NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del) AND SZT2-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 14, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004748750.1

Allele description [Variation Report for NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)]

NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)

Gene:

SZT2:SZT2 subunit of KICSTOR complex [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_001365999.1(SZT2):c.6120_6122del (p.Val2041del)

HGVS:

NC_000001.11:g.43437256_43437258del
NG_029091.1:g.52372_52374del
NM_001365999.1:c.6120_6122delMANE SELECT
NM_015284.4:c.5949_5951del
NP_001352928.1:p.Val2041del
NP_056099.3:p.Val1984del
NC_000001.10:g.43902925_43902927del
NC_000001.10:g.43902927_43902929del
NM_015284.3:c.5949_5951del
NM_015284.3:c.5949_5951delTGT
p.Val1984del

Protein change:

V1984del

Links:

dbSNP: rs746200792

NCBI 1000 Genomes Browser:

rs746200792

Molecular consequence:

NM_001365999.1:c.6120_6122del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_015284.4:c.5949_5951del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: SZT2-related disorder
Synonyms:: SZT2-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005367074	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Likely pathogenic (May 14, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005367074

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Likely pathogenic
(May 14, 2024)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005367074.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The SZT2 c.5949_5951delTGT variant is predicted to result in an in-frame deletion (p.Val1984del). This variant has been reported in the compound heterozygous state and homozygous state in at least four individuals with epileptic encephalopathy (Uittenbogaard et al. 2018. PubMed ID: 30564332; Calhoun et al. 2022. PubMed ID: 35773235). In vitro studies suggest that this variant alters protein function (Uittenbogaard et al. 2018. PubMed ID: 30564332). This variant is reported in 0.087% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Taken together, this variant is interpreted as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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