NM_001365999.1(SZT2):c.4972T>A (p.Leu1658Ile) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 27, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002316781.9

Allele description [Variation Report for NM_001365999.1(SZT2):c.4972T>A (p.Leu1658Ile)]

NM_001365999.1(SZT2):c.4972T>A (p.Leu1658Ile)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_001365999.1(SZT2):c.4972T>A (p.Leu1658Ile)

HGVS:

NC_000001.11:g.43431320T>A
NG_029091.1:g.46436T>A
NM_001365999.1:c.4972T>AMANE SELECT
NM_015284.4:c.4801T>A
NP_001352928.1:p.Leu1658Ile
NP_056099.3:p.Leu1601Ile
NC_000001.10:g.43896991T>A
NM_015284.3:c.4801T>A

Protein change:

L1601I

Links:

dbSNP: rs745970630

NCBI 1000 Genomes Browser:

rs745970630

Molecular consequence:

NM_001365999.1:c.4972T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015284.4:c.4801T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000850510	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 27, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000850510

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 27, 2017)

germline

clinical testing

Citation Link

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 Ambry Genetics, SCV000850510.4

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

Description

The p.L1601I variant (also known as c.4801T>A), located in coding exon 33 of the SZT2 gene, results from a T to A substitution at nucleotide position 4801. The leucine at codon 1601 is replaced by isoleucine, an amino acid with highly similar properties. This amino acid position is conserved through mammals but not in all available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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