NC_000016.10:g.(?_1523498)_(2064447_?)del AND Tuberous sclerosis 2

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 22, 2019
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:: RCV001032344.1

Allele description

NC_000016.10:g.(?_1523498)_(2064447_?)del

Genes:

JPT2:Jupiter microtubule associated homolog 2 [Gene - OMIM - HGNC]
NDUFB10:NADH:ubiquinone oxidoreductase subunit B10 [Gene - OMIM - HGNC]
NOXO1:NADPH oxidase organizer 1 [Gene - OMIM - HGNC]
NHERF2:NHERF family PDZ scaffold protein 2 [Gene - OMIM - HGNC]
NME3:NME/NM23 nucleoside diphosphate kinase 3 [Gene - OMIM - HGNC]
NUBP2:NUBP iron-sulfur cluster assembly factor 2, cytosolic [Gene - OMIM - HGNC]
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
CRAMP1:cramped chromatin regulator homolog 1 [Gene - HGNC]
EME2:essential meiotic structure-specific endonuclease subunit 2 [Gene - OMIM - HGNC]
FAHD1:fumarylacetoacetate hydrolase domain containing 1 [Gene - OMIM - HGNC]
GFER:growth factor, augmenter of liver regeneration [Gene - OMIM - HGNC]
HS3ST6:heparan sulfate-glucosamine 3-sulfotransferase 6 [Gene - OMIM - HGNC]
HAGH:hydroxyacylglutathione hydrolase [Gene - OMIM - HGNC]
IGFALS:insulin like growth factor binding protein acid labile subunit [Gene - OMIM - HGNC]
IFT140:intraflagellar transport 140 [Gene - OMIM - HGNC]
MEIOB:meiosis specific with OB-fold [Gene - OMIM - HGNC]
MSRB1:methionine sulfoxide reductase B1 [Gene - OMIM - HGNC]
MRPS34:mitochondrial ribosomal protein S34 [Gene - OMIM - HGNC]
MAPK8IP3:mitogen-activated protein kinase 8 interacting protein 3 [Gene - OMIM - HGNC]
NPW:neuropeptide W [Gene - OMIM - HGNC]
NTHL1:nth like DNA glycosylase 1 [Gene - OMIM - HGNC]
RPL3L:ribosomal protein L3 like [Gene - OMIM - HGNC]
RPS2:ribosomal protein S2 [Gene - OMIM - HGNC]
RNF151:ring finger protein 151 [Gene - HGNC]
SNHG9:small nucleolar RNA host gene 9 [Gene - HGNC]
SPSB3:splA/ryanodine receptor domain and SOCS box containing 3 [Gene - OMIM - HGNC]
SYNGR3:synaptogyrin 3 [Gene - OMIM - HGNC]
TBL3:transducin beta like 3 [Gene - OMIM - HGNC]
TMEM204:transmembrane protein 204 [Gene - OMIM - HGNC]
ZNF598:zinc finger protein 598, E3 ubiquitin ligase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Chr16: 1573499 - 2114448 (on Assembly GRCh37)

Preferred name:

NC_000016.10:g.(?_1523498)_(2064447_?)del

HGVS:

NC_000016.10:g.(?_1523498)_(2064447_?)del
NC_000016.9:g.(?_1573499)_(2114448_?)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
SCV001195651	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 22, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17287951, 20498439, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001195651

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 22, 2019)

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

Biallelic TSC gene inactivation in tuberous sclerosis complex.

Crino PB, Aronica E, Baltuch G, Nathanson KL.

Neurology. 2010 May 25;74(21):1716-23. doi: 10.1212/WNL.0b013e3181e04325.

PubMed [citation]

PMID:: 20498439
PMCID:: PMC2882213

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001195651.1

#	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 exons 1-15 of the TSC2 gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 15 of the TSC2 gene. This is expected to result in an absent or disrupted protein product. Similar deletions has been observed in individuals affected with tuberous sclerosis (PMID:20498439, 17287951). Loss-of-function variants in TSC2 are known to be pathogenic (PMID: 10205261, 17304050). 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: Mar 26, 2023

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