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NM_001365999.1(SZT2):c.184A>G (p.Ser62Gly) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 19, 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:
RCV000523881.1

Allele description [Variation Report for NM_001365999.1(SZT2):c.184A>G (p.Ser62Gly)]

NM_001365999.1(SZT2):c.184A>G (p.Ser62Gly)

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.184A>G (p.Ser62Gly)
HGVS:
  • NC_000001.11:g.43403631A>G
  • NG_029091.1:g.18747A>G
  • NM_001365999.1:c.184A>GMANE SELECT
  • NM_015284.4:c.184A>G
  • NP_001352928.1:p.Ser62Gly
  • NP_056099.3:p.Ser62Gly
  • NC_000001.10:g.43869302A>G
  • NM_015284.3:c.184A>G
Protein change:
S62G
Links:
dbSNP: rs1553138470
NCBI 1000 Genomes Browser:
rs1553138470
Molecular consequence:
  • NM_001365999.1:c.184A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015284.4:c.184A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000619270GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jul 19, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000619270.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The S62G variant in the SZT2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The S62G variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S62G variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret S62G as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022