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NM_000548.5(TSC2):c.5185C>T (p.Arg1729Cys) AND Hereditary cancer-predisposing syndrome

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Jun 5, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000567321.11

Allele description [Variation Report for NM_000548.5(TSC2):c.5185C>T (p.Arg1729Cys)]

NM_000548.5(TSC2):c.5185C>T (p.Arg1729Cys)

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.5185C>T (p.Arg1729Cys)
HGVS:
  • NC_000016.10:g.2088251C>T
  • NG_005895.1:g.43946C>T
  • NG_008617.1:g.54970G>A
  • NM_000548.5:c.5185C>TMANE SELECT
  • NM_001077183.3:c.4984C>T
  • NM_001114382.3:c.5116C>T
  • NM_001318827.2:c.4876C>T
  • NM_001318829.2:c.4840C>T
  • NM_001318831.2:c.4453C>T
  • NM_001318832.2:c.5017C>T
  • NM_001363528.2:c.4987C>T
  • NM_001370404.1:c.5053C>T
  • NM_001370405.1:c.5044C>T
  • NM_021055.3:c.5056C>T
  • NP_000539.2:p.Arg1729Cys
  • NP_001070651.1:p.Arg1662Cys
  • NP_001107854.1:p.Arg1706Cys
  • NP_001305756.1:p.Arg1626Cys
  • NP_001305758.1:p.Arg1614Cys
  • NP_001305760.1:p.Arg1485Cys
  • NP_001305761.1:p.Arg1673Cys
  • NP_001350457.1:p.Arg1663Cys
  • NP_001357333.1:p.Arg1685Cys
  • NP_001357334.1:p.Arg1682Cys
  • NP_066399.2:p.Arg1686Cys
  • LRG_487t1:c.5185C>T
  • LRG_487:g.43946C>T
  • NC_000016.9:g.2138252C>T
  • NM_000548.3:c.5185C>T
  • NM_000548.4:c.5185C>T
  • p.(Arg1729Cys)
Protein change:
R1485C
Links:
Tuberous sclerosis database (TSC2): TSC2_00659; dbSNP: rs45517409
NCBI 1000 Genomes Browser:
rs45517409
Molecular consequence:
  • NM_000548.5:c.5185C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077183.3:c.4984C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001114382.3:c.5116C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318827.2:c.4876C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318829.2:c.4840C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318831.2:c.4453C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318832.2:c.5017C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363528.2:c.4987C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370404.1:c.5053C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370405.1:c.5044C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021055.3:c.5056C>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
SCV000664729Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jun 8, 2018) 		germlineclinical testing

Citation Link,

SCV002534026Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)		Benign
(Jun 5, 2021) 		germlinecuration

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV000664729.5

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

From Sema4, Sema4, SCV002534026.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024