NM_000548.5(TSC2):c.2647C>T (p.Gln883Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 15, 2022
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:: RCV002255124.2

Allele description [Variation Report for NM_000548.5(TSC2):c.2647C>T (p.Gln883Ter)]

NM_000548.5(TSC2):c.2647C>T (p.Gln883Ter)

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.2647C>T (p.Gln883Ter)

HGVS:

NC_000016.10:g.2076075C>T
NG_005895.1:g.31770C>T
NM_000548.5:c.2647C>TMANE SELECT
NM_001077183.3:c.2647C>T
NM_001114382.3:c.2647C>T
NM_001318827.2:c.2536C>T
NM_001318829.2:c.2500C>T
NM_001318831.2:c.2047C>T
NM_001318832.2:c.2680C>T
NM_001363528.2:c.2647C>T
NM_001370404.1:c.2647C>T
NM_001370405.1:c.2647C>T
NM_021055.3:c.2647C>T
NP_000539.2:p.Gln883Ter
NP_001070651.1:p.Gln883Ter
NP_001107854.1:p.Gln883Ter
NP_001305756.1:p.Gln846Ter
NP_001305758.1:p.Gln834Ter
NP_001305760.1:p.Gln683Ter
NP_001305761.1:p.Gln894Ter
NP_001350457.1:p.Gln883Ter
NP_001357333.1:p.Gln883Ter
NP_001357334.1:p.Gln883Ter
NP_066399.2:p.Gln883Ter
LRG_487t1:c.2647C>T
LRG_487:g.31770C>T
NC_000016.9:g.2126076C>T
NM_000548.3:c.2647C>T
NM_000548.4:c.2647C>T
p.(Gln883*)

Protein change:

Q683*

Links:

Tuberous sclerosis database (TSC2): TSC2_00913; dbSNP: rs45476100

NCBI 1000 Genomes Browser:

rs45476100

Molecular consequence:

NM_000548.5:c.2647C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001077183.3:c.2647C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001114382.3:c.2647C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318827.2:c.2536C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318829.2:c.2500C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318831.2:c.2047C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318832.2:c.2680C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001363528.2:c.2647C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370404.1:c.2647C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370405.1:c.2647C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_021055.3:c.2647C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002526567	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 15, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002526567

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jun 15, 2022)

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, SCV002526567.2

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 24271014, 31160751, 32017698, 26540169)

#	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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