NC_000016.9:g.(?_2003468)_(2126543_?)del AND Tuberous sclerosis 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 13, 2020
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:: RCV001949704.6

Allele description [Variation Report for NC_000016.9:g.(?_2003468)_(2126543_?)del]

NC_000016.9:g.(?_2003468)_(2126543_?)del

Genes:

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]
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
GFER:growth factor, augmenter of liver regeneration [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]
SYNGR3:synaptogyrin 3 [Gene - OMIM - HGNC]
TBL3:transducin beta like 3 [Gene - OMIM - HGNC]
ZNF598:zinc finger protein 598, E3 ubiquitin ligase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Chr16: 2003468 - 2126543 (on Assembly GRCh37)

Preferred name:

NC_000016.9:g.(?_2003468)_(2126543_?)del

HGVS:

NC_000016.9:g.(?_2003468)_(2126543_?)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
SCV002243947	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 13, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10205261, 17304050, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002243947

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 13, 2020)

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

Comprehensive mutation analysis of TSC1 and TSC2-and phenotypic correlations in 150 families with tuberous sclerosis.

Jones AC, Shyamsundar MM, Thomas MW, Maynard J, Idziaszczyk S, Tomkins S, Sampson JR, Cheadle JP.

Am J Hum Genet. 1999 May;64(5):1305-15. Review.

PubMed [citation]

PMID:: 10205261
PMCID:: PMC1377866

Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States.

Au KS, Williams AT, Roach ES, Batchelor L, Sparagana SP, Delgado MR, Wheless JW, Baumgartner JE, Roa BB, Wilson CM, Smith-Knuppel TK, Cheung MY, Whittemore VH, King TM, Northrup H.

Genet Med. 2007 Feb;9(2):88-100.

PubMed [citation]

PMID:: 17304050

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002243947.4

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with TSC2-related conditions. This variant results in the deletion of exon(s) 1-24 and part of exon 25 (c.-94626_2796del) of the TSC2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TSC2 are known to be pathogenic (PMID: 10205261, 17304050).

#	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: Sep 29, 2024

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