NM_000548.5(TSC2):c.4613C>T (p.Pro1538Leu) AND Tuberous sclerosis 2

Germline classification:: Benign (1 submission)
Last evaluated:: Aug 22, 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:: RCV001341252.7

Allele description [Variation Report for NM_000548.5(TSC2):c.4613C>T (p.Pro1538Leu)]

NM_000548.5(TSC2):c.4613C>T (p.Pro1538Leu)

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.4613C>T (p.Pro1538Leu)

HGVS:

NC_000016.10:g.2085273C>T
NG_005895.1:g.40968C>T
NM_000548.5:c.4613C>TMANE SELECT
NM_001077183.3:c.4412C>T
NM_001114382.3:c.4544C>T
NM_001318827.2:c.4304C>T
NM_001318829.2:c.4268C>T
NM_001318831.2:c.3881C>T
NM_001318832.2:c.4445C>T
NM_001363528.2:c.4415C>T
NM_001370404.1:c.4481C>T
NM_001370405.1:c.4484C>T
NM_021055.3:c.4484C>T
NP_000539.2:p.Pro1538Leu
NP_001070651.1:p.Pro1471Leu
NP_001107854.1:p.Pro1515Leu
NP_001305756.1:p.Pro1435Leu
NP_001305758.1:p.Pro1423Leu
NP_001305760.1:p.Pro1294Leu
NP_001305761.1:p.Pro1482Leu
NP_001350457.1:p.Pro1472Leu
NP_001357333.1:p.Pro1494Leu
NP_001357334.1:p.Pro1495Leu
NP_066399.2:p.Pro1495Leu
LRG_487t1:c.4613C>T
LRG_487:g.40968C>T
NC_000016.9:g.2135274C>T
NM_000548.3:c.4613C>T

Protein change:

P1294L

Links:

dbSNP: rs753060862

NCBI 1000 Genomes Browser:

rs753060862

Molecular consequence:

NM_000548.5:c.4613C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.4412C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.4544C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.4304C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.4268C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.3881C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.4445C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.4415C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.4481C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.4484C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.4484C>T - 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
SCV001535112	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Aug 22, 2022)	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

SCV001535112

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Aug 22, 2022)

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, SCV001535112.4

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

#	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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