NM_000548.5(TSC2):c.5173G>T (p.Val1725Leu) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 3, 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:: RCV003170922.2

Allele description [Variation Report for NM_000548.5(TSC2):c.5173G>T (p.Val1725Leu)]

NM_000548.5(TSC2):c.5173G>T (p.Val1725Leu)

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.5173G>T (p.Val1725Leu)

HGVS:

NC_000016.10:g.2088239G>T
NG_005895.1:g.43934G>T
NG_008617.1:g.54982C>A
NM_000548.5:c.5173G>TMANE SELECT
NM_001077183.3:c.4972G>T
NM_001114382.3:c.5104G>T
NM_001318827.2:c.4864G>T
NM_001318829.2:c.4828G>T
NM_001318831.2:c.4441G>T
NM_001318832.2:c.5005G>T
NM_001363528.2:c.4975G>T
NM_001370404.1:c.5041G>T
NM_001370405.1:c.5032G>T
NM_001406663.1:c.5170G>T
NM_001406664.1:c.5101G>T
NM_001406665.1:c.5095G>T
NM_001406667.1:c.5065G>T
NM_001406668.1:c.5062G>T
NM_001406670.1:c.4993G>T
NM_001406671.1:c.4963G>T
NM_001406673.1:c.4960G>T
NM_001406675.1:c.4957G>T
NM_001406676.1:c.4954G>T
NM_001406677.1:c.4915G>T
NM_001406678.1:c.4861G>T
NM_001406679.1:c.4825G>T
NM_001406680.1:c.4573G>T
NM_001406681.1:c.4513G>T
NM_001406682.1:c.4504G>T
NM_001406683.1:c.4504G>T
NM_001406684.1:c.4501G>T
NM_001406685.1:c.4375G>T
NM_001406686.1:c.4375G>T
NM_001406687.1:c.4372G>T
NM_001406688.1:c.4372G>T
NM_001406689.1:c.3760G>T
NM_001406690.1:c.3700G>T
NM_001406691.1:c.3697G>T
NM_001406692.1:c.3631G>T
NM_001406693.1:c.3631G>T
NM_001406694.1:c.3631G>T
NM_001406695.1:c.3628G>T
NM_001406696.1:c.3628G>T
NM_001406697.1:c.3628G>T
NM_001406698.1:c.3370G>T
NM_021055.3:c.5044G>T
NP_000539.2:p.Val1725Leu
NP_000539.2:p.Val1725Leu
NP_001070651.1:p.Val1658Leu
NP_001107854.1:p.Val1702Leu
NP_001305756.1:p.Val1622Leu
NP_001305758.1:p.Val1610Leu
NP_001305760.1:p.Val1481Leu
NP_001305761.1:p.Val1669Leu
NP_001350457.1:p.Val1659Leu
NP_001357333.1:p.Val1681Leu
NP_001357334.1:p.Val1678Leu
NP_001393592.1:p.Val1724Leu
NP_001393593.1:p.Val1701Leu
NP_001393594.1:p.Val1699Leu
NP_001393596.1:p.Val1689Leu
NP_001393597.1:p.Val1688Leu
NP_001393599.1:p.Val1665Leu
NP_001393600.1:p.Val1655Leu
NP_001393602.1:p.Val1654Leu
NP_001393604.1:p.Val1653Leu
NP_001393605.1:p.Val1652Leu
NP_001393606.1:p.Val1639Leu
NP_001393607.1:p.Val1621Leu
NP_001393608.1:p.Val1609Leu
NP_001393609.1:p.Val1525Leu
NP_001393610.1:p.Val1505Leu
NP_001393611.1:p.Val1502Leu
NP_001393612.1:p.Val1502Leu
NP_001393613.1:p.Val1501Leu
NP_001393614.1:p.Val1459Leu
NP_001393615.1:p.Val1459Leu
NP_001393616.1:p.Val1458Leu
NP_001393617.1:p.Val1458Leu
NP_001393618.1:p.Val1254Leu
NP_001393619.1:p.Val1234Leu
NP_001393620.1:p.Val1233Leu
NP_001393621.1:p.Val1211Leu
NP_001393622.1:p.Val1211Leu
NP_001393623.1:p.Val1211Leu
NP_001393624.1:p.Val1210Leu
NP_001393625.1:p.Val1210Leu
NP_001393626.1:p.Val1210Leu
NP_001393627.1:p.Val1124Leu
NP_066399.2:p.Val1682Leu
LRG_487t1:c.5173G>T
LRG_487:g.43934G>T
LRG_487p1:p.Val1725Leu
NC_000016.9:g.2138240G>T
NM_000548.3:c.5173G>T
NR_176225.1:n.5125G>T
NR_176226.1:n.5373G>T
NR_176227.1:n.5301G>T
NR_176228.1:n.5122G>T
NR_176229.1:n.5047G>T

Protein change:

V1124L

Molecular consequence:

NM_000548.5:c.5173G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.4972G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.5104G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.4864G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.4828G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.4441G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.5005G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.4975G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5041G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5032G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406663.1:c.5170G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406664.1:c.5101G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406665.1:c.5095G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406667.1:c.5065G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406668.1:c.5062G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406670.1:c.4993G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406671.1:c.4963G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406673.1:c.4960G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406675.1:c.4957G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406676.1:c.4954G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406677.1:c.4915G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406678.1:c.4861G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406679.1:c.4825G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406680.1:c.4573G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406681.1:c.4513G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406682.1:c.4504G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406683.1:c.4504G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406684.1:c.4501G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406685.1:c.4375G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406686.1:c.4375G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406687.1:c.4372G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406688.1:c.4372G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406689.1:c.3760G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406690.1:c.3700G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406691.1:c.3697G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406692.1:c.3631G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406693.1:c.3631G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406694.1:c.3631G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406695.1:c.3628G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406696.1:c.3628G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406697.1:c.3628G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406698.1:c.3370G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.5044G>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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ANGPT2 [Sus scrofa]
ANGPT2 [Sus scrofa]
Gene ID:396730

Gene
396730[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003861779	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 3, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003861779

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 3, 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, SCV003861779.2

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

Description

The p.V1725L variant (also known as c.5173G>T), located in coding exon 40 of the TSC2 gene, results from a G to T substitution at nucleotide position 5173. The valine at codon 1725 is replaced by leucine, an amino acid with highly similar properties. This amino acid position is conserved. 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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