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NM_000548.5(TSC2):c.1839+2T>C AND Tuberous sclerosis 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 26, 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:
RCV000524605.7

Allele description [Variation Report for NM_000548.5(TSC2):c.1839+2T>C]

NM_000548.5(TSC2):c.1839+2T>C

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.1839+2T>C
HGVS:
  • NC_000016.10:g.2070580T>C
  • NG_005895.1:g.26275T>C
  • NM_000548.5:c.1839+2T>CMANE SELECT
  • NM_001077183.3:c.1839+2T>C
  • NM_001114382.3:c.1839+2T>C
  • NM_001318827.2:c.1728+2T>C
  • NM_001318829.2:c.1692+2T>C
  • NM_001318831.2:c.1239+2T>C
  • NM_001318832.2:c.1872+2T>C
  • NM_001363528.2:c.1839+2T>C
  • NM_001370404.1:c.1839+2T>C
  • NM_001370405.1:c.1839+2T>C
  • NM_001406663.1:c.1839+2T>C
  • NM_001406664.1:c.1839+2T>C
  • NM_001406665.1:c.1839+2T>C
  • NM_001406667.1:c.1929+2T>C
  • NM_001406668.1:c.1929+2T>C
  • NM_001406670.1:c.1728+2T>C
  • NM_001406671.1:c.1827+2T>C
  • NM_001406673.1:c.1827+2T>C
  • NM_001406675.1:c.1692+2T>C
  • NM_001406676.1:c.1692+2T>C
  • NM_001406677.1:c.1782+2T>C
  • NM_001406678.1:c.1728+2T>C
  • NM_001406679.1:c.1692+2T>C
  • NM_001406680.1:c.1239+2T>C
  • NM_001406681.1:c.1377+2T>C
  • NM_001406682.1:c.1239+2T>C
  • NM_001406683.1:c.1239+2T>C
  • NM_001406684.1:c.1239+2T>C
  • NM_001406685.1:c.1239+2T>C
  • NM_001406686.1:c.1239+2T>C
  • NM_001406687.1:c.1239+2T>C
  • NM_001406688.1:c.1239+2T>C
  • NM_001406689.1:c.495+2T>C
  • NM_001406690.1:c.495+2T>C
  • NM_001406691.1:c.495+2T>C
  • NM_001406692.1:c.495+2T>C
  • NM_001406693.1:c.495+2T>C
  • NM_001406694.1:c.495+2T>C
  • NM_001406695.1:c.495+2T>C
  • NM_001406696.1:c.495+2T>C
  • NM_001406697.1:c.495+2T>C
  • NM_001406698.1:c.237+2T>C
  • NM_021055.3:c.1839+2T>C
  • LRG_487t1:c.1839+2T>C
  • LRG_487:g.26275T>C
  • NC_000016.9:g.2120581T>C
  • NM_000548.3:c.1839+2T>C
Links:
dbSNP: rs1555505211
NCBI 1000 Genomes Browser:
rs1555505211
Molecular consequence:
  • NM_000548.5:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001077183.3:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001114382.3:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318827.2:c.1728+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318829.2:c.1692+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318831.2:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318832.2:c.1872+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001363528.2:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370404.1:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370405.1:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406663.1:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406664.1:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406665.1:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406667.1:c.1929+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406668.1:c.1929+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406670.1:c.1728+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406671.1:c.1827+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406673.1:c.1827+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406675.1:c.1692+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406676.1:c.1692+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406677.1:c.1782+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406678.1:c.1728+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406679.1:c.1692+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406680.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406681.1:c.1377+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406682.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406683.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406684.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406685.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406686.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406687.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406688.1:c.1239+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406689.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406690.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406691.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406692.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406693.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406694.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406695.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406696.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406697.1:c.495+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406698.1:c.237+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_021055.3:c.1839+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000644287Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 26, 2017) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Response to everolimus is seen in TSC-associated SEGAs and angiomyolipomas independent of mutation type and site in TSC1 and TSC2.

Kwiatkowski DJ, Palmer MR, Jozwiak S, Bissler J, Franz D, Segal S, Chen D, Sampson JR.

Eur J Hum Genet. 2015 Dec;23(12):1665-72. doi: 10.1038/ejhg.2015.47. Epub 2015 Mar 18.

PubMed [citation]
PMID:
25782670
PMCID:
PMC4795200

LOVD v.2.0: the next generation in gene variant databases.

Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT.

Hum Mutat. 2011 May;32(5):557-63. doi: 10.1002/humu.21438. Epub 2011 Feb 22.

PubMed [citation]
PMID:
21520333
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000644287.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Loss-of-function variants in TSC2 are known to be pathogenic. This particular variant has been reported in individuals affected with tuberous sclerosis complex (TSC), in the literature (PMID: 25782670) and in the Leiden Open-source Variation Database (PMID: 21520333). For these reasons, this variant has been classified as Pathogenic. This sequence change affects a donor splice site in intron 17 of the TSC2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024