NM_000548.5(TSC2):c.1826G>T (p.Ser609Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 14, 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:: RCV003297172.2

Allele description [Variation Report for NM_000548.5(TSC2):c.1826G>T (p.Ser609Ile)]

NM_000548.5(TSC2):c.1826G>T (p.Ser609Ile)

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.1826G>T (p.Ser609Ile)

HGVS:

NC_000016.10:g.2070565G>T
NG_005895.1:g.26260G>T
NM_000548.5:c.1826G>TMANE SELECT
NM_001077183.3:c.1826G>T
NM_001114382.3:c.1826G>T
NM_001318827.2:c.1715G>T
NM_001318829.2:c.1679G>T
NM_001318831.2:c.1226G>T
NM_001318832.2:c.1859G>T
NM_001363528.2:c.1826G>T
NM_001370404.1:c.1826G>T
NM_001370405.1:c.1826G>T
NM_001406663.1:c.1826G>T
NM_001406664.1:c.1826G>T
NM_001406665.1:c.1826G>T
NM_001406667.1:c.1916G>T
NM_001406668.1:c.1916G>T
NM_001406670.1:c.1715G>T
NM_001406671.1:c.1814G>T
NM_001406673.1:c.1814G>T
NM_001406675.1:c.1679G>T
NM_001406676.1:c.1679G>T
NM_001406677.1:c.1769G>T
NM_001406678.1:c.1715G>T
NM_001406679.1:c.1679G>T
NM_001406680.1:c.1226G>T
NM_001406681.1:c.1364G>T
NM_001406682.1:c.1226G>T
NM_001406683.1:c.1226G>T
NM_001406684.1:c.1226G>T
NM_001406685.1:c.1226G>T
NM_001406686.1:c.1226G>T
NM_001406687.1:c.1226G>T
NM_001406688.1:c.1226G>T
NM_001406689.1:c.482G>T
NM_001406690.1:c.482G>T
NM_001406691.1:c.482G>T
NM_001406692.1:c.482G>T
NM_001406693.1:c.482G>T
NM_001406694.1:c.482G>T
NM_001406695.1:c.482G>T
NM_001406696.1:c.482G>T
NM_001406697.1:c.482G>T
NM_001406698.1:c.224G>T
NM_021055.3:c.1826G>T
NP_000539.2:p.Ser609Ile
NP_000539.2:p.Ser609Ile
NP_001070651.1:p.Ser609Ile
NP_001107854.1:p.Ser609Ile
NP_001305756.1:p.Ser572Ile
NP_001305758.1:p.Ser560Ile
NP_001305760.1:p.Ser409Ile
NP_001305761.1:p.Ser620Ile
NP_001350457.1:p.Ser609Ile
NP_001357333.1:p.Ser609Ile
NP_001357334.1:p.Ser609Ile
NP_001393592.1:p.Ser609Ile
NP_001393593.1:p.Ser609Ile
NP_001393594.1:p.Ser609Ile
NP_001393596.1:p.Ser639Ile
NP_001393597.1:p.Ser639Ile
NP_001393599.1:p.Ser572Ile
NP_001393600.1:p.Ser605Ile
NP_001393602.1:p.Ser605Ile
NP_001393604.1:p.Ser560Ile
NP_001393605.1:p.Ser560Ile
NP_001393606.1:p.Ser590Ile
NP_001393607.1:p.Ser572Ile
NP_001393608.1:p.Ser560Ile
NP_001393609.1:p.Ser409Ile
NP_001393610.1:p.Ser455Ile
NP_001393611.1:p.Ser409Ile
NP_001393612.1:p.Ser409Ile
NP_001393613.1:p.Ser409Ile
NP_001393614.1:p.Ser409Ile
NP_001393615.1:p.Ser409Ile
NP_001393616.1:p.Ser409Ile
NP_001393617.1:p.Ser409Ile
NP_001393618.1:p.Ser161Ile
NP_001393619.1:p.Ser161Ile
NP_001393620.1:p.Ser161Ile
NP_001393621.1:p.Ser161Ile
NP_001393622.1:p.Ser161Ile
NP_001393623.1:p.Ser161Ile
NP_001393624.1:p.Ser161Ile
NP_001393625.1:p.Ser161Ile
NP_001393626.1:p.Ser161Ile
NP_001393627.1:p.Ser75Ile
NP_066399.2:p.Ser609Ile
LRG_487t1:c.1826G>T
LRG_487:g.26260G>T
LRG_487p1:p.Ser609Ile
NC_000016.9:g.2120566G>T
NM_000548.3:c.1826G>T
NR_176225.1:n.1936G>T
NR_176226.1:n.2155G>T
NR_176227.1:n.2155G>T
NR_176228.1:n.1936G>T
NR_176229.1:n.1936G>T

Protein change:

S161I

Molecular consequence:

NM_000548.5:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.1715G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.1679G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.1859G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406663.1:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406664.1:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406665.1:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406667.1:c.1916G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406668.1:c.1916G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406670.1:c.1715G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406671.1:c.1814G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406673.1:c.1814G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406675.1:c.1679G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406676.1:c.1679G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406677.1:c.1769G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406678.1:c.1715G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406679.1:c.1679G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406680.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406681.1:c.1364G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406682.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406683.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406684.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406685.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406686.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406687.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406688.1:c.1226G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406689.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406690.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406691.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406692.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406693.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406694.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406695.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406696.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406697.1:c.482G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406698.1:c.224G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.1826G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_176225.1:n.1936G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176226.1:n.2155G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176227.1:n.2155G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176228.1:n.1936G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176229.1:n.1936G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003998682	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003998682

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 14, 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, SCV003998682.2

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

Description

The p.S609I variant (also known as c.1826G>T), located in coding exon 16 of the TSC2 gene, results from a G to T substitution at nucleotide position 1826. The serine at codon 609 is replaced by isoleucine, an amino acid with dissimilar properties. This amino acid position is well 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: Nov 3, 2024

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