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.

31 entries on 1 page. Showing entries 1 - 31.
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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)     

Published as     

ISCN     

DB-ID     

Variant remarks     

Reference     

ClinVar ID     

dbSNP ID     

Origin     

Segregation     

Frequency     

Re-site     

VIP     

Methylation     

Template     

Technique     

Tissue     

Remarks     

Disease     

ID_report     

Reference     

Remarks     

Gender     

Consanguinity     

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Population     

Age at death     

VIP     

Data_av     

Treatment     

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Owner     
+/. - c.4544_4547del r.(?) p.(Asn1515SerfsTer60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del TSC2(NM_000548.3):c.4544_4547delACAA (p.N1515Sfs*60) - TSC2_000590 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic (dominant) g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547delACAA - TSC2_000590 4bp deletion of ACAA originally Kwiatkowski database - - Germline - - - - - DNA SEQ Blood - TSC - originally Kwiatkowski database variant reported 3 times in Harvard db; 2/3 reported represented by this entry; the 3rd report is represented by case in Dabora, 2001 ? - - - - - - - 2 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4559 del 4bp - TSC2_000590 4bp deletion of ACAA (according to HGVS nomenclature) reported as deletion of CAAA PubMed: Maheshwar, 1997, PubMed: Jones, 1999 - - Germline - - - - - DNA SSCA Blood - TSC 147 PubMed: Maheshwar, 1997, PubMed: Jones, 1999 seen in 1/173 cases; same patient reported in both papers by Jones, 1999 ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547delACAA - TSC2_000590 4bp deletion of ACAA; variant reported 3 times in Harvard db PubMed: Dabora, 2001 - - Germline - - - - - DNA DHPLC Blood - TSC BG1901 PubMed: Dabora, 2001 - ? - - - - - - - 3 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4562_4565delACAA - TSC2_000590 4bp deletion of ACAA PubMed: Langkau, 2002 - - Germline - - - - - DNA SSCA Blood - TSC T2324P1 PubMed: Langkau, 2002 - ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA; variant reported not seen in 100 control chromosomes PubMed: Ali, 2005 - - Germline - - - - - DNA SSCA Blood - TSC TS-10 PubMed: Ali, 2005 patient also has 3 TSC1 variants reported as c.663+35T>C; c.965T>C and c.2829C>T ? - India - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4541_4544delCAAA - TSC2_000590 4bp deletion of ACAA (according to HGVS nomenclature) reported as deletion of CAAA PubMed: Hung, 2006 - - Germline - - - - - DNA DHPLC Blood - TSC 77 PubMed: Hung, 2006 - ? - Taiwan Taiwanese - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4562-4565delACAA - TSC2_000590 4bp deletion of ACAA; found with TSC2 missense c.1387A>G, TSC2 c.5161-10A>C and TSC2 c.5161-28_5161-25del unpublished - - Germline - - - - - DNA DHPLC Blood - TSC - unpublished patient has TSC2 missense c.1387A>G, TSC2 frameshift c.4544_4547del, TSC2 c.5161-10A>C and TSC2 c.5161-28_5161-25del; different patient to that in Jones, 1999 ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547delACAA - TSC2_000590 4bp deletion of ACAA PubMed: Au, 2007 - - Germline - - - - - DNA SEQ Blood - TSC TS00-157 PubMed: Au, 2007 another case ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4475_4478del, Ser1492fsX1574 (without exon 31); c.4544_4547delACAA - TSC2_000590 4bp deletion of ACAA PubMed: Au, 1998, PubMed: Au, 2007 - - Germline - - - - - DNA SSCA Blood - TSC TS93-020 PubMed: Au, 1998, PubMed: Au, 2007 - ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del del4475N4, N1492FS1551X (without exon 31) - TSC2_000590 4bp deletion of ACAA PubMed: Yamashita, 2000 - - Germline - - - - - DNA SSCA Blood - TSC 13 PubMed: Yamashita, 2000 patient also has 2 silent TSC1 variants c.972G>A and c.1371T>C ? - - Japanese - - - - 1 Rosemary Ekong
?/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - VUS g.2135002_2135005del g.2085001_2085004del c.4541-4544delCAAA - TSC2_000590 4bp deletion of ACAA (according to HGVS nomenclature) reported as deletion of CAAA; reported that numbering of the base position uses A in the starting ATG as +1 PubMed: Li, 2011 - - Germline - - - - - DNA DHPLC Blood - TSC - PubMed: Li, 2011 TS affected patient M - China Han, Hunan province - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547delACAA - TSC2_000590 4bp deletion of ACAA unpublished - - De novo - - - - - DNA SEQ Blood - TSC - unpublished TS affected; both unaffected parents and another family member tested and they do not have the variant F - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547del4 - TSC2_000590 4bp deletion of ACAA PubMed: Sancak, 2005 - - Germline - - - - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 different patient; diagnosed with definite TSC ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547del4 - TSC2_000590 4bp deletion of ACAA unpublished - - Germline - - - - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547del4 - TSC2_000590 4bp deletion of ACAA; found with TSC2 intronic variant c.4006-8C>T PubMed: Sancak, 2005 - - Germline - - - - - DNA SEQ Blood - TSC - PubMed: Sancak, 2005 diagnosed with definite TSC; patient has TSC2 intronic variant c.4006-8C>T and TSC2 frameshift c.4544_4547del ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del c.4544_4547delACAA - TSC2_000590 4bp deletion of ACAA unpublished - - De novo - - - - - DNA SEQ Blood - TSC - unpublished sibling has LD; both parents and sibling tested and variant not found; referred for diagnostic TS testing M - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA PubMed: Kwiatkowski, 2015 - - Germline - - - - - DNA SEQ Blood - TSC - PubMed: Kwiatkowski, 2015 2 different patients who have subependymal giant cell astrocytomas associated with tuberous sclerosis complex ? - - - - - - - 2 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA PubMed: Kwiatkowski, 2015 - - Germline - - - - - DNA SEQ Blood - TSC - PubMed: Kwiatkowski, 2015 patient has TSC with AML ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4544_4547delACAA - TSC2_000590 4bp deletion of ACAA PubMed: Peron 2018 - - De novo - - - - - DNA DHPLC, SEQ Blood - TSC P60 PubMed: Peron 2018 1 affected in 1 generation; parents tested and variant not found (Migone, personal communication) ? - Italy - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4544_4547delACAA - TSC2_000590 4bp deletion of ACAA unpublished - - De novo - - - - - DNA SEQ Blood - TSC - unpublished 1 affected in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4544_4547delACAA - TSC2_000590 4bp deletion of ACAA unpublished - - De novo - - - - - DNA SEQ Blood - TSC - unpublished 1 affected in 1 generation; parents tested and variant not found ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 1515-1516delfs - TSC2_000590 4bp deletion of ACAA; found with TSC2 silent variant c.3126G>C and TSC2 intronic variant c.3883+8C>G; entire TSC1 and TSC2 genes sequenced; TSC MLPA done unpublished - - Germline - - - - - DNA SEQ, MLPA Blood - TSC - unpublished TS affected patient with TSC2 silent variant c.3126G>C, TSC2 intronic variant c.3883+8C>G and TSC2 frameshift c.4544_4547del M - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA unpublished - - Germline - - - - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested F - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA unpublished - - Germline - - - - - DNA DHPLC, SEQ Blood - TSC - unpublished two relatives tested negative F - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA unpublished - - Germline - - - - - DNA DHPLC, SEQ Blood - TSC - unpublished No other family member tested F - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic g.2135002_2135005del g.2085001_2085004del 4544-4547 4pb deletion - TSC2_000590 4bp deletion of ACAA unpublished - - Germline - - - - - DNA SEQ Blood - TSC - unpublished patient with clinical diagnosis of TS; no FH of TS ? - - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Paternal (confirmed) - pathogenic g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 4bp deletion of ACAA; found with TSC2 missense c.1946T>C unpublished - - Germline - - - - - DNA DHPLC, SEQ Blood - TSC - unpublished proband has TSC2 missense c.1946T>C and TSC2 frameshift c.4544_4547del; 2 affected siblings and one parent reported as unaffected were tested; all have both variants that are present in the proband F - - - - - - - 4 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown - pathogenic (dominant) g.2135002_2135005del - exon 34 - TSC2_000590 4bp deletion of ACAA unpublished - - Germline ? - - - - DNA DHPLC, SEQ Blood Diagnostic testing TSC - unpublished No other family member tested F ? - - - - - - 1 Rosemary Ekong
+/. 35 c.4544_4547del r.(?) p.(Asn1515Serfs*60) - - Unknown ACMG pathogenic (dominant) g.2135002_2135005del g.2085001_2085004del - - TSC2_000590 delACAA PubMed: Milon 2024; PubMed: Milon 2024 - - Germline - - - - - DNA SEQ, SEQ-NG-IT Amniocytes - TSC - PubMed: Milon 2024; PubMed: Milon 2024 no family history of TSC; prenatally diagnosed cardiac rhabdomyoma (≥2); one parent tested negative - - - - - - - - 1 Sarah Prestwich
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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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