NM_000548.5(TSC2):c.3986G>A (p.Arg1329His) AND Tuberous sclerosis syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Apr 27, 2017
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:: RCV000054856.15

Allele description [Variation Report for NM_000548.5(TSC2):c.3986G>A (p.Arg1329His)]

NM_000548.5(TSC2):c.3986G>A (p.Arg1329His)

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.3986G>A (p.Arg1329His)

Other names:

NM_000548.3(TSC2):c.3986G>A(p.Arg1329His); NM_001077183.1(TSC2):c.3785G>A(p.Arg1262His); NM_001114382.1(TSC2):c.3917G>A(p.Arg1306His)

HGVS:

NC_000016.10:g.2083797G>A
NG_005895.1:g.39492G>A
NM_000548.5:c.3986G>AMANE SELECT
NM_001077183.3:c.3785G>A
NM_001114382.3:c.3917G>A
NM_001318827.2:c.3677G>A
NM_001318829.2:c.3641G>A
NM_001318831.2:c.3254G>A
NM_001318832.2:c.3818G>A
NM_001363528.2:c.3788G>A
NM_001370404.1:c.3854G>A
NM_001370405.1:c.3857G>A
NM_021055.3:c.3857G>A
NP_000539.2:p.Arg1329His
NP_001070651.1:p.Arg1262His
NP_001107854.1:p.Arg1306His
NP_001305756.1:p.Arg1226His
NP_001305758.1:p.Arg1214His
NP_001305760.1:p.Arg1085His
NP_001305761.1:p.Arg1273His
NP_001350457.1:p.Arg1263His
NP_001357333.1:p.Arg1285His
NP_001357334.1:p.Arg1286His
NP_066399.2:p.Arg1286His
LRG_487t1:c.3986G>A
LRG_487:g.39492G>A
NC_000016.9:g.2133798G>A
NM_000548.3:c.3986G>A
NM_000548.4:c.3986G>A
P49815:p.Arg1329His
p.R1329H
p.(Arg1329His)

Protein change:

R1085H

Links:

Tuberous sclerosis database (TSC2): TSC2_00092; UniProtKB: P49815#VAR_008029; dbSNP: rs45517323

NCBI 1000 Genomes Browser:

rs45517323

Molecular consequence:

NM_000548.5:c.3986G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.3785G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.3917G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.3677G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.3641G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.3254G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.3818G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.3788G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.3854G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.3857G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.3857G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Tuberous sclerosis syndrome (TSC)
Synonyms:: Tuberous sclerosis
Identifiers:: MONDO: MONDO:0001734; MedGen: C0041341; OMIM: PS191100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000066332	Tuberous sclerosis database (TSC2)	no classification provided (Tuberous Sclerosis Database Assertion Criteria 2015)	not provided	germline	curation	PubMed (4) [See all records that cite these PMIDs] 10732801, 15798777, 16114042, 17304050 Citation Link,
SCV000395640	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16114042, 10732801 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000066332

Tuberous sclerosis database (TSC2)

no classification provided

(Tuberous Sclerosis Database Assertion Criteria 2015)

not provided

germline

curation

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV000395640

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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
not provided	germline	yes	6	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Mutational analysis of the TSC1 and TSC2 genes in a diagnostic setting: genotype--phenotype correlations and comparison of diagnostic DNA techniques in Tuberous Sclerosis Complex.

Sancak O, Nellist M, Goedbloed M, Elfferich P, Wouters C, Maat-Kievit A, Zonnenberg B, Verhoef S, Halley D, van den Ouweland A.

Eur J Hum Genet. 2005 Jun;13(6):731-41.

PubMed [citation]

PMID:: 15798777

Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States.

Au KS, Williams AT, Roach ES, Batchelor L, Sparagana SP, Delgado MR, Wheless JW, Baumgartner JE, Roa BB, Wilson CM, Smith-Knuppel TK, Cheung MY, Whittemore VH, King TM, Northrup H.

Genet Med. 2007 Feb;9(2):88-100.

PubMed [citation]

PMID:: 17304050

See all PubMed Citations (4)

Details of each submission

From Tuberous sclerosis database (TSC2), SCV000066332.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (4)

#	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 Illumina Laboratory Services, Illumina, SCV000395640.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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: Nov 24, 2024

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