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NM_000548.5(TSC2):c.1839+1G>T AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 3, 2018
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:
RCV000498860.2

Allele description [Variation Report for NM_000548.5(TSC2):c.1839+1G>T]

NM_000548.5(TSC2):c.1839+1G>T

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+1G>T
HGVS:
  • NC_000016.10:g.2070579G>T
  • NG_005895.1:g.26274G>T
  • NM_000548.5:c.1839+1G>TMANE SELECT
  • NM_001077183.3:c.1839+1G>T
  • NM_001114382.3:c.1839+1G>T
  • NM_001318827.2:c.1728+1G>T
  • NM_001318829.2:c.1692+1G>T
  • NM_001318831.2:c.1239+1G>T
  • NM_001318832.2:c.1872+1G>T
  • NM_001363528.2:c.1839+1G>T
  • NM_001370404.1:c.1839+1G>T
  • NM_001370405.1:c.1839+1G>T
  • NM_001406663.1:c.1839+1G>T
  • NM_001406664.1:c.1839+1G>T
  • NM_001406665.1:c.1839+1G>T
  • NM_001406667.1:c.1929+1G>T
  • NM_001406668.1:c.1929+1G>T
  • NM_001406670.1:c.1728+1G>T
  • NM_001406671.1:c.1827+1G>T
  • NM_001406673.1:c.1827+1G>T
  • NM_001406675.1:c.1692+1G>T
  • NM_001406676.1:c.1692+1G>T
  • NM_001406677.1:c.1782+1G>T
  • NM_001406678.1:c.1728+1G>T
  • NM_001406679.1:c.1692+1G>T
  • NM_001406680.1:c.1239+1G>T
  • NM_001406681.1:c.1377+1G>T
  • NM_001406682.1:c.1239+1G>T
  • NM_001406683.1:c.1239+1G>T
  • NM_001406684.1:c.1239+1G>T
  • NM_001406685.1:c.1239+1G>T
  • NM_001406686.1:c.1239+1G>T
  • NM_001406687.1:c.1239+1G>T
  • NM_001406688.1:c.1239+1G>T
  • NM_001406689.1:c.495+1G>T
  • NM_001406690.1:c.495+1G>T
  • NM_001406691.1:c.495+1G>T
  • NM_001406692.1:c.495+1G>T
  • NM_001406693.1:c.495+1G>T
  • NM_001406694.1:c.495+1G>T
  • NM_001406695.1:c.495+1G>T
  • NM_001406696.1:c.495+1G>T
  • NM_001406697.1:c.495+1G>T
  • NM_001406698.1:c.237+1G>T
  • NM_021055.3:c.1839+1G>T
  • LRG_487t1:c.1839+1G>T
  • LRG_487:g.26274G>T
  • NC_000016.9:g.2120580G>T
  • NM_000548.3:c.1839+1G>T
  • p.?
Links:
Tuberous sclerosis database (TSC2): TSC2_01122; dbSNP: rs45438400
NCBI 1000 Genomes Browser:
rs45438400
Molecular consequence:
  • NM_000548.5:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001077183.3:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001114382.3:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318827.2:c.1728+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318829.2:c.1692+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318831.2:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318832.2:c.1872+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001363528.2:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370404.1:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370405.1:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406663.1:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406664.1:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406665.1:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406667.1:c.1929+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406668.1:c.1929+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406670.1:c.1728+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406671.1:c.1827+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406673.1:c.1827+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406675.1:c.1692+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406676.1:c.1692+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406677.1:c.1782+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406678.1:c.1728+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406679.1:c.1692+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406680.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406681.1:c.1377+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406682.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406683.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406684.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406685.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406686.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406687.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406688.1:c.1239+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406689.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406690.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406691.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406692.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406693.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406694.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406695.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406696.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406697.1:c.495+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406698.1:c.237+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_021055.3:c.1839+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000589551GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Dec 3, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000589551.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1839+1 G>T splice site variant in the TSC2 gene has been reported multiple timespreviously reported in association with TSC (Crino et al., 2010; TSC2 LOVD). This pathogenic variant destroys the canonical splice donor site in intron 17, and is expected to cause abnormal gene splicing. The c.1839+1 G>T variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Therefore, the presence of c.1839+1 G>T is consistent with the diagnosis of TSC in this individual.

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

Last Updated: Sep 29, 2024