsv950702 CNV duplication 24416366
nsv958630 CNV deletion 24416366

Variation tolerance for SZT2 Gene

Residual Variation Intolerance Score: 0.295% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.53; 85.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SZT2 Gene

Human Gene Mutation Database (HGMD)
SZT2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SZT2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SZT2 Gene

Disorders for SZT2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SZT2 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

UniProtKB/Swiss-Prot

SZT2_HUMAN
  • Epileptic encephalopathy, early infantile, 18 (EIEE18) [MIM:615476]: A severe autosomal recessive neurologic disorder characterized by lack of psychomotor development apparent from birth, dysmorphic facial features, early onset of refractory seizures, and thick corpus callosum and persistent cavum septum pellucidum on brain imaging. {ECO:0000269 PubMed:23932106}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SZT2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SZT2
genes like me logo Genes that share disorders with SZT2: view

No data available for Genatlas for SZT2 Gene

Publications for SZT2 Gene

  1. KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1. (PMID: 28199306) Wolfson RL … Sabatini DM (Nature 2017) 2 3 4 60
  2. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PMID: 9455484) Seki N … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4 60
  3. SZT2 dictates GATOR control of mTORC1 signalling. (PMID: 28199315) Peng M … Li MO (Nature 2017) 3 4 60
  4. An amino acid deletion inSZT2 in a family with non-syndromic intellectual disability. (PMID: 24324832) Falcone M … Tekin M (PloS one 2013) 3 4 60
  5. Biallelic SZT2 mutations cause infantile encephalopathy with epilepsy and dysmorphic corpus callosum. (PMID: 23932106) Basel-Vanagaite L … Borck G (American journal of human genetics 2013) 3 4 60

Products for SZT2 Gene

Sources for SZT2 Gene

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