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NM_000548.5(TSC2):c.[4570-18_4570-6del;4570-5CA[3]] AND Tuberous sclerosis 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 1, 2022
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:
RCV002274868.2

Alleles description [Variation Report for NM_000548.5(TSC2):c.[4570-18_4570-6del;4570-5CA[3]]]

NM_000548.5(TSC2):c.4570-18_4570-6del

Gene:
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_000548.5(TSC2):c.4570-18_4570-6del
HGVS:
  • NC_000016.10:g.2085212_2085224del
  • NG_005895.1:g.40907_40919del
  • NM_000548.5:c.4570-18_4570-6delMANE SELECT
  • NM_001077183.3:c.4369-18_4369-6del
  • NM_001114382.3:c.4501-18_4501-6del
  • NM_001318827.2:c.4261-18_4261-6del
  • NM_001318829.2:c.4225-18_4225-6del
  • NM_001318831.2:c.3838-18_3838-6del
  • NM_001318832.2:c.4402-18_4402-6del
  • NM_001363528.2:c.4372-18_4372-6del
  • NM_001370404.1:c.4438-18_4438-6del
  • NM_001370405.1:c.4441-18_4441-6del
  • NM_021055.3:c.4441-18_4441-6del
  • LRG_487:g.40907_40919del
  • NC_000016.9:g.2135213_2135225del
Links:
dbSNP: rs2151549002
NCBI 1000 Genomes Browser:
rs2151549002
Molecular consequence:
  • NM_000548.5:c.4570-18_4570-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077183.3:c.4369-18_4369-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001114382.3:c.4501-18_4501-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318827.2:c.4261-18_4261-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318829.2:c.4225-18_4225-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318831.2:c.3838-18_3838-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318832.2:c.4402-18_4402-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363528.2:c.4372-18_4372-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001370404.1:c.4438-18_4438-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001370405.1:c.4441-18_4441-6del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_021055.3:c.4441-18_4441-6del - intron variant - [Sequence Ontology: SO:0001627]
Functional consequence:
sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071]
Observations:
1

NM_000548.5(TSC2):c.4570-5CA[3]

Gene:
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_000548.5(TSC2):c.4570-5CA[3]
HGVS:
  • NC_000016.10:g.2085225CA[3]
  • NG_005895.1:g.40920CA[3]
  • NM_000548.5:c.4570-5CA[3]MANE SELECT
  • NM_001077183.3:c.4369-5CA[3]
  • NM_001114382.3:c.4501-5CA[3]
  • NM_001318827.2:c.4261-5CA[3]
  • NM_001318829.2:c.4225-5CA[3]
  • NM_001318831.2:c.3838-5CA[3]
  • NM_001318832.2:c.4402-5CA[3]
  • NM_001363528.2:c.4372-5CA[3]
  • NM_001370404.1:c.4438-5CA[3]
  • NM_001370405.1:c.4441-5CA[3]
  • NM_021055.3:c.4441-5CA[3]
  • LRG_487:g.40920CA[3]
  • NC_000016.9:g.2135226CA[3]
  • NM_000548.5:c.4570-3_4570-2dupMANE SELECT
Links:
dbSNP: rs2090619495
NCBI 1000 Genomes Browser:
rs2090619495
Molecular consequence:
  • NM_000548.5:c.4570-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001077183.3:c.4369-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001114382.3:c.4501-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001318827.2:c.4261-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001318829.2:c.4225-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001318831.2:c.3838-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001318832.2:c.4402-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001363528.2:c.4372-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001370404.1:c.4438-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001370405.1:c.4441-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_021055.3:c.4441-5CA[3] - splice acceptor variant - [Sequence Ontology: SO:0001574]
Functional consequence:
sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071]
Observations:
1

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
SCV002559891Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Aug 1, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Japanesegermlineyes1not providednot providednot providednot providedclinical 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 Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, SCV002559891.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Japanese1not providednot providedclinical testing PubMed (1)

Description

This 13 base pairs deletion and 2 base paires duplication in the TSC2 intron 35 causes splicing abnormalities.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jan 26, 2024