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NM_000548.5(TSC2):c.5393C>T (p.Ser1798Phe) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 23, 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:
RCV002348346.2

Allele description [Variation Report for NM_000548.5(TSC2):c.5393C>T (p.Ser1798Phe)]

NM_000548.5(TSC2):c.5393C>T (p.Ser1798Phe)

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.5393C>T (p.Ser1798Phe)
HGVS:
  • NC_000016.10:g.2088579C>T
  • NG_005895.1:g.44274C>T
  • NG_008617.1:g.54642G>A
  • NM_000548.5:c.5393C>TMANE SELECT
  • NM_001077183.3:c.5192C>T
  • NM_001114382.3:c.5324C>T
  • NM_001318827.2:c.5084C>T
  • NM_001318829.2:c.5048C>T
  • NM_001318831.2:c.4661C>T
  • NM_001318832.2:c.5225C>T
  • NM_001363528.2:c.5195C>T
  • NM_001370404.1:c.5261C>T
  • NM_001370405.1:c.5252C>T
  • NM_021055.3:c.5264C>T
  • NP_000539.2:p.Ser1798Phe
  • NP_001070651.1:p.Ser1731Phe
  • NP_001107854.1:p.Ser1775Phe
  • NP_001305756.1:p.Ser1695Phe
  • NP_001305758.1:p.Ser1683Phe
  • NP_001305760.1:p.Ser1554Phe
  • NP_001305761.1:p.Ser1742Phe
  • NP_001350457.1:p.Ser1732Phe
  • NP_001357333.1:p.Ser1754Phe
  • NP_001357334.1:p.Ser1751Phe
  • NP_066399.2:p.Ser1755Phe
  • LRG_487t1:c.5393C>T
  • LRG_487:g.44274C>T
  • NC_000016.9:g.2138580C>T
  • NM_000548.3:c.5393C>T
Protein change:
S1554F
Links:
dbSNP: rs2091216208
NCBI 1000 Genomes Browser:
rs2091216208
Molecular consequence:
  • NM_000548.5:c.5393C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077183.3:c.5192C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001114382.3:c.5324C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318827.2:c.5084C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318829.2:c.5048C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318831.2:c.4661C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318832.2:c.5225C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363528.2:c.5195C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370404.1:c.5261C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370405.1:c.5252C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021055.3:c.5264C>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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002642827Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Sep 23, 2019) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002642827.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.S1798F variant (also known as c.5393C>T), located in coding exon 41 of the TSC2 gene, results from a C to T substitution at nucleotide position 5393. The serine at codon 1798 is replaced by phenylalanine, an amino acid with highly 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024