NM_000368.5(TSC1):c.1460C>G (p.Ser487Cys) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Oct 1, 2020
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:: RCV000034602.8

Allele description

NM_000368.5(TSC1):c.1460C>G (p.Ser487Cys)

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.1460C>G (p.Ser487Cys)

Other names:

p.S487C:TCT>TGT

HGVS:

NC_000009.12:g.132906118G>C
NG_012386.1:g.43516C>G
NM_000368.5:c.1460C>GMANE SELECT
NM_001162426.2:c.1457C>G
NM_001162427.2:c.1307C>G
NM_001362177.2:c.1097C>G
NP_000359.1:p.Ser487Cys
NP_000359.1:p.Ser487Cys
NP_001155898.1:p.Ser486Cys
NP_001155899.1:p.Ser436Cys
NP_001349106.1:p.Ser366Cys
LRG_486t1:c.1460C>G
LRG_486:g.43516C>G
LRG_486p1:p.Ser487Cys
NC_000009.11:g.135781505G>C
NM_000368.3:c.1460C>G
NM_000368.4:c.1460C>G
p.(Ser487Cys)

Protein change:

S366C

Links:

Tuberous sclerosis database (TSC1): TSC1_00343; dbSNP: rs118203532

NCBI 1000 Genomes Browser:

rs118203532

Molecular consequence:

NM_000368.5:c.1460C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001162426.2:c.1457C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001162427.2:c.1307C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001362177.2:c.1097C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000043515	Biesecker Lab/Clinical Genomics Section,National Institutes of Health - ClinSeq	no assertion criteria provided	variant of unknown significance (Jul 13, 2012)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV000243461	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Apr 18, 2019)	germline	clinical testing	Citation Link,
SCV001502115	CeGaT Praxis fuer Humangenetik Tuebingen	criteria provided, single submitter (Praxis fuer Humangenetik Tuebingen - Variant Classification Criteria)	Likely benign (Oct 1, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000043515

Biesecker Lab/Clinical Genomics Section,National Institutes of Health - ClinSeq

no assertion criteria provided

variant of unknown significance
(Jul 13, 2012)

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV000243461

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Apr 18, 2019)

germline

clinical testing

Citation Link,

SCV001502115

CeGaT Praxis fuer Humangenetik Tuebingen

criteria provided, single submitter

(Praxis fuer Humangenetik Tuebingen - Variant Classification Criteria)

Likely benign
(Oct 1, 2020)

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	no	1	not provided	not provided	566	not provided	research
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.

Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG.

Am J Hum Genet. 2012 Jul 13;91(1):97-108. doi: 10.1016/j.ajhg.2012.05.021. Epub 2012 Jun 14.

PubMed [citation]

PMID:: 22703879
PMCID:: PMC3397257

Details of each submission

From Biesecker Lab/Clinical Genomics Section,National Institutes of Health - ClinSeq, SCV000043515.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (1)

Description

The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See PubMed ID:22703879 for details.

Description

Converted during submission to Uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	566	not provided	discovery		1	not provided	not provided	not provided

From GeneDx, SCV000243461.12

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

Description

This variant is associated with the following publications: (PMID: 21309039, 27153395, 16554133, 23514105, 22703879, 31054281)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001502115.3

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jan 11, 2022

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