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.

14147 entries on 142 pages. Showing entries 1 - 100.
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+/. 15i_22i c.(1599+1_1600-1)_(2545+1_2546-1)[3] r.? p.? - - Unknown - pathogenic (dominant) g.(2114429_2115519)_(2124391_2125799)[3] g.(2064428_2065518)_(2074390_2075798)[3] triplication of exons 15-21 inclusive - TSC2_001632 triplication of exons 16-22 inclusive resulting in 4 alleles (heterozygous triplication); signal ratios for probes in exons 16-22 reported as 2x above control levels indicating 4 alleles; reported as triplication of exons 15-21 (based on 41 exons) unpublished - - De novo ? 1/4 individuals tested has the variant - - - DNA MCA, SEQ Blood - - - unpublished patient with MRI changes reported to be consistent with TSC; both parents and a sibling are apparently unaffected and all 3 tested negative for the variant F ? - - - - - - 1 Rosemary Ekong
+/. _1_42_ c.-106_*102{0} r.0? p.0? - - Unknown ACMG pathogenic (dominant) g.2088737_2264526del - NC_000016.9: g.2088737_2264526del - TSC2_001689 175790bp multigene deletion; entire TSC2 deleted (ex 1-42) + 9254bp upstream of TSC2 and 125814bp downstream of TSC2; upstream deletion involves NTHL1 gene and downstream deletion involves entire PKD1, RAB26, TRAF7, CASKIN1, MLST8 and BRICD5 genes PubMed: Ogorek, 2020 - - Germline ? - - - - DNA MLPA, SEQ, SEQ-NG-I Blood Targeted massive parallel sequencing, mean target coverage of 327× to 1614× (median 716×), MLPA TSC2 P337-B1 probe mix used, Genome sequencing also done, deletion confirmed by PCR across breakpoints, gel electrophoresis and Sanger sequencing TSC 01-004 PubMed: Ogorek, 2020 infant with drug resistant epilepsy; no history of TSC in the family; patient had first subclinical/clinical seizures at day 85 during the study M ? - - - - - - 1 Rosemary Ekong
+/+ _1_42_ c.-106_*102{0} r.0? p.0? - - Unknown - pathogenic (dominant) g.2097990_2138713{0} g.2047989_2088712{0} - - TSC2_001689 175790bp multigene deletion; entire TSC2 deleted (ex 1-42) + 9254bp upstream of TSC2 and 125814bp downstream of TSC2; upstream deletion involves NTHL1 gene and downstream deletion involves entire PKD1, RAB26, TRAF7, CASKIN1, MLST8 and BRICD5 genes - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_12i c.-106_1258-159{0} r.? p.? - - Unknown ACMG pathogenic (dominant) g.2095658_2112339del g.2045657_2062338del NC_000016.9: g.2095658_2112339del - TSC2_001692 16682bp deletion; TSC2 exons 1-12 deleted + 2333bp upstream of TSC2; deletion ends in TSC2 intron 12; upstream deletion involves NTHL1 gene; variant at 7% MAF PubMed: Ogorek, 2020 - - Unknown ? - - - - DNA MLPA, SEQ, SEQ-NG-I Blood Targeted massive parallel sequencing, mean target coverage of 327× to 1614× (median 716×), MLPA TSC2 P337-B1 probe mix used, Genome sequencing also done, deletion confirmed by PCR across breakpoints, gel electrophoresis and Sanger sequencing TSC 01-057 PubMed: Ogorek, 2020 infant (mosaic) with drug resistant epilepsy; no history of TSC in the family; patient had first subclinical/clinical seizures at day 118 during the study M ? - - - - - - 1 Rosemary Ekong
+/+ _1_12i c.-106_1258-159{0} r.? p.? - - Unknown - pathogenic (dominant) g.2095658_2112339del g.2045657_2062338del - - TSC2_001692 16682bp deletion; TSC2 exons 1-12 deleted + 2333bp upstream of TSC2; deletion ends in TSC2 intron 12; upstream deletion involves NTHL1 gene - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/+ _1_16i c.-106_1716+1900{0} r.? p.? - - Unknown - pathogenic (dominant) g.2097990_2117536{0} g.2047989_2067535{0} - - TSC2_001690 71010bp multigene deletion; TSC2 exons 1-16 deleted + 51464bp upstream of TSC2; deletion ends in TSC2 intron 16; upstream deletion involves SLC9A3R2, NPW and NTHL1 genes - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. 37_38 c.4663_4989{0} r.(?) p.(Ser1555_Lys1663del) - - Unknown ACMG pathogenic (dominant) g.2136194_2136872{0} g.2086193_2086871{0} exon 37‐38 del - TSC2_001940 exons 37-38 deleted; breakpoints verified by long-range PCR; variant found at different VAFs; mosaic PubMed: Ye 2022 - - Somatic - - - - - DNA PCRlr, SEQ-NG-I Blood, Saliva, Buccal Breakpoints verified by long-range PCR TSC CHN‐11 PubMed: Ye 2022 patient reported to have 5 major TSC features (not specified) ? - - - - - - - 1 Rosemary Ekong
+?/+? 37_38 c.4663_4989{0} r.(?) p.(Ser1555_Lys1663del) GAP domain - Unknown - likely pathogenic (dominant) g.2136194_2136872{0} g.2086193_2086871{0} - - TSC2_001940 exons 37-38 deleted; breakpoints verified by long-range PCR - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. 38i_42_ c.4990-299_*102{0} r.? p.? - - Unknown ACMG pathogenic (dominant) g.2137565_2139331del g.2087564_2089330del NC_000016.9: g.2137565_2139331del - TSC2_001694 1767bp deletion; exons 39-42 deleted + 619bp downstream of TSC2, which includes part of PKD1 gene; deletion starts in TSC2 intron 38; variant at 32% MAF PubMed: Ogorek, 2020 - - Unknown ? - - - - DNA MLPA, SEQ, SEQ-NG-I Blood Targeted massive parallel sequencing, mean target coverage of 327× to 1614× (median 716×), MLPA TSC2 P337-B1 probe mix used, Genome sequencing also done, deletion confirmed by PCR across breakpoints, gel electrophoresis and Sanger sequencing TSC 01-058 PubMed: Ogorek, 2020 infant; no history of TSC in the family; patient had first subclinical/clinical seizures at day 260 during the study M ? - - - - - - 1 Rosemary Ekong
+/+ 38i_42_ c.4990-299_*102{0} r.? p.? - - Unknown - pathogenic (dominant) g.2137565_2139331del g.2087564_2089330del - - TSC2_001694 1767bp deletion; exons 39-42 deleted + 619bp downstream of TSC2, which includes part of PKD1 gene; deletion starts in TSC2 intron 38 - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. 39i_42_ c.5068+11_*102{0} r.? p.? - - Unknown ACMG pathogenic (dominant) g.2137951_2138954del g.2087950_2088953del NC_000016.9: g.2137951_2138954del, exon 39-41 deleted - TSC2_001693 1004bp deletion; exons 40-42 deleted + 242bp downstream of TSC2, which includes part of PKD1 gene; deletion starts in TSC2 intron 39; variant at 11% MAF PubMed: Ogorek, 2020 - - Unknown ? - - - - DNA MLPA, SEQ, SEQ-NG-I Blood Targeted massive parallel sequencing, mean target coverage of 327× to 1614× (median 716×), MLPA TSC2 P337-B1 probe mix used, Genome sequencing also done, deletion confirmed by PCR across breakpoints, gel electrophoresis and Sanger sequencing TSC 01-053 PubMed: Ogorek, 2020 infant is a mosaic; patient did not have subclinical or clinical seizures during the study F ? - - - - - - 1 Rosemary Ekong
+/+ 39i_42_ c.5068+11_*102{0} r.? p.? - - Unknown - pathogenic (dominant) g.2137951_2138954del g.2087950_2088953del - - TSC2_001693 1004bp deletion; exons 40-42 deleted + 242bp downstream of TSC2, which includes part of PKD1 gene; deletion starts in TSC2 intron 39 - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1 c.(?_-106)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)del g.(?_2047989)del deletion 5'UTR - TSC2_003645 deletion of region 5' of TSC2 gene; breakpoints undetermined; TSC2 MLPA kits P046-C1-1011 and P337-A2-0510 used Journal: 10.4236/ajmb.2014.43018 - - Germline - - - - - DNA MLPA Blood - TSC 890819 Journal: 10.4236/ajmb.2014.43018 patient with clinical diagnosis of TSC ? - Iran - - - - - 1 Rosemary Ekong
?/? _1 c.(?_-106)del r.? p.? - - Unknown - VUS g.(?_2097990)del g.(?_2047989)del - - TSC2_003645 deletion of region 5' of TSC2 gene; breakpoints undetermined - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-4447C>G r.(?) p.(=) - - Unknown - likely benign g.2093649C>G g.2043648C>G NTHL1(NM_002528.7):c.604G>C (p.E202Q) - NTHL1_000017 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-4426C>T r.(?) p.(=) - - Unknown - likely benign g.2093670C>T g.2043669C>T NTHL1(NM_002528.7):c.583G>A (p.D195N) - NTHL1_000189 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-4398G>A r.(?) p.(=) - - Unknown - likely benign g.2093698G>A - NTHL1(NM_002528.7):c.555C>T (p.S185=) - NTHL1_000393 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-4368C>T r.(?) p.(=) - - Unknown - pathogenic g.2093728C>T - NTHL1(NM_002528.7):c.526-1G>A - NTHL1_000228 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-4359_-4358del r.(?) p.(=) - - Unknown - likely benign g.2093737_2093738del - NTHL1(NM_002528.7):c.526-11_526-10delCT - NTHL1_000232 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-4359_-4358del r.(?) p.(=) - - Unknown - VUS g.2093737_2093738del - NTHL1(NM_002528.7):c.526-11_526-10delCT - NTHL1_000232 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-4353G>C r.(?) p.(=) - - Unknown - likely benign g.2093743G>C g.2043742G>C NTHL1(NM_002528.7):c.526-16C>G - NTHL1_000004 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-3494C>T r.(?) p.(=) - - Unknown - likely benign g.2094602C>T - NTHL1(NM_002528.7):c.525+29G>A - NTHL1_000383 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-3443A>G r.(?) p.(=) - - Unknown - likely benign g.2094653A>G g.2044652A>G NTHL1(NM_001318194.1):c.173T>C (p.(Ile58Thr)), NTHL1(NM_002528.7):c.503T>C (p.I168T) - NTHL1_000012 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-3443A>G r.(?) p.(=) - - Unknown - VUS g.2094653A>G g.2044652A>G NTHL1(NM_001318194.1):c.173T>C (p.(Ile58Thr)), NTHL1(NM_002528.7):c.503T>C (p.I168T) - NTHL1_000012 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-3443A>G r.(?) p.(=) - - Unknown - VUS g.2094653A>G g.2044652A>G NTHL1(NM_001318194.1):c.173T>C (p.(Ile58Thr)), NTHL1(NM_002528.7):c.503T>C (p.I168T) - NTHL1_000012 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-3443A>G r.(?) p.(=) - - Unknown - VUS g.2094653A>G g.2044652A>G NTHL1(NM_001318194.1):c.173T>C (p.(Ile58Thr)), NTHL1(NM_002528.7):c.503T>C (p.I168T) - NTHL1_000012 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-3443A>G r.(?) p.(=) - - Unknown - likely benign g.2094653A>G - NTHL1(NM_001318194.1):c.173T>C (p.(Ile58Thr)), NTHL1(NM_002528.7):c.503T>C (p.I168T) - NTHL1_000012 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-3416G>A r.(?) p.(=) - - Unknown - VUS g.2094680G>A g.2044679G>A NTHL1(NM_002528.5):c.500C>T (p.(Thr167Ile)) - NTHL1_000005 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-3374C>T r.(?) p.(=) - - Unknown - likely benign g.2094722C>T g.2044721C>T NTHL1(NM_002528.7):c.434G>A (p.R145Q) - NTHL1_000208 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_3i c.-2600_226-765delinsN[273] r.(?) p.? - - Unknown - pathogenic g.2095496_2102578delinsN[273] g.2045495_2052577delinsN[273] c.-2600_226-765del6561ins273 - TSC2_003588 del 7083bp and ins 273bp (NG_005895.1:g.1190_8272delins273); starts upstream of untranslated ex 1, includes promoter region (Kobayashi et al, 1997; Mamm Genome. 1997, 8:554-8), ending in intron 3; inserted seq available on request unpublished - - Germline - - - - - DNA SEQ Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/+ _1_3i c.-2600_226-765delinsN[273] r.? p.? - - Unknown - pathogenic (dominant) g.2095496_2102578delinsN[273] g.2045495_2052577delinsN[273] - - TSC2_003588 exons 1-3 deleted; 7083bp deletion and 273bp insertion (NG_005895.1:g.1190_8272delins273); starts upstream of untranslated ex 1, includes promoter region (Kobayashi et al, 1997; Mamm Genome. 1997, 8:554-8), ending in intron 3 - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-1894A>G r.(?) p.(=) - - Unknown - VUS g.2096202A>G g.2046201A>G NTHL1(NM_002528.7):c.281T>C (p.M94T) - NTHL1_000023 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-1887G>A r.(?) p.(=) - - Unknown - VUS g.2096209G>A g.2046208G>A NTHL1(NM_002528.7):c.274C>T (p.R92C) - NTHL1_000006 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-1887G>A r.(?) p.(=) - - Unknown - VUS g.2096209G>A g.2046208G>A NTHL1(NM_002528.7):c.274C>T (p.R92C) - NTHL1_000006 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-1887G>A r.(?) p.(=) - - Unknown - likely benign g.2096209G>A g.2046208G>A NTHL1(NM_002528.7):c.274C>T (p.R92C) - NTHL1_000006 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-1887G>A r.(?) p.(=) - - Unknown - VUS g.2096209G>A - NTHL1(NM_002528.7):c.274C>T (p.R92C) - NTHL1_000006 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-1857G>A r.(?) p.(=) - - Unknown - pathogenic g.2096239G>A g.2046238G>A NTHL1(NM_001318193.1):c.268C>T (p.(Gln90Ter)), NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-1857G>A r.(?) p.(=) - - Unknown - pathogenic g.2096239G>A g.2046238G>A NTHL1(NM_001318193.1):c.268C>T (p.(Gln90Ter)), NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-1857G>A r.(?) p.(=) - - Unknown - pathogenic g.2096239G>A g.2046238G>A NTHL1(NM_001318193.1):c.268C>T (p.(Gln90Ter)), NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-1857G>A r.(?) p.(=) - - Unknown - pathogenic g.2096239G>A g.2046238G>A NTHL1(NM_001318193.1):c.268C>T (p.(Gln90Ter)), NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-1857G>A r.(?) p.(=) - - Unknown - pathogenic g.2096239G>A - NTHL1(NM_001318193.1):c.268C>T (p.(Gln90Ter)), NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-1857G>A r.(?) p.(=) - - Unknown - pathogenic g.2096239G>A - NTHL1(NM_001318193.1):c.268C>T (p.(Gln90Ter)), NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-1857G>A r.(?) p.(=) - - Unknown - pathogenic g.2096239G>A - NTHL1(NM_001318193.1):c.268C>T (p.(Gln90Ter)), NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-1765C>T r.(?) p.(=) - - Unknown - likely benign g.2096331C>T g.2046330C>T NTHL1(NM_002528.5):c.176G>A (p.(Arg59Gln)) - NTHL1_000007 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-1763C>T r.(?) p.(=) - - Unknown - likely benign g.2096333C>T - NTHL1(NM_002528.7):c.150G>A (p.P50=) - NTHL1_000213 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-1759C>T r.(?) p.(=) - - Unknown - VUS g.2096337C>T - NTHL1(NM_002528.5):c.170G>A (p.(Arg57His)) - NTHL1_000261 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-1754C>T r.(?) p.(=) - - Unknown - likely benign g.2096342C>T g.2046341C>T NTHL1(NM_002528.7):c.141G>A (p.V47=) - NTHL1_000024 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-1751G>A r.(?) p.(=) - - Unknown - likely benign g.2096345G>A g.2046344G>A NTHL1(NM_002528.7):c.138C>T (p.P46=) - NTHL1_000025 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-1713C>T r.(?) p.(=) - - Unknown - VUS g.2096383C>T - NTHL1(NM_001318193.1):c.140-16G>A (p.(=)) - NTHL1_000191 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.-1712G>A r.(?) p.(=) - - Unknown - benign g.2096384G>A g.2046383G>A NTHL1(NM_002528.7):c.116-17C>T - NTHL1_000008 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.-1712G>A r.(?) p.(=) - - Unknown - benign g.2096384G>A - NTHL1(NM_002528.7):c.116-17C>T - NTHL1_000008 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.-1712G>A r.(?) p.(=) - - Unknown - benign g.2096384G>A - NTHL1(NM_002528.7):c.116-17C>T - NTHL1_000008 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_1 c.-827_-84del r.(?) p.? - - Unknown - pathogenic g.2097269_2098012del g.2047268_2048011del c.-106-722_-85del; 744nt del includes part exon 1; sent seq in this nomenclature = c.-106-723_-86del - TSC2_003410 744nt del involving 23nt at 5' end of untranslated exon 1 and upstream sequence; HGVS compliant description = NG_005895.1:g.2963_3706del (considers most 3' nts as affected); variant at 50% freq; NGS read depth >500x PubMed: Tyburczy, 2015 - - De novo - - - - - DNA SEQ-NG-I Saliva - TSC P33 PubMed: Tyburczy, 2015 8 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 M - - - - - - - 1 Rosemary Ekong
?/? _1_1 c.-827_-84del r.(?) p.? - - Unknown - VUS g.2097269_2098012del g.2047268_2048011del - - TSC2_003410 744nt deletion involving 23nt at 5' end of untranslated exon 1 and upstream sequence; involves the core promoter region (Kobayashi et al, 1997. DOI: 10.1007/s003359900502); HGVS compliant description = NG_005895.1:g.2963_3706del - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.-403C>T r.(?) p.(=) - - Unknown - benign g.2097693C>T g.2047692C>T NTHL1(NM_002528.7):c.115+17G>A - NTHL1_000255 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-387C>T r.(?) p.(=) - - Unknown - pathogenic g.2097709C>T - NTHL1(NM_002528.7):c.115+1G>A - NTHL1_000230 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.-387C>T r.(?) p.(=) - - Unknown - pathogenic g.2097709C>T - NTHL1(NM_002528.7):c.115+1G>A - NTHL1_000230 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.-384G>A r.(?) p.(=) - - Unknown - benign g.2097712G>A g.2047711G>A NTHL1(NM_002528.7):c.113C>T (p.A38V) - NTHL1_000231 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-315A>G r.(?) p.(=) - - Unknown - likely benign g.2097781A>G - NTHL1(NM_002528.7):c.44T>C (p.L15P) - NTHL1_000262 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-300G>C r.(?) p.(=) - - Unknown - likely benign g.2097796G>C g.2047795G>C NTHL1(NM_002528.7):c.29C>G (p.T10S) - NTHL1_000256 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-270C>T r.(?) p.(=) - - Unknown - VUS g.2097826C>T - NTHL1(NM_001318193.1):c.23G>A (p.(Gly8Asp)) - NTHL1_000402 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-267G>C r.(?) p.(=) - - Unknown - likely benign g.2097829G>C - - - NTHL1_000394 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.-256A>C r.(?) p.(=) - - Unknown - VUS g.2097840A>C - TSC2(NM_000548.5):c.-256A>C - NTHL1_000308 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.-235T>C r.(?) p.(=) - - Unknown - likely benign g.2097861T>C g.2047860T>C NTHL1(NM_002528.7):c.-37A>G - NTHL1_000257 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. _1 c.-115G>T r.(?) p.(=) - - Unknown - benign g.2097981G>T g.2047980G>T -636G>T - TSC2_002760 cDNA sequenced in proband and sibling; balanced allelic expression found; variant is 9 bases 5' of the untranslated exon 1 unpublished - - Germline - - MmeI+ - - DNA, RNA SEQ Blood - TSC - unpublished variant seen in proband and a healthy sibling; reported that proband does not fulfil TSC diagnostic criteria and no definite disease-causing variant seen in proband; the one parent tested does not have this variant ? - - - - - - - 2 Rosemary Ekong
-?/-? _1 c.-115G>T r.(?) p.(=) - - Unknown - likely benign g.2097981G>T g.2047980G>T - - TSC2_002760 variant is 9 bases 5' of the untranslated exon 1 and is between 2 cETS binding sites in the core promoter region (Kobayashi et al, 1997. DOI: 10.1007/s003359900502) - - - SUMMARY record - - MmeI+ - - - - - - - - - - - - - - - - - - - -
+/. _1_2i c.(?_-106)_(138+1_139-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_( 2098755_ 2100400)del - NM_000548.3:c.(?_-29) _(225_?)del - TSC2_002459 exons 1-2 deleted; ~25% mosaic; breakpoints not determined; reported that variant description is based on 42 exons which includes the noncoding exon 1 PubMed: Byers 2018 - - Germline ? - - - - DNA MLPA Blood, Skin cultured skin fibroblasts from hypopigmented macule and normal skin tested, Array-CGH from buccal swab normal, Sanger SEQ of blood DNA negative TSC - PubMed: Byers 2018 patient with germline mosaicism and multiple TSC features; at 4yrs old speech was at the 12-month level - Dx of ASD; brain MRI at 3yrs 2mths showed multiple TSC features; renal USS and cardiac ECG normal; mother, father and a paternal half-brother examined and no signs of TSC reported M ? United States - - - - - 1 Rosemary Ekong
+/+ _1_2i c.(?_-106)_(138+1_139-1)del r.0? p.0? - - Unknown - likely pathogenic (dominant) g.(?_2097990)_( 2098755_ 2100400)del - - - TSC2_002459 exons 1-2 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_2i c.(?_-106)_(138+1_139-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2098755_2100400)del g.(?_2047989)_(2048754_2050399)del deletion exon 1 and upstream - TSC2_002459 deletion involves exon 2 and upstream region; boundaries of deletion not determined unpublished - - Germline - - - - - DNA MLPA Blood - TSC - unpublished No other family member tested M - - - - - - - 1 Rosemary Ekong
+/. _1_3i c.(?_-106)_(225+1_226-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2100488_2103342)del g.(?_2047989)_(2050487_2053341)del deletion exon 1 to 2 and upstream - TSC2_003018 deletion involves upstream region and exons 1-3 unpublished - - Germline - - - - - DNA MLPA Blood - TSC - unpublished No other family member tested F - - - - - - - 1 Rosemary Ekong
+?/+? _1_3i c.(?_-106)_(225+1_226-1)del r.0? p.0? - - Unknown - likely pathogenic (dominant) g.(?_2097990)_(2100488_2103342)del g.(?_2047989)_(2050487_2053341)del - - TSC2_003018 exons 1-3 deleted, including region upstream of TSC2 - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_3i c.(?_-106)_(225+1_226-1)del r.0? p.0? - - Unknown ACMG pathogenic (dominant) g.(?_2097990)_(2100488_2103342)del g.(?_2047989)_(2050487_2053341)del - - TSC2_003018 exons 1-3 deletion found with deletion of exons 6-42 in RPKM data of NGS analysis and in MLPA; exons 4-5 present in both analyses; MLPA of all exons for TSC1 and TSC2, exons 35 and 45 only for PKD1 PubMed: Milon 2024; PubMed: Milon 2024 - - De novo - - - - - DNA MLPA, SEQ, SEQ-NG-IT Amniocytes - TSC - PubMed: Milon 2024; PubMed: Milon 2024 no family history of TSC; prenatally diagnosed cardiac rhabdomyoma (≥2) and cortical tubers (≥2); both parents tested negative; termination of pregnancy at 27+4 - - - - - - - - 1 Sarah Prestwich
+/. _1_10i c.(?_-106)_(975+1_976-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2108875_2110670)del g.(?_2047989)_(2058874_2060669)del Exons 1-10, TSC2del e1-e10 p.? - TSC2_003688 exons 1-10 deleted PubMed: Rosset, 2017 - - Germline - - - - - DNA SEQ-NG-IT Blood - TSC 12 PubMed: Rosset, 2017 - ? - Brazil - - - - - 1 Rosemary Ekong
+/+ _1_10i c.(?_-106)_(975+1_976-1)del r.0? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2108875_2110670)del g.(?_2047989)_(2058874_2060669)del - - TSC2_003688 exons 1-10 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_11i c.(?_-106)_(1119+1_1120-1)del r.0? p.0? - - Maternal (confirmed) - pathogenic g.(?_2097990)_(2110815_2111871)del g.(?_2047989)_(2060814_2061870)del deletion exon 1-11 - TSC2_003519 exons 1-11 deleted PubMed: Bai, 2017 - - Germline - - - - - DNA SEQ-NG-I, MLPA Blood - TSC 8 PubMed: Bai, 2017 affected child and affected mother have the variant ? - China - - - - - 2 Rosemary Ekong
+/+ _1_11i c.(?_-106)_(1119+1_1120-1)del r.0? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2110815_2111871)del g.(?_2047989)_(2060814_2061870)del - - TSC2_003519 exons 1-11 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_13i c.(?_-106)_(1361+1_1362-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2112602_2112972)del g.(?_2047989)_(2062601_2062971)del exons 1-12 deleted; TSC2del 5'1-e12; [TSC2.-9465_14050del23515; -9466_14051ins37(inv63261_63297)] - TSC2_003432 TSC2 exons 1-13 deleted; 23,515bp deletion extends ~10kb 5' of TSC2 and involves NTHL1 gene, with insertion of 37bp from PKD1 gene; breakpoints flanked by nts. C and CCTG PubMed: Kozlowski, 2007 - - Germline - - - - - DNA MLPA Blood - TSC BHM15501 PubMed: Kozlowski, 2007 patient with clinical diagnosis of TSC; other family members with TS but no indication if tested ? - - - - - - - 1 Rosemary Ekong
+/+ _1_13i c.(?_-106)_(1361+1_1362-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2112602_2112972)del g.(?_2047989)_(2062601_2062971)del - - TSC2_003432 exons 1-13 deleted; 23,515bp deletion extends ~10kb 5' of TSC2 and involves NTHL1 gene, with insertion of 37bp from PKD1 gene - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_15i c.(?_-106)_(1599+1_1600-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2114429_2115519)del g.(?_2047989)_(2064428_2065518)del TSC2del 5'3-e14 - TSC2_003475 ex 1-15 del; del extends >15kb 5' of TSC2, involves SLC9A3R2 and NTHL1 genes, ends in intron 15 PubMed: Au, 2007, PubMed: Kozlowski, 2007 - - Germline - - - - - DNA MLPA, Southern Blood - TSC TS00-353 PubMed: Au, 2007, PubMed: Kozlowski, 2007 - ? - - - - - - - 1 Rosemary Ekong
+/. _1_15i c.(?_-106)_(1599+1_1600-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2114429_2115519)del g.(?_2047989)_(2064428_2065518)del TSC2 del ex1-15 - TSC2_003475 MLPA kits TSC2 P046 and P337 used (42 exons) PubMed: Suspitsin, 2018 - - De novo - - - - - DNA SEQ-NG-I Blood - TSC MG67 PubMed: Suspitsin, 2018 18 mth old index with clinical signs of TSC F - Russia Slavic - - - - 1 Rosemary Ekong
+/+ _1_15i c.(?_-106)_(1599+1_1600-1)del r.0? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2114429_2115519)del g.(?_2047989)_(2064428_2065518)del - - TSC2_003475 exons 1-15 deleted; deletion extends >15kb 5' of TSC2, involves SLC9A3R2 and NTHL1 genes, ends in intron 15 - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_15i c.(?_-106)_(1599+1_1600-1)del r.? p.? - - Unknown ACMG pathogenic (dominant) g.(?_2097990)_(2114429_2115519)del g.(?_2047989)_(2064428_2065518)del - - TSC2_003475 exons 1 to 15 deleted; mosaic variant detected in amniocytes and postnatal blood sample; minor allele frequency 20% PubMed: Milon 2024; PubMed: Milon 2024 - - De novo - - - - - DNA MLPA, SEQ, SEQ-NG-IT Amniocytes, Blood - TSC - PubMed: Milon 2024; PubMed: Milon 2024 no family history of TSC; prenatally diagnosed cardiac rhabdomyoma (≥2); one parent tested negative; Birth at 33+0 - - - - - - - - 1 Sarah Prestwich
+/. _1_16i c.(?_-106)_(1716+1_1717-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2115637_2120456)del g.(?_2047989)_(2065636_2070455)del TSC2 del 5'3-e15 - TSC2_003382 ex 1-16 deletion previously reported as exons 4 and 7 deleted (Dabora, 2001); deletion refined in Kozlowski (2007) to a deletion that extends >15kb 5' of TSC2, involves SLC9A3R2 and NTHL1 genes, and ends in intron 16 PubMed: Dabora, 2001, PubMed: Kozlowski, 2007 - - Germline - - - - - DNA MLPA, PCRq Blood - TSC ONK116-1 PubMed: Dabora, 2001, PubMed: Kozlowski, 2007 same patient reported in both papers ? - - - - - - - 1 Rosemary Ekong
+/. _1_16i c.(?_-106)_(1716+1_1717-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2115637_2120456)del g.(?_2047989)_(2065636_2070455)del exons 1 to 15 and 5' region of TSC2 - TSC2_003382 16.9kb MLPA deletion involving exons 1-16 and 5' region of TSC2 (extend of deletion not determined); confirmed as a 210kb deletion by karyomapping PubMed: GimÈnez, 2015 - - De novo - - - - - DNA MLPA Blood - TSC - PubMed: GimÈnez, 2015 32 yr old diagnosed with TSC; reported as having renal symptoms; no other family member has the deletion F - - - - - - - 1 Rosemary Ekong
+/. _1_16i c.(?_-106)_(1716+1_1717-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2115637_2120456)del g.(?_2047989)_(2065636_2070455)del Exons 1-16 Deletion - TSC2_003382 exons 1-16 deleted; found in cortical tuber PubMed: Wang, 2020 - - Somatic - - - - - DNA SEQ Brain tuber - TSC - PubMed: Wang, 2020 cortical tuber from patient with TSC analysed F ? China - - - - - 1 Rosemary Ekong
+/+ _1_16i c.(?_-106)_(1716+1_1717-1)del r.0? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2115637_2120456)del g.(?_2047989)_(2065636_2070455)del - - TSC2_003382 exons 1-16 deleted; deletion extends >15kb 5' of TSC2, involves SLC9A3R2 and NTHL1 genes, and ends in intron 16 - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_16i c.(?_-106)_(1716+1_1717-1)del r.? p.? - - Unknown ACMG pathogenic (dominant) g.(?_2097990)_(2115637_2120456)del g.(?_2047989)_(2065636_2070455)del - - TSC2_003382 exons 1-16 deleted; MLPA of all exons for TSC1 and TSC2, exons 30, 40 and 46 only for PKD1 PubMed: Milon 2024; PubMed: Milon 2024 - - De novo - - - - - DNA MLPA Amniocytes - TSC - PubMed: Milon 2024; PubMed: Milon 2024 no family history of TSC; prenatally diagnosed cardiac rhabdomyoma (≥2); both parents tested negative; termination of pregnancy at 24+0 - - - - - - - - 1 Sarah Prestwich
+/. _1_20i c.(?_-106)_(2220+1_2221-1)del r.? p.? - - Unknown ACMG pathogenic (dominant) g.(?_2097990)_(2122365_2122849)del g.(?_2047989)_(2072364_2072848)del 1-20, Exons 1–20 deleted - TSC2_001917 MLPA kit P046–C1 used PubMed: Ng, 2022 - - Germline - - - - - DNA MLPA Blood all exons, adjacent splice sites and 10 intronic bases flanking each exon analysed, variants verified by Sanger sequencing. TSC - PubMed: Ng, 2022 patient with definite TSC - - Hong Kong China - - - - 1 Rosemary Ekong
+/+ _1_20i c.(?_-106)_(2220+1_2221-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2122365_2122849)del g.(?_2047989)_(2072364_2072848)del - - TSC2_001917 - - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_27i c.(?_-106)_(3131+1_3132-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2129198_2129276)del g.(?_2047989)_(2079197_2079275)del TSC2 del ex 1-27 - TSC2_003689 exons 1-27 deleted; MLPA kits TSC2 P046 and P337 used (42 exons) PubMed: Suspitsin, 2018 - - De novo - - - - - DNA SEQ-NG-I Blood - TSC MG164 PubMed: Suspitsin, 2018 1yr 6mth old index with clinical signs of TSC F - Russia Slavic - - - - 1 Rosemary Ekong
+/+ _1_27i c.(?_-106)_(3131+1_3132-1)del r.0? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2129198_2129276)del g.(?_2047989)_(2079197_2079275)del - - TSC2_003689 exons 1-27 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_27i c.(?_-106)_(3131+1_3132-1)dup r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2129198_2129276dup g.(?_2047989)_(2079197_2079275dup duplication 5'UTR and exon 27 - TSC2_003686 suspected duplication of region 5' of TSC2 gene and TSC2 exon 27; TSC2 MLPA kits P046-C1-1011 and P337-A2-0510 used Journal: 10.4236/ajmb.2014.43018 - - Germline - - - - - DNA MLPA Blood - TSC 890801 Journal: 10.4236/ajmb.2014.43018 patient with clinical diagnosis of TSC ? - Iran - - - - - 1 Rosemary Ekong
?/? _1_27i c.(?_-106)_(3131+1_3132-1)dup r.0? p.? - - Unknown - VUS g.(?_2097990)_(2129198_2129276)dup g.(?_2047989)_(2079197_2079275)dup - - TSC2_003686 exons 1-27 duplicated; duplication of region 5' of TSC2 gene and TSC2 exon 27 - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_29i c.(?_-106)_(3397+1_3398-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2129671_2130165)del g.(?_2047989)_(2079670_2080164)del Del 1-29 exons - TSC2_003690 exons 1-29 deleted; variant confirmed by Sanger sequencing PubMed: Papadopoulou, 2018 - - Germline - - - - - DNA SEQ-NG-R, SEQ Blood - TSC 2 PubMed: Papadopoulou, 2018 patient diagnosed with TSC at 5yrs, last reviewed at 12yrs; seizures controlled F - - - - - - - 1 Rosemary Ekong
+/+ _1_29i c.(?_-106)_(3397+1_3398-1)del r.0? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2129671_2130165)del g.(?_2047989)_(2079670_2080164)del - - TSC2_003690 exons 1-29 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_30i c.-106_3610+163del{0} r.0? p.0? - - Unknown ACMG pathogenic (dominant) g.2091899_2130541del g.2041898_2080540del - - TSC2_004777 - PubMed: Duan 2024 - - Germline yes - - - - DNA MLPA-ms, SEQ, SEQ-PB - - TSC - PubMed: Duan 2024 - F no China - - - - - 1 Jing Duan
+/. _1_34i c.(?_-106)_(4493+1_4494-1)del r.0? p.0? - - Unknown - pathogenic g.(?_2097990)_(2134717_2134951)del g.(?_2047989)_(2084716_2084950)del c.(?_1)_4493+?del - TSC2_003759 exons 1-34 deleted (based on 42 exons) unpublished - - Germline - - - - - DNA MLPA Blood - TSC - unpublished - ? - - - - - - - 1 Rosemary Ekong
+/+ _1_34i c.(?_-106)_(4493+1_4494-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2134717_2134951)del g.(?_2047989)_(2084716_2084950)del - - TSC2_003759 exons 1-34 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
+/. _1_37i c.(?_-106)_(4849+1_4850-1)del r.? p.? - - Unknown - pathogenic g.(?_2097990)_(2136381_2136732)del - Exons 1-37 - TSC2_004242 exons 1-37 deleted PubMed: Lin 2019 - - Germline ? - - - - DNA MLPA Blood MLPA kit P046-C1 used TSC - PubMed: Lin 2019 clinically diagnosed with TSC; TSC features not specified ? ? China - - - - - 1 Rosemary Ekong
+/+ _1_37i c.(?_-106)_(4849+1_4850-1)del r.? p.? - - Unknown - pathogenic (dominant) g.(?_2097990)_(2136381_2136729)del - - - TSC2_004242 exons 1-37 deleted - - - SUMMARY record - - - - - - - - - - - - - - - - - - - - - - -
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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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