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

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Nov 1, 2023
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:: RCV000034602.22

Allele description [Variation Report for NM_000368.5(TSC1):c.1460C>G (p.Ser487Cys)]

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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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 Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Nov 1, 2023)	germline	clinical testing	Citation Link,
SCV004221381	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (Jun 9, 2016)	unknown	clinical testing	PubMed (10) [See all records that cite these PMIDs] 23514105, 25722345, 21309039, 16554133, 22703879, 25498131, 27153395, 31054281, 30076350, 26467025

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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	6	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder.

Bahl S, Chiang C, Beauchamp RL, Neale BM, Daly MJ, Gusella JF, Talkowski ME, Ramesh V.

Mol Autism. 2013 Mar 20;4(1):5. doi: 10.1186/2040-2392-4-5.

PubMed [citation]

PMID:: 23514105
PMCID:: PMC3610211

Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility.

Wang Y, Cheng H, Pan Z, Ren J, Liu Z, Xue Y.

J Mol Cell Biol. 2015 Jun;7(3):187-202. doi: 10.1093/jmcb/mjv013. Epub 2015 Feb 26.

PubMed [citation]

PMID:: 25722345

See all PubMed Citations (10)

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 Center for Human Genetics Tuebingen, SCV001502115.13

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	clinical testing	not provided

Description

TSC1: BS1

#	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		6	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004221381.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

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

Last Updated: Jun 2, 2024

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