NM_000548.5(TSC2):c.5199C>A (p.Thr1733=) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 18, 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:: RCV004022584.1

Allele description [Variation Report for NM_000548.5(TSC2):c.5199C>A (p.Thr1733=)]

NM_000548.5(TSC2):c.5199C>A (p.Thr1733=)

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.5199C>A (p.Thr1733=)

HGVS:

NC_000016.10:g.2088265C>A
NG_005895.1:g.43960C>A
NG_008617.1:g.54956G>T
NM_000548.5:c.5199C>AMANE SELECT
NM_001077183.3:c.4998C>A
NM_001114382.3:c.5130C>A
NM_001318827.2:c.4890C>A
NM_001318829.2:c.4854C>A
NM_001318831.2:c.4467C>A
NM_001318832.2:c.5031C>A
NM_001363528.2:c.5001C>A
NM_001370404.1:c.5067C>A
NM_001370405.1:c.5058C>A
NM_021055.3:c.5070C>A
NP_000539.2:p.Thr1733=
NP_001070651.1:p.Thr1666=
NP_001107854.1:p.Thr1710=
NP_001305756.1:p.Thr1630=
NP_001305758.1:p.Thr1618=
NP_001305760.1:p.Thr1489=
NP_001305761.1:p.Thr1677=
NP_001350457.1:p.Thr1667=
NP_001357333.1:p.Thr1689=
NP_001357334.1:p.Thr1686=
NP_066399.2:p.Thr1690=
LRG_487t1:c.5199C>A
LRG_487:g.43960C>A
NC_000016.9:g.2138266C>A
NM_000548.3:c.5199C>A

Links:

dbSNP: rs778378296

NCBI 1000 Genomes Browser:

rs778378296

Molecular consequence:

NM_000548.5:c.5199C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077183.3:c.4998C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001114382.3:c.5130C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318827.2:c.4890C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318829.2:c.4854C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318831.2:c.4467C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318832.2:c.5031C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363528.2:c.5001C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370404.1:c.5067C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370405.1:c.5058C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_021055.3:c.5070C>A - synonymous variant - [Sequence Ontology: SO:0001819]

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

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PREDICTED: Homo sapiens calcitonin receptor like receptor (CALCRL), transcript v...
PREDICTED: Homo sapiens calcitonin receptor like receptor (CALCRL), transcript variant X1, mRNA
gi|2217324926|ref|XM_005246232.4|

Nucleotide
Homo sapiens abhydrolase domain containing 11 (ABHD11), transcript variant 10, n...
Homo sapiens abhydrolase domain containing 11 (ABHD11), transcript variant 10, non-coding RNA
gi|1887096829|ref|NR_135627.2|

Nucleotide
vomeronasal 2, receptor 32 precursor [Mus musculus]
vomeronasal 2, receptor 32 precursor [Mus musculus]
gi|157311608|ref|NP_001098533.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004971747	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 18, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004971747

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 18, 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, SCV004971747.1

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

Description

The c.5199C>A (p.T1733T) alteration is located in exon 41 (coding exon 40) of the TSC2 gene. This alteration consists of a C to A substitution at nucleotide position 5199. This nucleotide substitution does not change the amino acid at codon 1733. However, this change occurs in the last nucleotide of Exon 41 (c.5161_5259) which makes it likely to have some effect on normal mRNA splicing. Based on insufficient or conflicting evidence, 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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