NM_000548.5(TSC2):c.5338A>C (p.Thr1780Pro) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 8, 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:: RCV002350301.2

Allele description [Variation Report for NM_000548.5(TSC2):c.5338A>C (p.Thr1780Pro)]

NM_000548.5(TSC2):c.5338A>C (p.Thr1780Pro)

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.5338A>C (p.Thr1780Pro)

HGVS:

NC_000016.10:g.2088524A>C
NG_005895.1:g.44219A>C
NG_008617.1:g.54697T>G
NM_000548.5:c.5338A>CMANE SELECT
NM_001077183.3:c.5137A>C
NM_001114382.3:c.5269A>C
NM_001318827.2:c.5029A>C
NM_001318829.2:c.4993A>C
NM_001318831.2:c.4606A>C
NM_001318832.2:c.5170A>C
NM_001363528.2:c.5140A>C
NM_001370404.1:c.5206A>C
NM_001370405.1:c.5197A>C
NM_021055.3:c.5209A>C
NP_000539.2:p.Thr1780Pro
NP_001070651.1:p.Thr1713Pro
NP_001107854.1:p.Thr1757Pro
NP_001305756.1:p.Thr1677Pro
NP_001305758.1:p.Thr1665Pro
NP_001305760.1:p.Thr1536Pro
NP_001305761.1:p.Thr1724Pro
NP_001350457.1:p.Thr1714Pro
NP_001357333.1:p.Thr1736Pro
NP_001357334.1:p.Thr1733Pro
NP_066399.2:p.Thr1737Pro
LRG_487t1:c.5338A>C
LRG_487:g.44219A>C
NC_000016.9:g.2138525A>C
NM_000548.3:c.5338A>C
NM_000548.4:c.5338A>C

Protein change:

T1536P

Links:

dbSNP: rs989487316

NCBI 1000 Genomes Browser:

rs989487316

Molecular consequence:

NM_000548.5:c.5338A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.5137A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.5269A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.5029A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.4993A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.4606A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.5170A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.5140A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5206A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5197A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.5209A>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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002647043	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 8, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002647043

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 8, 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, SCV002647043.2

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

Description

The p.T1780P variant (also known as c.5338A>C), located in coding exon 41 of the TSC2 gene, results from an A to C substitution at nucleotide position 5338. The threonine at codon 1780 is replaced by proline, an amino acid with highly similar properties. This amino acid position is poorly 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: Oct 13, 2024

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