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.

32 entries on 1 page. Showing entries 1 - 32.
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Effect     
Exon     
AscendingDNA change (cDNA)     
RNA change     
Protein     
P-domain     
Predict-BioInf     
Allele     
Classification method     
Clinical classification     
DNA change (genomic) (hg19)     
DNA change (hg38)     
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ISCN     
DB-ID     
Variant remarks     
Reference     
ClinVar ID     
dbSNP ID     
Origin     
Segregation     
Frequency     
Re-site     
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Methylation     
Template     
Technique     
Tissue     
Remarks     
Disease     
ID_report     
Reference     
Remarks     
Gender     
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Age at death     
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+/. - c.976-15G>A r.(=) p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A TSC2(NM_000548.3):c.976-15G>A - TSC2_000184 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A intron 9 - TSC2_000184 splice variant; found with TSC1 silent variant c.3303G>A and TSC2 missense c.760G>A unpublished - - Germline - - +MscI, BanII- - - DNA SEQ Blood - TSC - unpublished sporadic case; patient has TSC1 silent variant c.3303G>A, TSC2 missense c.760G>A and TSC2 splice variant c.976-15G>A ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A p.A326_splice - TSC2_000184 MAF = 0.81 in AML; 16p LOH seen; normal sample also tested PubMed: Giannikou, 2016 - - Somatic - 0.81 - - - DNA, RNA RT-PCR, SEQ Renal angiomyolipoma - ? P2 PubMed: Giannikou, 2016 patient has diagnosis of LAM ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A exon 9 - TSC2_000184 - PubMed: Au, 2007 - - Germline - - +MscI, BanII- - - DNA SSCA Blood - TSC HOU29-02 PubMed: Au, 2007 - ? - - - - - - - 2 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 - PubMed: Dabora, 2001 - - Germline - - +MscI, BanII- - - DNA DHPLC Blood - TSC ONK171 PubMed: Dabora, 2001 2 affected members ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 - originally Kwiatkowski database - - Germline - - +MscI, BanII- - - DNA ? Blood - TSC - originally Kwiatkowski database reported 4 times in Harvard db; 2/4 reports represented by this entry; other 2/4 accounted for in Dabora, 2001; ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 - PubMed: Dabora, 2001 - - Germline - - +MscI, BanII- - - DNA DHPLC Blood - TSC BG1301 PubMed: Dabora, 2001 - ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.[=, 976_1119del, 976_1031del] p.[Ala326_Gln373del, Met327Hisfs*5] Hamartin binding domain - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 2 aberrantly spliced transcripts; (1) in-frame del of entire ex11, (2) first 56bp of ex11 del; stop codon after 6 novel aa in ex11; no gDNA deletion seen; variant not in 50 unaffecteds screened by RFLP PubMed: Mayer, 1999, PubMed: Mayer, 2000 - - Germline - - +MscI, BanII- - - DNA, RNA PTT Blood - TSC T10 PubMed: Mayer, 1999, PubMed: Mayer, 2000 patient is heterozygous for TSC2 1578C>T which creates TaaI site ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.[=, 976_1119del, 976_1031del] p.[Ala326_Gln373del, Met327Hisfs*5] Hamartin binding domain - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 2 aberrantly spliced transcripts; (1) in-frame del of entire ex11, (2) first 56bp of ex11 del; stop codon after 6 novel aa in ex11; no gDNA deletion seen; variant not in 50 unaffecteds screened by RFLP PubMed: Mayer, 1999, PubMed: Mayer, 2000 - - Germline - - +MscI, BanII- - - DNA, RNA PTT Blood - TSC T64 PubMed: Mayer, 1999, PubMed: Mayer, 2000 different patient ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 reported as a splice variant (see Mayer et al, 2000) unpublished - - De novo - - +MscI, BanII- - - DNA SEQ Blood - TSC - unpublished - F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A 994-15G>A, intron 9 - TSC2_000184 - unpublished - - Germline - - +MscI, BanII- - - DNA DHPLC Blood - TSC - unpublished - F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A intron 9 - TSC2_000184 splice variant; found with TSC2 missense c.3434C>T unpublished - - Germline - - +MscI, BanII- - - DNA SEQ Blood - TSC - unpublished patient has TSC2 splice variant c.976-15G>A and TSC2 missense c.3434C>T ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A intron 9 - TSC2_000184 splice variant unpublished - - Germline - - +MscI, BanII- - - DNA SEQ Blood - TSC - unpublished 4 different patients; 2/4 indicated as sporadic cases ? - - - - - - - 4 Rosemary Ekong
?/. 10i c.976-15G>A r.spl p.(=) - - Unknown - VUS g.2110656G>A g.2060655G>A c.976-15G>A, intron 9 - TSC2_000184 splice variant seen with TSC2 c.1120-93T>C; no gDNA variants in ex 10,11 & 12; ex11 deleted in cDNA from lymphoblastoid cell line of patient; no MLPA variants seen with kits P124 (TSC1) & P046 (TSC2) unpublished - - Germline - - +MscI, BanII- - - DNA, RNA MLPA, SEQ Blood - TSC - unpublished TS affected; probably sporadic case; no clinical information M - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - Germline - - +MscI, BanII- - - DNA SEQ Blood - TSC - unpublished 2 affected in 2 generations but only proband tested ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - Germline - - +MscI, BanII- - - DNA SEQ Blood - TSC - unpublished parents not tested ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - De novo - - +MscI, BanII- - - DNA SEQ Blood - TSC - unpublished 1 affected in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - Germline - - +MscI, BanII- - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - De novo - - +MscI, BanII- - - DNA DHPLC, SEQ Blood - TSC - unpublished variant is absent in both parents and 2 siblings tested F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - De novo - - +MscI, BanII- - - DNA DHPLC, SEQ Amniocytes - TSC - unpublished prenatally diagnosed cardiac rhabdomyoma in index; both parents and a sibling tested negative ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - Germline - - +MscI, BanII- - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested M - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant unpublished - - Germline - - +MscI, BanII- - - DNA DHPLC, SEQ Blood - TSC - unpublished variant absent in the one parent tested F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant found at 34% MAF; NGS read depth >500x PubMed: Tyburczy, 2015 - - De novo - 34% +MscI, BanII- - - DNA SEQ-NG-I, SEQ Saliva - TSC P8 PubMed: Tyburczy, 2015 7 year old TSC patient with NMI status (previous Sanger SEQ and TSC2 MLPA negative); reported as mosaic (34% MAF); no FH of TS; both parents tested and variant not found F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant in AF (8.9% MAF) + normal skin (0.63% MAF); seen with TSC2 nonsense c.1372C>T (7.3% MAF in AF) + TSC2 missense c.4490C>T (1.3% MAF in AF + normal skin MAF 0.61%); freq in blood & saliva similar to normal controls; NGS read depth >500x PubMed: Tyburczy, 2015; PubMed: Giannikou, 2019 - - De novo - - +MscI, BanII- - - DNA SEQ-NG-I Angiofibroma, normal skin amplicon NGS TSC P14 PubMed: Tyburczy, 2015; PubMed: Giannikou, 2019 23 year old TSC patient with NMI status (previous Sanger SEQ and TSC2 MLPA negative); no FH of TS; has TSC2 splice variant c.976-15G>A, TSC2 nonsense c.1372C>T and TSC2 missense c.4490C>T in facial angiofibroma; both parents tested and variants not found M - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant detected at 50% freq; NGS read depth >500x PubMed: Tyburczy, 2015 - - De novo - 50% +MscI, BanII- - - DNA SEQ-NG-I Blood, saliva - TSC P18 PubMed: Tyburczy, 2015 2 year old TSC patient with NMI status (previous Sanger SEQ and TSC2 MLPA negative); no FH of TS; both parents tested and variant not found F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant detected at 50% freq; NGS read depth >500x PubMed: Tyburczy, 2015 - - De novo - 50% +MscI, BanII- - - DNA SEQ-NG-I Blood - TSC P37 PubMed: Tyburczy, 2015 7 year old TSC patient with NMI status (previous Sanger SEQ and TSC2 MLPA negative); no FH of TS; both parents tested and variant not found F - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.? - - Unknown - pathogenic g.2110656G>A g.2060655G>A p.A326_splice - TSC2_000184 splice variant; found with TSC2 nonsense c.3310C>T; MAF =0.23; no normal sample available for comparison PubMed: Giannikou, 2016 - - Somatic - 0.23 - - - DNA SEQ-NG Renal angiomyolipoma WES TSC P10 PubMed: Giannikou, 2016 TSC2 splice variant c.976-15G>A and TSC2 nonsense c.3310C>T found in the same sample (2 hit) ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 predicted splice variant unpublished - - De novo - - - - - DNA SEQ Blood - TSC - unpublished both parents tested and variant absent ? - - - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant reported as a missense; variant identified in NGS and verified by Sanger sequencing PubMed: Wang, 2017 - - Germline - - - - - DNA SEQ-NG, SEQ Blood - TSC 9 PubMed: Wang, 2017 5 yr old patient with clinical TSC F - China - - - - - 1 Rosemary Ekong
+/. 10i c.976-15G>A r.spl p.(=) - - Unknown - pathogenic g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant PubMed: Rosset, 2017 - - Germline - - - - - DNA SEQ-NG-IT Blood - TSC 18 PubMed: Rosset, 2017 - ? - Brazil - - - - - 1 Rosemary Ekong
+/+ 10i c.976-15G>A r.[976_1119del;976_1031del];[=] p.[Ala326_Gln373del;Met327Hisfs*5] - likely to affect splicing Unknown - pathogenic (dominant) g.2110656G>A g.2060655G>A - - TSC2_000184 splice variant; evidence of abnormal transcripts reported in mRNA - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. 10i c.976-15G>A r.spl p.? - - Unknown ACMG pathogenic (dominant) g.2110656G>A g.2060655G>A - - TSC2_000184 - PubMed: Ye, 2022 - - Germline - - - - - DNA SEQ-NG Blood - TSC - PubMed: Ye, 2022 - F - - - - - - - 1 Zimeng Ye
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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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