NM_000548.5(TSC2):c.5251C>T (p.Arg1751Cys) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 17, 2023
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:: RCV001023801.11

Allele description [Variation Report for NM_000548.5(TSC2):c.5251C>T (p.Arg1751Cys)]

NM_000548.5(TSC2):c.5251C>T (p.Arg1751Cys)

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.5251C>T (p.Arg1751Cys)

HGVS:

NC_000016.10:g.2088317C>T
NG_005895.1:g.44012C>T
NG_008617.1:g.54904G>A
NM_000548.5:c.5251C>TMANE SELECT
NM_001077183.3:c.5050C>T
NM_001114382.3:c.5182C>T
NM_001318827.2:c.4942C>T
NM_001318829.2:c.4906C>T
NM_001318831.2:c.4519C>T
NM_001318832.2:c.5083C>T
NM_001363528.2:c.5053C>T
NM_001370404.1:c.5119C>T
NM_001370405.1:c.5110C>T
NM_021055.3:c.5122C>T
NP_000539.2:p.Arg1751Cys
NP_001070651.1:p.Arg1684Cys
NP_001107854.1:p.Arg1728Cys
NP_001305756.1:p.Arg1648Cys
NP_001305758.1:p.Arg1636Cys
NP_001305760.1:p.Arg1507Cys
NP_001305761.1:p.Arg1695Cys
NP_001350457.1:p.Arg1685Cys
NP_001357333.1:p.Arg1707Cys
NP_001357334.1:p.Arg1704Cys
NP_066399.2:p.Arg1708Cys
LRG_487t1:c.5251C>T
LRG_487:g.44012C>T
NC_000016.9:g.2138318C>T
NM_000548.3:c.5251C>T
NM_000548.4:c.5251C>T

Protein change:

R1507C

Links:

dbSNP: rs781630603

NCBI 1000 Genomes Browser:

rs781630603

Molecular consequence:

NM_000548.5:c.5251C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.5050C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.5182C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.4942C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.4906C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.4519C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.5083C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.5053C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5119C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5110C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.5122C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001185723	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jan 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001185723

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jan 17, 2023)

germline

clinical testing

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

Citation Link

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

TSC2 rare germline variants in non-tuberous sclerosis patients with neuroendocrine neoplasias.

Asprino PF, Linck RDM, Cesar J, Freitas FP, Koyama FC, Riechelmann RSP, Costa FP, Hoff PMG, Galante PAF, Meyer D, Camargo AA, Sabbaga J.

Endocr Relat Cancer. 2018 Feb;25(2):L1-L5. doi: 10.1530/ERC-17-0286. Epub 2017 Nov 22. No abstract available.

PubMed [citation]

PMID:: 29167182
PMCID:: PMC5763421

Details of each submission

From Ambry Genetics, SCV001185723.5

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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 3, 2024

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