NM_000368.5(TSC1):c.2066G>C (p.Arg689Pro) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 9, 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:: RCV001014297.4

Allele description [Variation Report for NM_000368.5(TSC1):c.2066G>C (p.Arg689Pro)]

NM_000368.5(TSC1):c.2066G>C (p.Arg689Pro)

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.2066G>C (p.Arg689Pro)

HGVS:

NC_000009.12:g.132903793C>G
NG_012386.1:g.45841G>C
NM_000368.5:c.2066G>CMANE SELECT
NM_001162426.2:c.2063G>C
NM_001162427.2:c.1913G>C
NM_001362177.2:c.1703G>C
NP_000359.1:p.Arg689Pro
NP_001155898.1:p.Arg688Pro
NP_001155899.1:p.Arg638Pro
NP_001349106.1:p.Arg568Pro
LRG_486t1:c.2066G>C
LRG_486:g.45841G>C
NC_000009.11:g.135779180C>G
NM_000368.4:c.2066G>C

Protein change:

R568P

Links:

dbSNP: rs200827913

NCBI 1000 Genomes Browser:

rs200827913

Molecular consequence:

NM_000368.5:c.2066G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001162426.2:c.2063G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001162427.2:c.1913G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001362177.2:c.1703G>C - 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
SCV001174991	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 9, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001174991

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 9, 2022)

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, SCV001174991.5

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

Description

The p.R689P variant (also known as c.2066G>C), located in coding exon 15 of the TSC1 gene, results from a G to C substitution at nucleotide position 2066. The arginine at codon 689 is replaced by proline, an amino acid with dissimilar properties. This amino acid position is poorly 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: Sep 29, 2024

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