NM_000548.5(TSC2):c.2653A>G (p.Ile885Val) AND Tuberous sclerosis 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 1, 2024
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:: RCV000644070.10

Allele description [Variation Report for NM_000548.5(TSC2):c.2653A>G (p.Ile885Val)]

NM_000548.5(TSC2):c.2653A>G (p.Ile885Val)

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.2653A>G (p.Ile885Val)

HGVS:

NC_000016.10:g.2076081A>G
NG_005895.1:g.31776A>G
NM_000548.5:c.2653A>GMANE SELECT
NM_001077183.3:c.2653A>G
NM_001114382.3:c.2653A>G
NM_001318827.2:c.2542A>G
NM_001318829.2:c.2506A>G
NM_001318831.2:c.2053A>G
NM_001318832.2:c.2686A>G
NM_001363528.2:c.2653A>G
NM_001370404.1:c.2653A>G
NM_001370405.1:c.2653A>G
NM_021055.3:c.2653A>G
NP_000539.2:p.Ile885Val
NP_001070651.1:p.Ile885Val
NP_001107854.1:p.Ile885Val
NP_001305756.1:p.Ile848Val
NP_001305758.1:p.Ile836Val
NP_001305760.1:p.Ile685Val
NP_001305761.1:p.Ile896Val
NP_001350457.1:p.Ile885Val
NP_001357333.1:p.Ile885Val
NP_001357334.1:p.Ile885Val
NP_066399.2:p.Ile885Val
LRG_487t1:c.2653A>G
LRG_487:g.31776A>G
NC_000016.9:g.2126082A>G
NM_000548.3:c.2653A>G

Protein change:

I685V

Links:

dbSNP: rs1555508581

NCBI 1000 Genomes Browser:

rs1555508581

Molecular consequence:

NM_000548.5:c.2653A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.2653A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.2653A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.2542A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.2506A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.2053A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.2686A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.2653A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.2653A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.2653A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.2653A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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PREDICTED: Homo sapiens ankyrin repeat domain 52 (ANKRD52), transcript variant X...
PREDICTED: Homo sapiens ankyrin repeat domain 52 (ANKRD52), transcript variant X1, mRNA
gi|2217288615|ref|XM_017019183.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000765760	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 1, 2024)	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

SCV000765760

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 1, 2024)

germline

clinical testing

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

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000765760.7

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

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 885 of the TSC2 protein (p.Ile885Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. ClinVar contains an entry for this variant (Variation ID: 535859). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TSC2 protein function with a negative predictive value of 95%. 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: Sep 29, 2024

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