NM_000548.5(TSC2):c.5404G>A (p.Asp1802Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 21, 2019
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:: RCV001024046.3

Allele description [Variation Report for NM_000548.5(TSC2):c.5404G>A (p.Asp1802Asn)]

NM_000548.5(TSC2):c.5404G>A (p.Asp1802Asn)

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.5404G>A (p.Asp1802Asn)

HGVS:

NC_000016.10:g.2088590G>A
NG_005895.1:g.44285G>A
NG_008617.1:g.54631C>T
NM_000548.5:c.5404G>AMANE SELECT
NM_001077183.3:c.5203G>A
NM_001114382.3:c.5335G>A
NM_001318827.2:c.5095G>A
NM_001318829.2:c.5059G>A
NM_001318831.2:c.4672G>A
NM_001318832.2:c.5236G>A
NM_001363528.2:c.5206G>A
NM_001370404.1:c.5272G>A
NM_001370405.1:c.5263G>A
NM_021055.3:c.5275G>A
NP_000539.2:p.Asp1802Asn
NP_001070651.1:p.Asp1735Asn
NP_001107854.1:p.Asp1779Asn
NP_001305756.1:p.Asp1699Asn
NP_001305758.1:p.Asp1687Asn
NP_001305760.1:p.Asp1558Asn
NP_001305761.1:p.Asp1746Asn
NP_001350457.1:p.Asp1736Asn
NP_001357333.1:p.Asp1758Asn
NP_001357334.1:p.Asp1755Asn
NP_066399.2:p.Asp1759Asn
LRG_487t1:c.5404G>A
LRG_487:g.44285G>A
NC_000016.9:g.2138591G>A
NM_000548.3:c.5404G>A

Protein change:

D1558N

Links:

dbSNP: rs1596464614

NCBI 1000 Genomes Browser:

rs1596464614

Molecular consequence:

NM_000548.5:c.5404G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.5203G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.5335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.5095G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.5059G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.4672G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.5236G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.5206G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5272G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5263G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.5275G>A - 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
SCV001185999	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 21, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001185999

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 21, 2019)

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, SCV001185999.4

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

Description

The p.D1802N variant (also known as c.5404G>A), located in coding exon 41 of the TSC2 gene, results from a G to A substitution at nucleotide position 5404. The aspartic acid at codon 1802 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is highly 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: May 1, 2024

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