NM_006516.4(SLC2A1):c.398_399delinsTT (p.Cys133Phe) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 1, 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:: RCV000519895.1

Allele description [Variation Report for NM_006516.4(SLC2A1):c.398_399delinsTT (p.Cys133Phe)]

NM_006516.4(SLC2A1):c.398_399delinsTT (p.Cys133Phe)

Gene:

SLC2A1:solute carrier family 2 member 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_006516.4(SLC2A1):c.398_399delinsTT (p.Cys133Phe)

HGVS:

NC_000001.11:g.42930743_42930744delinsAA
NG_008232.1:g.33433_33434delinsTT
NM_006516.4:c.398_399delinsTTMANE SELECT
NP_006507.2:p.Cys133Phe
LRG_1132:g.33433_33434delinsTT
NC_000001.10:g.43396414_43396415delinsAA
NM_006516.2:c.398_399delGCinsTT

Protein change:

C133F

Links:

dbSNP: rs1553156161

NCBI 1000 Genomes Browser:

rs1553156161

Molecular consequence:

NM_006516.4:c.398_399delinsTT - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000619866	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Aug 1, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000619866

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Aug 1, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000619866.1

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

Description

The c.398_399delGCinsTT variant in the SLC2A1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant results in the replacement of a Cysteine residue with a Phenylalanine residue, denoted Cys133Phe. The c.398_399delGCinsTT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position that is not conserved. However, this variant results in 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, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret c.398_399delGCinsTT as a likely pathogenic variant.

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

Last Updated: Apr 23, 2022

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