NM_000548.5(TSC2):c.1823GCA[3] (p.Ser609dup) AND Tuberous sclerosis 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 2019
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:: RCV001213061.5

Allele description [Variation Report for NM_000548.5(TSC2):c.1823GCA[3] (p.Ser609dup)]

NM_000548.5(TSC2):c.1823GCA[3] (p.Ser609dup)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.1823GCA[3] (p.Ser609dup)

HGVS:

NC_000016.10:g.2070562GCA[3]
NG_005895.1:g.26257GCA[3]
NM_000548.5:c.1823GCA[3]MANE SELECT
NM_001077183.3:c.1823GCA[3]
NM_001114382.3:c.1823GCA[3]
NM_001318827.2:c.1712GCA[3]
NM_001318829.2:c.1676GCA[3]
NM_001318831.2:c.1223GCA[3]
NM_001318832.2:c.1856GCA[3]
NM_001363528.2:c.1823GCA[3]
NM_001370404.1:c.1823GCA[3]
NM_001370405.1:c.1823GCA[3]
NM_021055.3:c.1823GCA[3]
NP_000539.2:p.Ser609dup
NP_001070651.1:p.Ser609dup
NP_001107854.1:p.Ser609dup
NP_001305756.1:p.Ser572dup
NP_001305758.1:p.Ser560dup
NP_001305760.1:p.Ser409dup
NP_001305761.1:p.Ser620dup
NP_001350457.1:p.Ser609dup
NP_001357333.1:p.Ser609dup
NP_001357334.1:p.Ser609dup
NP_066399.2:p.Ser609dup
LRG_487:g.26257GCA[3]
NC_000016.9:g.2120561_2120562insAGC
NC_000016.9:g.2120563GCA[3]
p.(Ser609dup)

Links:

Tuberous sclerosis database (TSC2): TSC2_00821; dbSNP: rs137854260

NCBI 1000 Genomes Browser:

rs137854260

Molecular consequence:

NM_000548.5:c.1823GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001077183.3:c.1823GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001114382.3:c.1823GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001318827.2:c.1712GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001318829.2:c.1676GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001318831.2:c.1223GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001318832.2:c.1856GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001363528.2:c.1823GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001370404.1:c.1823GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001370405.1:c.1823GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_021055.3:c.1823GCA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Name:: Tuberous sclerosis 2 (TSC2)
Identifiers:: MONDO: MONDO:0013199; MedGen: C1860707; Orphanet: 805; OMIM: 613254

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001384677	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15483652, 21520333, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001384677

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 2019)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

Distinct effects of single amino-acid changes to tuberin on the function of the tuberin-hamartin complex.

Nellist M, Sancak O, Goedbloed MA, Rohe C, van Netten D, Mayer K, Tucker-Williams A, van den Ouweland AM, Halley DJ.

Eur J Hum Genet. 2005 Jan;13(1):59-68.

PubMed [citation]

PMID:: 15483652

LOVD v.2.0: the next generation in gene variant databases.

Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT.

Hum Mutat. 2011 May;32(5):557-63. doi: 10.1002/humu.21438. Epub 2011 Feb 22.

PubMed [citation]

PMID:: 21520333

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001384677.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has been reported to affect TSC2 protein function (PMID: 15483652). This variant has been reported in individual(s) in the Leiden Open-source Variation Database (PMID: 21520333). ClinVar contains an entry for this variant (Variation ID: 49176). This variant is not present in population databases (ExAC no frequency). This variant, c.1826_1828dup, results in the insertion of 1 amino acid(s) to the TSC2 protein (p.Ser609dup), but otherwise preserves the integrity of the reading frame.

#	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: Sep 29, 2024

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