NM_000548.5(TSC2):c.4620C>A (p.Tyr1540Ter) AND Tuberous sclerosis 2

Germline classification:: Pathogenic (1 submission)
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:: RCV001831715.2

Allele description [Variation Report for NM_000548.5(TSC2):c.4620C>A (p.Tyr1540Ter)]

NM_000548.5(TSC2):c.4620C>A (p.Tyr1540Ter)

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.4620C>A (p.Tyr1540Ter)

HGVS:

NC_000016.10:g.2085280C>A
NG_005895.1:g.40975C>A
NM_000548.5:c.4620C>AMANE SELECT
NM_001077183.3:c.4419C>A
NM_001114382.3:c.4551C>A
NM_001318827.2:c.4311C>A
NM_001318829.2:c.4275C>A
NM_001318831.2:c.3888C>A
NM_001318832.2:c.4452C>A
NM_001363528.2:c.4422C>A
NM_001370404.1:c.4488C>A
NM_001370405.1:c.4491C>A
NM_021055.3:c.4491C>A
NP_000539.2:p.Tyr1540Ter
NP_001070651.1:p.Tyr1473Ter
NP_001107854.1:p.Tyr1517Ter
NP_001305756.1:p.Tyr1437Ter
NP_001305758.1:p.Tyr1425Ter
NP_001305760.1:p.Tyr1296Ter
NP_001305761.1:p.Tyr1484Ter
NP_001350457.1:p.Tyr1474Ter
NP_001357333.1:p.Tyr1496Ter
NP_001357334.1:p.Tyr1497Ter
NP_066399.2:p.Tyr1497Ter
LRG_487t1:c.4620C>A
LRG_487:g.40975C>A
NC_000016.9:g.2135281C>A
NM_000548.3:c.4620C>A
p.(Tyr1540*)

Protein change:

Y1296*

Links:

Tuberous sclerosis database (TSC2): TSC2_00595; dbSNP: rs45455897

NCBI 1000 Genomes Browser:

rs45455897

Molecular consequence:

NM_000548.5:c.4620C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001077183.3:c.4419C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001114382.3:c.4551C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318827.2:c.4311C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318829.2:c.4275C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318831.2:c.3888C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001318832.2:c.4452C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001363528.2:c.4422C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370404.1:c.4488C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370405.1:c.4491C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_021055.3:c.4491C>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV002097032	Suma Genomics, Suma Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002097032

Suma Genomics, Suma Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

de novo

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Suma Genomics, Suma Genomics, SCV002097032.1

#	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	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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