NM_000548.5(TSC2):c.5220G>A (p.Trp1740Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 25, 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:: RCV000493371.1

Allele description [Variation Report for NM_000548.5(TSC2):c.5220G>A (p.Trp1740Ter)]

NM_000548.5(TSC2):c.5220G>A (p.Trp1740Ter)

Gene:

TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.5220G>A (p.Trp1740Ter)

HGVS:

NC_000016.10:g.2088286G>A
NG_005895.1:g.43981G>A
NG_008617.1:g.54935C>T
NM_000548.5:c.5220G>AMANE SELECT
NM_001077183.3:c.5019G>A
NM_001114382.3:c.5151G>A
NM_001318827.2:c.4911G>A
NM_001318829.2:c.4875G>A
NM_001318831.2:c.4488G>A
NM_001318832.2:c.5052G>A
NM_001363528.2:c.5022G>A
NM_001370404.1:c.5088G>A
NM_001370405.1:c.5079G>A
NM_021055.3:c.5091G>A
NP_000539.2:p.Trp1740Ter
NP_001070651.1:p.Trp1673Ter
NP_001107854.1:p.Trp1717Ter
NP_001305756.1:p.Trp1637Ter
NP_001305758.1:p.Trp1625Ter
NP_001305760.1:p.Trp1496Ter
NP_001305761.1:p.Trp1684Ter
NP_001350457.1:p.Trp1674Ter
NP_001357333.1:p.Trp1696Ter
NP_001357334.1:p.Trp1693Ter
NP_066399.2:p.Trp1697Ter
LRG_487t1:c.5220G>A
LRG_487:g.43981G>A
NC_000016.9:g.2138287G>A
NM_000548.3:c.5220G>A
p.(Trp1740*)

Protein change:

W1496*

Links:

Tuberous sclerosis database (TSC2): TSC2_00299; dbSNP: rs45517411

NCBI 1000 Genomes Browser:

rs45517411

Molecular consequence:

NM_000548.5:c.5220G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001077183.3:c.5019G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001114382.3:c.5151G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318827.2:c.4911G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318829.2:c.4875G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318831.2:c.4488G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318832.2:c.5052G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001363528.2:c.5022G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370404.1:c.5088G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370405.1:c.5079G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_021055.3:c.5091G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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cytochrome c oxidase subunit I, partial (mitochondrion) [Xerocrassa rhithymna]
cytochrome c oxidase subunit I, partial (mitochondrion) [Xerocrassa rhithymna]
gi|258517643|gb|ACV73311.1|

Protein
COX2 [Dogania subplana]
COX2 [Dogania subplana]
Gene ID:803313

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000583283	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (May 25, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000583283

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(May 25, 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, SCV000583283.4

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

Description

The W1740X nonsense variant in the TSC2 gene has been reported previously as a de novo change in an individual with TSC (Roberts et al., 2002; TSC2 LOVD). This pathogenic variant is predicted to cause loss of normal protein function through protein truncation as the last 68 amino acids of the TSC2 protein are lost. The W1740X variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server).

#	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: Sep 29, 2024

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