Full data view for gene TSC2

The curator’s expert opinion on the classification of a variant, can be found in the
SUMMARY record. Regarding the classification, please note that where there are several
records of the same variant, the classification of that variant may differ depending on the
submitter’s conclusion.
Information The variants shown are described using the NM_000548.3 transcript reference sequence.

37 entries on 1 page. Showing entries 1 - 37.
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Effect     

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AscendingDNA change (cDNA)     

RNA change     

Protein     

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Predict-BioInf     

Allele     

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DNA change (hg38)     

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Variant remarks     

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ID_report     

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+/. - c.3094C>T r.(?) p.(Arg1032Ter) - - Unknown - pathogenic g.2129160C>T g.2079159C>T TSC2(NM_000548.3):c.3094C>T (p.R1032*) - TSC2_000492 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - De novo ? 1/3 individuals tested has the variant TaqI- - - DNA SEQ Blood - TSC - unpublished clinical features not specified F ? - - - - - - 1 Rosemary Ekong
+/+ 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic (dominant) g.2129160C>T g.2079159C>T - - TSC2_000492 - - - - SUMMARY record - - TaqI- - - - - - - - - - - - - - - - - - - - -
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 both TSC1 and TSC2 genes tested; found with silent TSC1 c.3324C>T and intronic TSC2 c.3884-8C>T unpublished - - Germline - - -TaqI - - DNA MLPA, SEQ Blood - TSC - unpublished patient has one TSC1 and two TSC2 variants; none of the variants were present in the one parent tested M - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - PubMed: Dabora, 2001 - - Germline - - -TaqI - - DNA DHPLC Blood - TSC ONK761 PubMed: Dabora, 2001 2 affected family members ? - - - - - - - 2 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - PubMed: Dabora, 2001 - - Germline - - -TaqI - - DNA DHPLC Blood - TSC ONK161 PubMed: Dabora, 2001 more than 2 affected family members ? - - - - - - - 3 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T 3112C>T - TSC2_000492 - PubMed: Jones, 2000 - - Germline - - -TaqI - - DNA DHPLC Blood - TSC 249 PubMed: Jones, 2000 - ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T p.Gln1032X - TSC2_000492 variant not detected by SSCA PubMed: Au, 2007 - - Germline - - -TaqI - - DNA SEQ Blood - TSC TS93-011 PubMed: Au, 2007 - ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T p.Gly1032X - TSC2_000492 variant not detected by SSCA PubMed: Au, 2007 - - Germline - - -TaqI - - DNA SEQ Blood - TSC TS94-013 PubMed: Au, 2007 2nd case ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA DHPLC Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 both TSC1 and TSC2 genes tested unpublished - - De novo - 1/3 individuals tested has the variant TaqI- - - DNA SEQ Blood - TSC - unpublished No family history of TSC; both parents tested and variant not found F - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - PubMed: Tsai, 2011 - - Germline - - -TaqI - - DNA SEQ Blood - TSC 26 PubMed: Tsai, 2011 - ? - Taiwan - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - PubMed: You, 2013 - - Germline - - -TaqI - - DNA SEQ Blood - TSC 3 PubMed: You, 2013 6yr old patient; TSC reported as confirmed by diagnostic criteria and histopathological findings M - China - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - PubMed: Sancak, 2005 - - Germline - - -TaqI - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 2 different cases; both diagnosed with definite TSC ? - - - - - - - 4 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 found with TSC2 silent variant c.2031C>T PubMed: Sancak, 2005 - - Germline - - -TaqI - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 diagnosed with definite TSC; patient has TSC2 silent variant c.2031C>T and TSC2 nonsense variant c.3094C>T ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - De novo - - -TaqI - - DNA SEQ Blood - TSC - unpublished no family history of TS; both parents tested and variant not found; referred for ?TS F - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - De novo - - -TaqI - - DNA SEQ Blood - TSC - unpublished both parents tested and variant not found; referred for diagnostic TS testing M - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA SEQ Blood - TSC - unpublished parents not tested F - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - PubMed: Kwiatkowski, 2015 - - Germline - - -TaqI - - DNA SEQ Blood - TSC - PubMed: Kwiatkowski, 2015 5 different patients who have subependymal giant cell astrocytomas associated with tuberous sclerosis complex ? - - - - - - - 5 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T p.R1032* - TSC2_000492 variant reported as mutation; found with TSC2 silent variants c.1593C>T and c.4968C>T; non-contiguous TSC2 deletions reported were not tested in normal tissue from patient so not indicated here; TSC2 MLPA P046-C1 used PubMed: Yang, 2014 - - Somatic - - -TaqI - - DNA MLPA, SEQ Kidney - ? 19A/19B PubMed: Yang, 2014 27 yr old patient diagnosed with definite TSC; renal AML indicated at age 29; patient has TSC2 nonsence c.3094C>T and TSC2 silent variants c.1593C>T and c.4968C>T; non-contiguous TSC2 del reported were not tested in patient normal tissue so not indicated here F - Korea Korean - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T p.R1032* - TSC2_000492 variant reported as mutation; found with TSC2 silent variants c.228C>T, c.4780C>T and c.4968C>T; non-contiguous TSC2 deletions reported were not tested in normal tissue from patient so not indicated here; TSC2 MLPA P046-C1 used PubMed: Yang, 2014 - - Somatic - - -TaqI - - DNA MLPA, SEQ Kidney, Liver - ? 54A/54B PubMed: Yang, 2014 50-52 yr old patient diagnosed with probable TSC; reported as a TSC-AML patient and has TSC2 nonsence c.3094C>T and TSC2 silent variants c.228C>T, c.4780C>T and c.4968C>T F - Korea Korean - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested F - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - De novo - - -TaqI - - DNA DHPLC, SEQ Blood - TSC - unpublished both parents tested negative F - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA DHPLC, SEQ Blood - TSC - unpublished patient reported as a mosaic; No other family member tested M - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - De novo - - -TaqI - - DNA DHPLC, SEQ Blood - TSC - unpublished both parents tested negative for variant M - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA DHPLC, SEQ Blood - TSC - unpublished another family member has same variant F - - - - - - - 2 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - De novo - - -TaqI - - DNA DHPLC, SEQ Blood - TSC - unpublished both parents and a sibling tested negative M - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA SEQ Blood - TSC - unpublished patient with clinical diagnosis of TS; no FH of TS; parents not tested ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - Germline - - -TaqI - - DNA SEQ Blood - TSC - unpublished patient with clinical diagnosis of TS; no FH of TS ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T NC_000016.10:g.2079159C>T, exon23, NP_000539.2:p.Arg1032Ter - TSC2_000492 - unpublished - - Germline - - - - - DNA SEQ-NG-I Blood - TSC - unpublished diagnosed with definite TS; no information on clinical features ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 - unpublished - - De novo - - - - - DNA SEQ Blood - TSC - unpublished both parents tested and variant absent ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T p.Arg1032X - TSC2_000492 variant at MAF of 0.16; found with TSC2 c.3610G>A PubMed: Murphy, 2017 - - Somatic - - - - - DNA SEQ-NG-I Lung - LAM LAM2 PubMed: Murphy, 2017 patient with sporadic lymphangioleiomyomatosis and no TSC; has TSC2 c.3094C>T and TSC2 c.3610G>A in LAM cells; absence of clinical TSC concluded by absence of variants in control smooth muscle tissue of patient ? - (United States) - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T p.R1032* - TSC2_000492 variant (34% MAF) identified by NGS and verified by Sanger sequencing PubMed: Tyburczy, 2015 - - Somatic - - - - - DNA SEQ Blood - TSC Patient 1 PubMed: Tyburczy, 2015 patient diagnosed at 14 yrs old; has one germline and 4 somatic TSC variants; no intellectual disability; has renal findings on USS and CT; had bilateral nephrectomy at 24yrs and 27yrs; the five separate tumours analysed from this patient had five distinct second hit genetic events resulting in biallelic inactivation of TSC2; variants in other genes reported (see paper) F - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic g.2129160C>T g.2079159C>T - - TSC2_000492 found with TSC2 frameshift c.2859del (occurring in alternatively spliced exon) and TSC2 missense c.1624C>G unpublished - - Germline - - - - - DNA SEQ Blood - TSC - unpublished patients has TSC2 missense c.1624C>G, TSC2 frameshift c.2859del (occurring in alternatively spliced exon) and TSC2 nonsense c.3094C>T ? - - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic (dominant) g.2129160C>T - exon 26 - TSC2_000492 - unpublished - - Germline ? - - - - DNA DHPLC, SEQ Blood Diagnostic testing TSC - unpublished affected child not tested M ? - - - - - - 1 Rosemary Ekong
+/. 27 c.3094C>T r.(?) p.(Arg1032*) - - Unknown - pathogenic (dominant) g.2129160C>T g.2079159C>T - - TSC2_000492 variant at 54% MAF; somatic variants in other genes found (not specified) PubMed: Giannikou, 2020 - - Somatic ? - - - - DNA SEQ-NG-I Brain whole exome analysis of Subependymal giant cell astrocytomas, median coverage = 64x TSC SEGA-S18 PubMed: Giannikou, 2020 patient had surgery at 22y; also had treatment prior to surgery F ? - - - - - antiepileptic 1 Rosemary Ekong
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Assessment of functional consequences - Our conclusions on the functional consequences of variants are based on the type of variant, results of in vitro functional tests (doi: 10.1002/humu.21451; doi: 10.1002/humu.22202; doi: 10.1002/humu.23963), population frequencies, output from in silico splice site prediction algorithms, and any clinical/family data available to us. We also have output from protein prediction programs in this database for comparison purposes and they are not considered in our assessment of pathogenicity. PolyPhen Predictions - Note that these results are from PolyPhen-2 and only the HumDiv classification is shown.


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