NM_000548.5(TSC2):c.5197_5202delinsGAC (p.Thr1733del) AND Tuberous sclerosis 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 12, 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:: RCV000467027.3

Allele description [Variation Report for NM_000548.5(TSC2):c.5197_5202delinsGAC (p.Thr1733del)]

NM_000548.5(TSC2):c.5197_5202delinsGAC (p.Thr1733del)

Gene:

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

Variant type:

Indel

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.5197_5202delinsGAC (p.Thr1733del)

HGVS:

NC_000016.10:g.2088263_2088268delinsGAC
NG_005895.1:g.43958_43963delinsGAC
NG_008617.1:g.54953_54958delinsGTC
NM_000548.5:c.5197_5202delinsGACMANE SELECT
NM_001077183.3:c.4996_5001delinsGAC
NM_001114382.3:c.5128_5133delinsGAC
NM_001318827.2:c.4888_4893delinsGAC
NM_001318829.2:c.4852_4857delinsGAC
NM_001318831.2:c.4465_4470delinsGAC
NM_001318832.2:c.5029_5034delinsGAC
NM_001363528.2:c.4999_5004delinsGAC
NM_001370404.1:c.5065_5070delinsGAC
NM_001370405.1:c.5056_5061delinsGAC
NM_021055.3:c.5068_5073delinsGAC
NP_000539.2:p.Thr1733del
NP_001070651.1:p.Thr1666del
NP_001107854.1:p.Thr1710del
NP_001305756.1:p.Thr1630del
NP_001305758.1:p.Thr1618del
NP_001305760.1:p.Thr1489del
NP_001305761.1:p.Thr1677del
NP_001350457.1:p.Thr1667del
NP_001357333.1:p.Thr1689del
NP_001357334.1:p.Thr1686del
NP_066399.2:p.Thr1690del
LRG_487t1:c.5197_5202delinsGAC
LRG_487:g.43958_43963delinsGAC
NC_000016.9:g.2138264_2138269delinsGAC
NM_000548.3:c.5197_5202delinsGAC

Protein change:

T1489del

Links:

dbSNP: rs1064792922

NCBI 1000 Genomes Browser:

rs1064792922

Molecular consequence:

NM_000548.5:c.5197_5202delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001077183.3:c.4996_5001delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001114382.3:c.5128_5133delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318827.2:c.4888_4893delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318829.2:c.4852_4857delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318831.2:c.4465_4470delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318832.2:c.5029_5034delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001363528.2:c.4999_5004delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370404.1:c.5065_5070delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370405.1:c.5056_5061delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_021055.3:c.5068_5073delinsGAC - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

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

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gi|262070325|gb|GU063562.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000544310	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 12, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000544310

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 12, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000544310.4

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

Description

This variant, c.5197_5199delACC, results in the deletion of 1 amino acid of the TSC2 protein (p.Thr1733del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with TSC2-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. 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.

#	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: Nov 5, 2022

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