NM_000548.5(TSC2):c.122C>T (p.Thr41Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 12, 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:: RCV002368143.2

Allele description [Variation Report for NM_000548.5(TSC2):c.122C>T (p.Thr41Ile)]

NM_000548.5(TSC2):c.122C>T (p.Thr41Ile)

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.122C>T (p.Thr41Ile)

HGVS:

NC_000016.10:g.2048737C>T
NG_005895.1:g.4432C>T
NG_008412.1:g.4130G>A
NM_000548.5:c.122C>TMANE SELECT
NM_001077183.3:c.122C>T
NM_001114382.3:c.122C>T
NM_001318827.2:c.122C>T
NM_001318829.2:c.-10+672C>T
NM_001318831.2:c.-105C>T
NM_001318832.2:c.155C>T
NM_001363528.2:c.122C>T
NM_001370404.1:c.122C>T
NM_001370405.1:c.122C>T
NM_021055.3:c.122C>T
NP_000539.2:p.Thr41Ile
NP_001070651.1:p.Thr41Ile
NP_001107854.1:p.Thr41Ile
NP_001305756.1:p.Thr41Ile
NP_001305761.1:p.Thr52Ile
NP_001350457.1:p.Thr41Ile
NP_001357333.1:p.Thr41Ile
NP_001357334.1:p.Thr41Ile
NP_066399.2:p.Thr41Ile
LRG_487t1:c.122C>T
LRG_1366:g.4130G>A
LRG_487:g.4432C>T
NC_000016.9:g.2098738C>T
NM_000548.3:c.122C>T

Protein change:

T41I

Links:

dbSNP: rs1385450866

NCBI 1000 Genomes Browser:

rs1385450866

Molecular consequence:

NM_001318831.2:c.-105C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001318829.2:c.-10+672C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000548.5:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.155C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.122C>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
SCV002664638	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 12, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002664638

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 12, 2022)

germline

clinical testing

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

Details of each submission

From Ambry Genetics, SCV002664638.2

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

Description

The p.T41I variant (also known as c.122C>T), located in coding exon 1 of the TSC2 gene, results from a C to T substitution at nucleotide position 122. The threonine at codon 41 is replaced by isoleucine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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