NC_000016.10:g.(?_2081575)_(2104662_?)del AND Tuberous sclerosis 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 12, 2021
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:: RCV000805913.6

Allele description [Variation Report for NC_000016.10:g.(?_2081575)_(2104662_?)del]

NC_000016.10:g.(?_2081575)_(2104662_?)del

Genes:

PKD1-AS1:PKD1 antisense RNA 1 [Gene - HGNC]
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
MIR1225:microRNA 1225 [Gene - OMIM - HGNC]
PKD1:polycystin 1, transient receptor potential channel interacting [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NC_000016.10:g.(?_2081575)_(2104662_?)del

HGVS:

NC_000016.10:g.(?_2081575)_(2104662_?)del
NC_000016.9:g.(?_2131576)_(2154663_?)del

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
SCV000945888	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 12, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17287951, 24789117, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000945888

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 12, 2021)

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

Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations.

Kozlowski P, Roberts P, Dabora S, Franz D, Bissler J, Northrup H, Au KS, Lazarus R, Domanska-Pakiela D, Kotulska K, Jozwiak S, Kwiatkowski DJ.

Hum Genet. 2007 May;121(3-4):389-400. Epub 2007 Feb 8.

PubMed [citation]

PMID:: 17287951

Quick genetic screening using targeted next-generation sequencing in patients with tuberous sclerosis.

Liu Q, Huang Y, Zhang M, Wang LQ, Guo XN, Si N, Qi Z, Zhou XQ, Cui LY.

J Child Neurol. 2015 Apr;30(5):610-4. doi: 10.1177/0883073814531332. Epub 2014 Apr 30.

PubMed [citation]

PMID:: 24789117

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000945888.4

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

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 31-42 of the TSC2 gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. A similar copy number variant has been observed in individual(s) with tuberous sclerosis complex (PMID: 17287951). This variant is also known as exons 30-41. This variant disrupts a region of the TSC2 protein in which other variant(s) (p.Phe1803Leufs*42) have been determined to be pathogenic (PMID: 24789117). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	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: Nov 11, 2023

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