NM_000548.5(TSC2):c.1276C>T (p.Leu426=) AND Tuberous sclerosis 2

Germline classification:: 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:: RCV000225838.23

Allele description [Variation Report for NM_000548.5(TSC2):c.1276C>T (p.Leu426=)]

NM_000548.5(TSC2):c.1276C>T (p.Leu426=)

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.1276C>T (p.Leu426=)

Other names:

p.L426L:CTG>TTG; p.Leu426Leu

HGVS:

NC_000016.10:g.2062515C>T
NG_005895.1:g.18210C>T
NM_000548.5:c.1276C>TMANE SELECT
NM_001077183.3:c.1276C>T
NM_001114382.3:c.1276C>T
NM_001318827.2:c.1165C>T
NM_001318829.2:c.1129C>T
NM_001318831.2:c.676C>T
NM_001318832.2:c.1309C>T
NM_001363528.2:c.1276C>T
NM_001370404.1:c.1276C>T
NM_001370405.1:c.1276C>T
NM_021055.3:c.1276C>T
NP_000539.2:p.Leu426=
NP_001070651.1:p.Leu426=
NP_001107854.1:p.Leu426=
NP_001305756.1:p.Leu389=
NP_001305758.1:p.Leu377=
NP_001305760.1:p.Leu226=
NP_001305761.1:p.Leu437=
NP_001350457.1:p.Leu426=
NP_001357333.1:p.Leu426=
NP_001357334.1:p.Leu426=
NP_066399.2:p.Leu426=
LRG_487t1:c.1276C>T
LRG_487:g.18210C>T
NC_000016.9:g.2112516C>T
NM_000548.3:c.1276C>T
NM_000548.4:c.1276C>T
p.L426L
p.(=)

Links:

Tuberous sclerosis database (TSC2): TSC2_00063; dbSNP: rs45478593

NCBI 1000 Genomes Browser:

rs45478593

Molecular consequence:

NM_000548.5:c.1276C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077183.3:c.1276C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001114382.3:c.1276C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318827.2:c.1165C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318829.2:c.1129C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318831.2:c.676C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318832.2:c.1309C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363528.2:c.1276C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370404.1:c.1276C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370405.1:c.1276C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_021055.3:c.1276C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000285233	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]
SCV000677533	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (May 30, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10215407, 17304050, 26467025
SCV002041314	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]
SCV004360858	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Sep 20, 2022)	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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	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

Identification of a large insertion and two novel point mutations (3671del8 and S1221X) in tuberous sclerosis complex (TSC) patients. Mutations in brief no. 119. Online.

Wang Q, Verhoef S, Tempelaars AM, Bakker PL, Vrtel R, Hesseling-Janssen AL, Nellist M, Oranje AP, Stroink H, Lindhout D, Halley DJ, van den Ouweland AM.

Hum Mutat. 1998;11(4):331-2.

PubMed [citation]

PMID:: 10215407

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000285233.10

#	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 Athena Diagnostics, SCV000677533.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

#	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 Genome-Nilou Lab, SCV002041314.1

#	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, SCV004360858.1

#	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 8, 2024

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