NM_000548.5(TSC2):c.5383C>T (p.Arg1795Cys) AND Tuberous sclerosis 2

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Feb 1, 2024
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:: RCV000989443.17

Allele description [Variation Report for NM_000548.5(TSC2):c.5383C>T (p.Arg1795Cys)]

NM_000548.5(TSC2):c.5383C>T (p.Arg1795Cys)

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.5383C>T (p.Arg1795Cys)

Other names:

p.R1795C:CGC>TGC

HGVS:

NC_000016.10:g.2088569C>T
NG_005895.1:g.44264C>T
NG_008617.1:g.54652G>A
NM_000548.5:c.5383C>TMANE SELECT
NM_001077183.3:c.5182C>T
NM_001114382.3:c.5314C>T
NM_001318827.2:c.5074C>T
NM_001318829.2:c.5038C>T
NM_001318831.2:c.4651C>T
NM_001318832.2:c.5215C>T
NM_001363528.2:c.5185C>T
NM_001370404.1:c.5251C>T
NM_001370405.1:c.5242C>T
NM_021055.3:c.5254C>T
NP_000539.2:p.Arg1795Cys
NP_001070651.1:p.Arg1728Cys
NP_001107854.1:p.Arg1772Cys
NP_001305756.1:p.Arg1692Cys
NP_001305758.1:p.Arg1680Cys
NP_001305760.1:p.Arg1551Cys
NP_001305761.1:p.Arg1739Cys
NP_001350457.1:p.Arg1729Cys
NP_001357333.1:p.Arg1751Cys
NP_001357334.1:p.Arg1748Cys
NP_066399.2:p.Arg1752Cys
LRG_487t1:c.5383C>T
LRG_487:g.44264C>T
NC_000016.9:g.2138570C>T
NM_000548.3:c.5383C>T
p.R1795C
p.(Arg1795Cys)

Protein change:

R1551C

Links:

Tuberous sclerosis database (TSC2): TSC2_00666; dbSNP: rs45517423

NCBI 1000 Genomes Browser:

rs45517423

Molecular consequence:

NM_000548.5:c.5383C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.5182C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.5314C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.5074C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.5038C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.4651C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.5215C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.5185C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.5251C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.5242C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.5254C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Tuberous sclerosis 2 (TSC2)
Identifiers:: MONDO: MONDO:0013199; MedGen: C1860707; Orphanet: 805; OMIM: 613254

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000261971	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001139769	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV002040296	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 7, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004360948	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Mar 5, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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
not provided	germline	no	not provided	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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000261971.11

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

#	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

From Mendelics, SCV001139769.1

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

From Genome-Nilou Lab, SCV002040296.1

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

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

From Color Diagnostics, LLC DBA Color Health, SCV004360948.1

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

#	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: Oct 26, 2024

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