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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SZT2
SZT2 subunit of KICSTOR complex
Chromosome 1 Β· 1p34.2
NCBI Gene: 23334Ensembl: ENSG00000198198.17HGNC: HGNC:29040UniProt: Q5T011
44PubMed Papers
21Diseases
0Drugs
188Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
GATOR2 complexGATOR1 complexprotein bindingcellular response to amino acid starvationdevelopmental and epileptic encephalopathy, 18genetic developmental and epileptic encephalopathyRolandic epilepsyself-limited epilepsy with centrotemporal spikes
✦AI Summary

SZT2 is a scaffolding protein and core component of the KICSTOR complex, which functions as a critical negative regulator of mTORC1 signaling in response to amino acid and glucose availability 1. SZT2 localizes to lysosomal membranes where it recruits and positions the GATOR1 complex, facilitating GATOR1's interaction with RAG GTPases and GATOR2 12. The crescent-shaped SZT2 scaffold contains repetitive tandem units that bind other KICSTOR components; its N-terminal domain specifically interacts with GATOR1 through NPRL3 2. Loss of SZT2 results in constitutive mTORC1 localization and activation to lysosomes, even during nutrient deprivation 1. Beyond mTORC1 regulation, SZT2 interacts with autophagy and ciliogenesis-related proteins, suggesting broader cellular functions 3. Biallelic SZT2 mutations cause Developmental and Epileptic Encephalopathy 18 (DEE18), characterized by early-onset seizures (90% of cases), global developmental delay (95%), macrocephaly, craniofacial malformations, and corpus callosum abnormalities 45. Disease severity correlates with residual SZT2 protein activity, with truncating variants causing more severe phenotypes 5. mTORC1 hyperactivation from defective SZT2-GATOR1 positioning represents the primary pathogenic mechanism 6.

Sources cited
1
SZT2 is a KICSTOR component that recruits GATOR1 to lysosomes and is required for amino acid/glucose deprivation to inhibit mTORC1; SZT2 mutations increase mTORC1 signaling in tissues including brain neurons
PMID: 28199306
2
SZT2 forms a crescent-shaped scaffold with repetitive tandem units; its N-terminal domain binds GATOR1 through NPRL3; disruption hyperactivates mTORC1; SZT2 and C12orf66 interact with negatively charged lipids for lysosomal localization
PMID: 41198956
3
SZT2-related disease is a severe autosomal recessive DEE with clinical phenotypes including global developmental delay (95%), seizures (90%), craniofacial deformity (67.5%), corpus callosum malformation (45%), and hypotonia (55%)
PMID: 38134649
4
Biallelic SZT2 variants cause DEE18; protein-truncating variants cause severe developmental delay and refractory epilepsy; phenotypic severity relates to residual SZT2 protein activity
PMID: 35352205
5
SZT2 interactome analysis identified clusters related to autophagy, ciliogenesis, neurogenesis, and neurodegenerative processes; SZT2-ablated cells show increased mTORC1 activation reversible by rapamycin and elevated autophagic components
PMID: 34685691
6
SZT2 loss-of-function variants cause early-onset seizures (median 24 months), focal seizures, developmental delay, and macrocephaly; a recurrent in-frame deletion (p.Val1984del) is a founder variant in Ashkenazi Jewish populations
PMID: 35773235
Disease Associationsβ“˜21
developmental and epileptic encephalopathy, 18Open Targets
0.78Strong
genetic developmental and epileptic encephalopathyOpen Targets
0.67Moderate
Rolandic epilepsyOpen Targets
0.53Moderate
self-limited epilepsy with centrotemporal spikesOpen Targets
0.53Moderate
genetic disorderOpen Targets
0.53Moderate
Early infantile epileptic encephalopathy without suppression burstOpen Targets
0.46Moderate
developmental and epileptic encephalopathyOpen Targets
0.41Moderate
undetermined early-onset epileptic encephalopathyOpen Targets
0.38Weak
developmental disabilityOpen Targets
0.37Weak
non-syndromic intellectual disabilityOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.33Weak
SeizureOpen Targets
0.30Weak
hereditary spherocytosisOpen Targets
0.27Weak
hereditary spherocytosis type 3Open Targets
0.27Weak
hypertensionOpen Targets
0.23Weak
response to xenobiotic stimulusOpen Targets
0.17Weak
EncephaloceleOpen Targets
0.15Weak
Severe hydrocephalusOpen Targets
0.15Weak
infantile spasmsOpen Targets
0.13Weak
Global developmental delayOpen Targets
0.12Weak
Developmental and epileptic encephalopathy 18UniProt
Pathogenic Variants188
NM_001365999.1(SZT2):c.6724C>T (p.Arg2242Trp)Likely pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2026β†’ Residue 2242
NM_001365999.1(SZT2):c.8811dup (p.Ser2938fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 2938
NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18|SZT2-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 2041
NM_001365999.1(SZT2):c.5872C>T (p.Arg1958Ter)Pathogenic
not provided|Inborn genetic diseases|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2025β†’ Residue 1958
NM_001365999.1(SZT2):c.8659C>T (p.Arg2887Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2025β†’ Residue 2887
NM_001365999.1(SZT2):c.3640C>T (p.Arg1214Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2025β†’ Residue 1214
NM_001365999.1(SZT2):c.9286+1G>ALikely pathogenic
not provided
β˜…β˜…β˜†β˜†2025
NM_001365999.1(SZT2):c.4141C>T (p.Arg1381Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1381
NM_001365999.1(SZT2):c.2363C>G (p.Ser788Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2025β†’ Residue 788
NM_001365999.1(SZT2):c.4396C>T (p.Arg1466Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2025β†’ Residue 1466
NM_001365999.1(SZT2):c.3787C>T (p.Arg1263Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1263
NM_001365999.1(SZT2):c.203G>A (p.Trp68Ter)Pathogenic
Developmental and epileptic encephalopathy, 18|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 68
NM_001365999.1(SZT2):c.9040C>T (p.Arg3014Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2024β†’ Residue 3014
NM_001365999.1(SZT2):c.5905C>T (p.Arg1969Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2024β†’ Residue 1969
NM_001365999.1(SZT2):c.8062C>T (p.Arg2688Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 2688
NM_001365999.1(SZT2):c.2476C>T (p.Arg826Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 826
NM_001365999.1(SZT2):c.8811del (p.Ser2938fs)Pathogenic
not provided|Developmental and epileptic encephalopathy, 18|Inborn genetic diseases
β˜…β˜…β˜†β˜†2023β†’ Residue 2938
NM_001365999.1(SZT2):c.7488dup (p.Asp2497fs)Pathogenic
Developmental and epileptic encephalopathy, 18|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 2497
NM_001365999.1(SZT2):c.1091-1G>ALikely pathogenic
not provided|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2023
NM_001365999.1(SZT2):c.6139C>T (p.Arg2047Ter)Pathogenic
not provided|SZT2-related disorder|Developmental and epileptic encephalopathy, 18
β˜…β˜…β˜†β˜†2023β†’ Residue 2047
View on ClinVar β†—
Related Genes
LAMP1Protein interaction100%RRAGBProtein interaction100%SAMTORProtein interaction100%WDR24Protein interaction100%MIOSProtein interaction83%SEH1LProtein interaction81%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
98%
Lung
81%
Liver
69%
Heart
55%
Brain
35%
Gene Interaction Network
Click a node to explore
SZT2LAMP1RRAGBSAMTORWDR24MIOSSEH1L
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q5T011
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.58Moderately Constrained
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.52 [0.46–0.58]
RankingsWhere SZT2 stands among ~20K protein-coding genes
  • #9,661of 20,598
    Most Researched44
  • #374of 5,498
    Most Pathogenic Variants188 Β· top 10%
  • #3,904of 17,882
    Most Constrained (LOEUF)0.58 Β· top quartile
Genes detectedSZT2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Clinical phenotype and genetic characteristics of SZT2 related diseases: A case report and literature review.
PMID: 38134649
Seizure Β· 2024
1.00
2
KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1.
PMID: 28199306
Nature Β· 2017
0.90
3
Genetic analysis of developmental and epileptic encephalopathy caused by novel biallelic SZT2 gene mutations in three Chinese Han infants: a case series and literature review.
PMID: 35352205
Neurol Sci Β· 2022
0.80
4
A novel homozygous mutation in SZT2 gene in Saudi family with developmental delay, macrocephaly and epilepsy.
PMID: 30315519
Genes Genomics Β· 2018
0.70
5
mTORC1 functional assay reveals SZT2 loss-of-function variants and a founder in-frame deletion.
PMID: 35773235
Brain Β· 2022
0.60