SZT2 SZT2 subunit of KICSTOR complex [Homo sapiens (human)] - Gene

Summary

Official Symbol: SZT2provided by HGNC
Official Full Name: SZT2 subunit of KICSTOR complexprovided by HGNC
Primary source: HGNC:HGNC:29040
See related: Ensembl:ENSG00000198198 MIM:615463; AllianceGenome:HGNC:29040
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DEE18; KICS1; SZT2A; SZT2B; EIEE18; C1orf84; KIAA0467
Summary: 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]
Expression: Ubiquitous expression in ovary (RPKM 6.6), testis (RPKM 6.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p34.2

Exon count:: 72

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (43389899..43454247)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (43260449..43324500)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (43855570..43919918)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical phenotype and genetic characteristics of SZT2 related diseases: A case report and literature review.
Title: Clinical phenotype and genetic characteristics of SZT2 related diseases: A case report and literature review.
Induced Pluripotent Stem Cell (iPSC) Lines from a Family with Resistant Epileptic Encephalopathy Caused by Compound Heterozygous Mutations in SZT2 Gene.
Title: Induced Pluripotent Stem Cell (iPSC) Lines from a Family with Resistant Epileptic Encephalopathy Caused by Compound Heterozygous Mutations in SZT2 Gene.
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.
Title: 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.
The SZT2 Interactome Unravels New Functions of the KICSTOR Complex.
Title: The SZT2 Interactome Unravels New Functions of the KICSTOR Complex.
A novel possible familial cause of epilepsy of infancy with migrating focal seizures related to SZT2 gene variant.
Title: A novel possible familial cause of epilepsy of infancy with migrating focal seizures related to SZT2 gene variant.
Developmental and epileptic encephalopathy due to SZT2 genomic variants: Emerging features of a syndromic condition.
Title: Developmental and epileptic encephalopathy due to SZT2 genomic variants: Emerging features of a syndromic condition.
results expand the genotype and phenotypes of SZT2-related DEEs, suggesting that SZT2 mutations play a role in developmental delay and epileptic encephalopathy, with high susceptibility to SE and relatively specific MRI findings.
Title: Novel SZT2 mutations in three patients with developmental and epileptic encephalopathies.
The loss-of-function nature of SZT2 mutations in the patients, and consequent hyperactivation of mTORC1 signaling in response to both amino acid starvation and stimulation in their lymphoblastoid cell lines, is reported.
Title: Constitutive activation of mTORC1 signaling induced by biallelic loss-of-function mutations in SZT2 underlies a discernible neurodevelopmental disease.
in the third case, born to consanguineous parents, had unexpected compound heterozygous missense mutations. She showed microcephaly despite the other case and previous ones presenting with macrocephaly, suggesting that SZT2 mutations might affect head size.
Title: Novel biallelic SZT2 mutations in 3 cases of early-onset epileptic encephalopathy.
SZT2 heterozygote mutation results in early-onset epileptic encephalopathy and leukoencephalopathy.
Title: Mutations in SZT2 result in early-onset epileptic encephalopathy and leukoencephalopathy.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Developmental and epileptic encephalopathy, 18 MedGen: C3809624 OMIM: 615476 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80143 (e-PCR)
- UniSTS:91161

RH101946 (e-PCR)
- UniSTS:96281

Tbxas1 (e-PCR), detects polymorphism
- UniSTS:265585

G35510 (e-PCR)
- UniSTS:44150

G44325 (e-PCR)
- UniSTS:95114

RH103424 (e-PCR)
- UniSTS:97749

Clone Names

FLJ00408, FLJ10387, FLJ23425, FLJ34502, KIAA0467

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to amino acid starvation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to glucose starvation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in central nervous system development	ISS Inferred from Sequence or Structural Similarity more info
involved_in corpus callosum morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of TORC1 signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pigmentation	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to lysosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of superoxide dismutase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
part_of GATOR1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of GATOR2 complex	IDA Inferred from Direct Assay more info	PubMed
part_of KICSTOR complex	IDA Inferred from Direct Assay more info	PubMed
part_of KICSTOR complex	NAS Non-traceable Author Statement more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	NAS Non-traceable Author Statement more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
is_active_in peroxisome	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisome	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: KICSTOR complex protein SZT2

Names: SZT2 subunit KICSTOR complex; SZT2, KICSTOR complex subunit; seizure threshold 2 protein homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029091.1 RefSeqGene

Range

5015..69363

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001365999.1 → NP_001352928.1 KICSTOR complex protein SZT2 isoform 1

Status: REVIEWED

Source sequence(s)

AL139289, AL583862

Consensus CDS

CCDS90935.1

UniProtKB/Swiss-Prot

A0PJK5, A7E2X4, O75055, Q5JUY7, Q5T011, Q5T012, Q5XKC7, Q6ZNI8, Q6ZT24, Q7Z636, Q8NAY9, Q9H5H7, Q9UFQ8

Related

ENSP00000489255.1, ENST00000634258.3
NM_015284.4 → NP_056099.3 KICSTOR complex protein SZT2 isoform 2

Status: REVIEWED

Source sequence(s)

AB007936, AK131107, AL139289, AL583862, BC051343, BF826848, BU633294, BX423490, DY655545

Consensus CDS

CCDS30694.2

UniProtKB/Swiss-Prot

Q5T011

Related

ENSP00000457168.1, ENST00000562955.2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

43389899..43454247

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

43260449..43324500

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001012960.1: Suppressed sequence

Description

NM_001012960.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein, and it is a nonsense-mediated mRNA decay (NMD) candidate.
NM_001012961.1: Suppressed sequence

Description

NM_001012961.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
NM_182518.2: Suppressed sequence

Description

NM_182518.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein, and it is a nonsense-mediated mRNA decay (NMD) candidate.