NM_000548.5(TSC2):c.5341C>G (p.Pro1781Ala) AND Tuberous sclerosis 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 4, 2020
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:: RCV000644075.9

Allele description [Variation Report for NM_000548.5(TSC2):c.5341C>G (p.Pro1781Ala)]

NM_000548.5(TSC2):c.5341C>G (p.Pro1781Ala)

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.5341C>G (p.Pro1781Ala)

HGVS:

NC_000016.10:g.2088527C>G
NG_005895.1:g.44222C>G
NG_008617.1:g.54694G>C
NM_000548.5:c.5341C>GMANE SELECT
NM_001077183.3:c.5140C>G
NM_001114382.3:c.5272C>G
NM_001318827.2:c.5032C>G
NM_001318829.2:c.4996C>G
NM_001318831.2:c.4609C>G
NM_001318832.2:c.5173C>G
NM_001363528.2:c.5143C>G
NM_001370404.1:c.5209C>G
NM_001370405.1:c.5200C>G
NM_021055.3:c.5212C>G
NP_000539.2:p.Pro1781Ala
NP_001070651.1:p.Pro1714Ala
NP_001107854.1:p.Pro1758Ala
NP_001305756.1:p.Pro1678Ala
NP_001305758.1:p.Pro1666Ala
NP_001305760.1:p.Pro1537Ala
NP_001305761.1:p.Pro1725Ala
NP_001350457.1:p.Pro1715Ala
NP_001357333.1:p.Pro1737Ala
NP_001357334.1:p.Pro1734Ala
NP_066399.2:p.Pro1738Ala
LRG_487t1:c.5341C>G
LRG_487:g.44222C>G
NC_000016.9:g.2138528C>G
NM_000548.3:c.5341C>G

Protein change:

P1537A

Links:

dbSNP: rs1555441410

NCBI 1000 Genomes Browser:

rs1555441410

Molecular consequence:

NM_000548.5:c.5341C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.5140C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.5272C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.5032C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.4996C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.4609C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.5173C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.5143C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5209C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5200C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.5212C>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000765765	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 4, 2020)	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

SCV000765765

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 4, 2020)

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, SCV000765765.6

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

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with TSC2-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with alanine at codon 1781 of the TSC2 protein (p.Pro1781Ala). The proline residue is moderately conserved and there is a small physicochemical difference between proline and alanine.

#	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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