NM_000548.5(TSC2):c.482-4_482-3delinsGT AND Tuberous sclerosis 2

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 21, 2023
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:: RCV001047639.7

Allele description

NM_000548.5(TSC2):c.482-4_482-3delinsGT

Gene:

TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.482-4_482-3delinsGT

HGVS:

NC_000016.10:g.2055398_2055399delCCinsGT
NC_000016.10:g.2055398_2055399delinsGT
NG_005895.1:g.11093_11094delinsGT
NM_000548.5:c.482-4_482-3delinsGTMANE SELECT
NM_001077183.3:c.482-4_482-3delinsGT
NM_001114382.3:c.482-4_482-3delinsGT
NM_001318827.2:c.371-4_371-3delinsGT
NM_001318829.2:c.335-4_335-3delinsGT
NM_001318831.2:c.-1-798_-1-797delinsGT
NM_001318832.2:c.515-4_515-3delinsGT
NM_001363528.2:c.482-4_482-3delinsGT
NM_001370404.1:c.482-4_482-3delinsGT
NM_001370405.1:c.482-4_482-3delinsGT
NM_021055.3:c.482-4_482-3delinsGT
LRG_487t1:c.482-4_482-3delinsGT
LRG_487:g.11093_11094delinsGT
NC_000016.9:g.2105399_2105400delinsGT
NM_000548.3:c.482-4_482-3delinsGT

Links:

dbSNP: rs2085650597

NCBI 1000 Genomes Browser:

rs2085650597

Molecular consequence:

NM_000548.5:c.482-4_482-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001077183.3:c.482-4_482-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001114382.3:c.482-4_482-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001318827.2:c.371-4_371-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001318829.2:c.335-4_335-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001318831.2:c.-1-798_-1-797delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001318832.2:c.515-4_515-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001363528.2:c.482-4_482-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001370404.1:c.482-4_482-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_001370405.1:c.482-4_482-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]
NM_021055.3:c.482-4_482-3delinsGT - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

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ADAMTS-like protein 5 isoform 2 precursor [Rattus norvegicus]
ADAMTS-like protein 5 isoform 2 precursor [Rattus norvegicus]
gi|2186289543|ref|NP_001387894.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001211607	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 21, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001211607

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 21, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001211607.5

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). ClinVar contains an entry for this variant (Variation ID: 844721). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change falls in intron 5 of the TSC2 gene. It does not directly change the encoded amino acid sequence of the TSC2 protein. It affects a nucleotide within the consensus splice site.

#	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: Feb 28, 2024

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Relating variation to medicine