NM_000548.5(TSC2):c.119T>C (p.Ile40Thr) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 2, 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:: RCV000129975.3

Allele description [Variation Report for NM_000548.5(TSC2):c.119T>C (p.Ile40Thr)]

NM_000548.5(TSC2):c.119T>C (p.Ile40Thr)

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.119T>C (p.Ile40Thr)

HGVS:

NC_000016.10:g.2048734T>C
NG_005895.1:g.4429T>C
NG_008412.1:g.4133A>G
NM_000548.5:c.119T>CMANE SELECT
NM_001077183.3:c.119T>C
NM_001114382.3:c.119T>C
NM_001318827.2:c.119T>C
NM_001318829.2:c.-10+669T>C
NM_001318831.2:c.-108T>C
NM_001318832.2:c.152T>C
NM_001363528.2:c.119T>C
NM_001370404.1:c.119T>C
NM_001370405.1:c.119T>C
NM_021055.3:c.119T>C
NP_000539.2:p.Ile40Thr
NP_001070651.1:p.Ile40Thr
NP_001107854.1:p.Ile40Thr
NP_001305756.1:p.Ile40Thr
NP_001305761.1:p.Ile51Thr
NP_001350457.1:p.Ile40Thr
NP_001357333.1:p.Ile40Thr
NP_001357334.1:p.Ile40Thr
NP_066399.2:p.Ile40Thr
LRG_487t1:c.119T>C
LRG_1366:g.4133A>G
LRG_487:g.4429T>C
NC_000016.9:g.2098735T>C
NM_000548.3:c.119T>C
p.I40T

Protein change:

I40T

Links:

dbSNP: rs587781758

NCBI 1000 Genomes Browser:

rs587781758

Molecular consequence:

NM_001318831.2:c.-108T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001318829.2:c.-10+669T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000548.5:c.119T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.119T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.119T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.119T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.152T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.119T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.119T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.119T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.119T>C - 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

Recent activity

Clear Turn Off Turn On

Human DNA sequence from clone RP11-472K17 on chromosome 13, complete sequence
Human DNA sequence from clone RP11-472K17 on chromosome 13, complete sequence
gi|9864606|emb|AL390755.5|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000184799	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 2, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000184799

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 2, 2023)

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, SCV000184799.7

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

Description

The p.I40T variant (also known as c.119T>C), located in coding exon 1 of the TSC2 gene, results from a T to C substitution at nucleotide position 119. The isoleucine at codon 40 is replaced by threonine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. 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

ClinVar

Relating variation to medicine