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NM_000368.5(TSC1):c.3115A>C (p.Ser1039Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 2, 2022
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:
RCV002320347.1

Allele description [Variation Report for NM_000368.5(TSC1):c.3115A>C (p.Ser1039Arg)]

NM_000368.5(TSC1):c.3115A>C (p.Ser1039Arg)

Gene:
TSC1:TSC complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_000368.5(TSC1):c.3115A>C (p.Ser1039Arg)
HGVS:
  • NC_000009.12:g.132896615T>G
  • NG_012386.1:g.53019A>C
  • NM_000368.5:c.3115A>CMANE SELECT
  • NM_001162426.2:c.3112A>C
  • NM_001162427.2:c.2962A>C
  • NM_001362177.2:c.2752A>C
  • NP_000359.1:p.Ser1039Arg
  • NP_001155898.1:p.Ser1038Arg
  • NP_001155899.1:p.Ser988Arg
  • NP_001349106.1:p.Ser918Arg
  • LRG_486t1:c.3115A>C
  • LRG_486:g.53019A>C
  • NC_000009.11:g.135772002T>G
  • NM_000368.4:c.3115A>C
Protein change:
S1038R
Links:
dbSNP: rs1490199228
NCBI 1000 Genomes Browser:
rs1490199228
Molecular consequence:
  • NM_000368.5:c.3115A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001162426.2:c.3112A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001162427.2:c.2962A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362177.2:c.2752A>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002607865Ambry Genetics
criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)		Uncertain significance
(Feb 2, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Ambry Genetics, SCV002607865.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The p.S1039R variant (also known as c.3115A>C), located in coding exon 21 of the TSC1 gene, results from an A to C substitution at nucleotide position 3115. The serine at codon 1039 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated 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
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Feb 28, 2024