All variants in the TSC2 gene

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.

13321 entries on 134 pages. Showing entries 1 - 100.
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Effect     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

P-domain     

Predict/SIFT     

Predict/PolyPhen     

Predicted     

Type/DNA     

Predict/Splice     

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     

Owner     
+/. 15i_22i c.(1599+1_1600-1)_(2545+1_2546-1)[3] r.? p.? - - - - - - - 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reported as 2x above control levels indicating 4 alleles; reported as triplication of exons 15-21 (based on 41 exons) unpublished - - De novo ? 1/4 individuals tested has the variant - - - Rosemary Ekong
+/. _1_42_ c.-106_*102{0} r.0? p.0? - - - - - - 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 ? - - - - Rosemary Ekong
+/+ _1_42_ c.-106_*102{0} r.0? p.0? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1_12i c.-106_1258-159{0} r.? p.? - - - - - - 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 ? - - - - Rosemary Ekong
+/+ _1_12i c.-106_1258-159{0} r.? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1_16i c.-106_1716+1900{0} r.? p.? - - - - - - ACMG pathogenic (dominant) g.2046527_2117536del - NC_000016.9: g.2046527_2117536del, exon 1-15 - 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 PubMed: Ogorek, 2020 - - Germline ? - - - - Rosemary Ekong
+/+ _1_16i c.-106_1716+1900{0} r.? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1_16i c.-106_1717-2210{0} r.? p.? - - - - - - ACMG pathogenic (dominant) g.2086101_2118247del g.2036100_2068246del NC_000016.9: g.2086101_2118247del - TSC2_001691 32147bp deletion; TSC2 exons 1-16 deleted + 11890bp upstream of TSC2; deletion ends in TSC2 intron 16; upstream deletion involves NTHL1 gene PubMed: Ogorek, 2020 - - Germline ? - - - - Rosemary Ekong
+/+ _1_16i c.-106_1717-2210{0} r.? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.2086101_2118247del g.2036100_2068246del - - TSC2_001691 32147bp deletion; TSC2 exons 1-16 deleted + 11890bp upstream of TSC2; deletion ends in TSC2 intron 16; upstream deletion involves NTHL1 gene - - - SUMMARY record - - - - - Rosemary Ekong
+/. 38i_42_ c.4990-299_*102{0} r.? p.? - - - - - - 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 ? - - - - Rosemary Ekong
+/+ 38i_42_ c.4990-299_*102{0} r.? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. 39i_42_ c.5068+11_*102{0} r.? p.? - - - - - - 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 ? - - - - Rosemary Ekong
+/+ 39i_42_ c.5068+11_*102{0} r.? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1 c.(?_-106)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
?/? _1 c.(?_-106)del r.? p.? - - - deletion, large deletion, large - - VUS g.(?_2097990)del g.(?_2047989)del - - TSC2_003645 deletion of region 5' of TSC2 gene; breakpoints undetermined - - - SUMMARY record - - - - - Rosemary Ekong
-?/. - c.-4447C>G r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
-?/. - c.-4426C>T r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
+/. - c.-4368C>T r.(?) p.(=) - - - - - - - pathogenic g.2093728C>T - NTHL1(NM_002528.7):c.526-1G>A - NTHL1_000228 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_VUmc
-?/. - c.-4359_-4358del r.(?) p.(=) - - - - - - - likely benign g.2093737_2093738del - NTHL1(NM_002528.7):c.526-11_526-10delCT - NTHL1_000232 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
-?/. - c.-4353G>C r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
-?/. - c.-3443A>G r.(?) p.(=) - - - - - - - likely benign g.2094653A>G g.2044652A>G NTHL1(NM_002528.7):c.503T>C (p.I168T) - NTHL1_000012 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
?/. - c.-3443A>G r.(?) p.(=) - - - - - - - VUS g.2094653A>G g.2044652A>G NTHL1(NM_002528.7):c.503T>C (p.I168T) - NTHL1_000012 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Groningen
?/. - c.-3416G>A r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_Leiden
-?/. - c.-3374C>T r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
+/. _1_3i c.-2600_226-765delinsN[273] r.(?) p.? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_3i c.-2600_226-765delinsN[273] r.? p.? - - - - delins - - 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 - - - - - Rosemary Ekong
?/. - c.-1894A>G r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_Rotterdam
?/. - c.-1887G>A r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_Rotterdam
?/. - c.-1887G>A r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
+/. - c.-1857G>A r.(?) p.(=) - - - - - - - pathogenic g.2096239G>A g.2046238G>A NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+/. - c.-1857G>A r.(?) p.(=) - - - - - - - pathogenic g.2096239G>A g.2046238G>A NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Rotterdam
+?/. - c.-1857G>A r.(?) p.(=) - - - - - - - likely pathogenic g.2096239G>A g.2046238G>A NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_VUmc
+/. - c.-1857G>A r.(?) p.(=) - - - - - - - pathogenic g.2096239G>A - NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Groningen
+/. - c.-1857G>A r.(?) p.(=) - - - - - - - pathogenic g.2096239G>A - NTHL1(NM_002528.7):c.244C>T (p.Q82*) - NTHL1_000001 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Utrecht
-?/. - c.-1765C>T r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_Leiden
-?/. - c.-1763C>T r.(?) p.(=) - - - - - - - likely benign g.2096333C>T - NTHL1(NM_002528.7):c.150G>A (p.P50=) - NTHL1_000213 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
?/. - c.-1759C>T r.(?) p.(=) - - - - - - - VUS g.2096337C>T - NTHL1(NM_002528.5):c.170G>A (p.(Arg57His)) - NTHL1_000261 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Leiden
-?/. - c.-1754C>T r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_Rotterdam
-?/. - c.-1751G>A r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
-/. - c.-1712G>A r.(?) p.(=) - - - - - - - benign g.2096384G>A g.2046383G>A NTHL1(NM_002528.7):c.116-17C>T - NTHL1_000008 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+/. _1_1 c.-827_-84del r.(?) p.? - - - - - - - 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 - - - - - Rosemary Ekong
?/? _1_1 c.-827_-84del r.(?) p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
-/. - c.-403C>T r.(?) p.(=) - - - - - - - benign g.2097693C>T g.2047692C>T NTHL1(NM_002528.7):c.115+17G>A - NTHL1_000255 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
+/. - c.-387C>T r.(?) p.(=) - - - - - - - pathogenic g.2097709C>T - NTHL1(NM_002528.7):c.115+1G>A - NTHL1_000230 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Utrecht
-/. - c.-384G>A r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
-?/. - c.-315A>G r.(?) p.(=) - - - - - - - likely benign g.2097781A>G - NTHL1(NM_002528.7):c.44T>C (p.L15P) - NTHL1_000262 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
-?/. - c.-300G>C r.(?) p.(=) - - - - - - - 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 - - - - - VKGL-NL_AMC
?/. - c.-256A>C r.(?) p.(=) - - - - - - - VUS g.2097840A>C - TSC2(NM_000548.5):c.-256A>C - NTHL1_000308 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_Groningen
-?/. - c.-235T>C r.(?) p.(=) - - - - - - - likely benign g.2097861T>C g.2047860T>C NTHL1(NM_002528.7):c.-37A>G - NTHL1_000257 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - VKGL-NL_AMC
-/. _1 c.-115G>T r.(?) p.(=) - - - - - - - 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+ - - Rosemary Ekong
-?/-? _1 c.-115G>T r.(?) p.(=) - - - - substitution - - 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+ - - Rosemary Ekong
+/. _1_2i c.(?_-106)_(138+1_139-1)del r.0? p.0? - - - - deletion, large - - 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 ? - - - - Rosemary Ekong
+/+ _1_2i c.(?_-106)_(138+1_139-1)del r.0? p.0? - - - deletion, large deletion, large - - likely pathogenic (dominant) g.(?_2097990)_( 2098755_ 2100400)del - - - TSC2_002459 exons 1-2 deleted - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_2i c.(?_-106)_(138+1_139-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/. _1_3i c.(?_-106)_(225+1_226-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+?/+? _1_3i c.(?_-106)_(225+1_226-1)del r.0? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1_10i c.(?_-106)_(975+1_976-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_10i c.(?_-106)_(975+1_976-1)del r.0? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.(?_2097990)_(2108875_2110670)del g.(?_2047989)_(2058874_2060669)del - - TSC2_003688 exons 1-10 deleted - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_11i c.(?_-106)_(1119+1_1120-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_11i c.(?_-106)_(1119+1_1120-1)del r.0? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.(?_2097990)_(2110815_2111871)del g.(?_2047989)_(2060814_2061870)del - - TSC2_003519 exons 1-11 deleted - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_13i c.(?_-106)_(1361+1_1362-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_13i c.(?_-106)_(1361+1_1362-1)del r.? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1_15i c.(?_-106)_(1599+1_1600-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/. _1_15i c.(?_-106)_(1599+1_1600-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_15i c.(?_-106)_(1599+1_1600-1)del r.0? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1_16i c.(?_-106)_(1716+1_1717-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/. _1_16i c.(?_-106)_(1716+1_1717-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/. _1_16i c.(?_-106)_(1716+1_1717-1)del r.? p.? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_16i c.(?_-106)_(1716+1_1717-1)del r.0? p.? - - - deletion, large deletion, large - - 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 - - - - - Rosemary Ekong
+/. _1_20i c.(?_-106)_(2220+1_2221-1)del r.? p.? - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_20i c.(?_-106)_(2220+1_2221-1)del r.? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.(?_2097990)_(2122365_2122849)del g.(?_2047989)_(2072364_2072848)del - - TSC2_001917 - - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_27i c.(?_-106)_(3131+1_3132-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_27i c.(?_-106)_(3131+1_3132-1)del r.0? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.(?_2097990)_(2129198_2129276)del g.(?_2047989)_(2079197_2079275)del - - TSC2_003689 exons 1-27 deleted - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_27i c.(?_-106)_(3131+1_3132-1)dup r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
?/? _1_27i c.(?_-106)_(3131+1_3132-1)dup r.0? p.? - - - duplication, large duplication, large - - 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 - - - - - Rosemary Ekong
+/. _1_29i c.(?_-106)_(3397+1_3398-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_29i c.(?_-106)_(3397+1_3398-1)del r.0? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.(?_2097990)_(2129671_2130165)del g.(?_2047989)_(2079670_2080164)del - - TSC2_003690 exons 1-29 deleted - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_34i c.(?_-106)_(4493+1_4494-1)del r.0? p.0? - - - - - - - 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 - - - - - Rosemary Ekong
+/+ _1_34i c.(?_-106)_(4493+1_4494-1)del r.? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.(?_2097990)_(2134717_2134951)del g.(?_2047989)_(2084716_2084950)del - - TSC2_003759 exons 1-34 deleted - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_37i c.(?_-106)_(4849+1_4850-1)del r.? p.? - - - deletion, large deletion, large - - pathogenic g.(?_2097990)_(2136381_2136732)del - Exons 1-37 - TSC2_004242 exons 1-37 deleted PubMed: Lin 2019 - - Germline ? - - - - Rosemary Ekong
+/+ _1_37i c.(?_-106)_(4849+1_4850-1)del r.? p.? - - - deletion, large deletion, large - - pathogenic (dominant) g.(?_2097990)_(2136381_2136729)del - - - TSC2_004242 exons 1-37 deleted - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(1000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(1000) - - - TSC2_001442 ~1kb intragenic deletion in patient and affected parent (2/2 affecteds); variant identified using cDNA probe E0.7 PubMed: European TSC consortium 1993 - - Germline yes - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(1000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(1000) - - - TSC2_001442 ~1kb intragenic deletion in patient but absent in both parents PubMed: Jones 1997 - - De novo no 1/6 chromosomes - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(1000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(1000) - 1kb deletion - TSC2_001442 deletion 1kb found using cDNA probe 4.9E0.7; variant in more than one affected PubMed: European TSC consortium 1993 - - Germline yes - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(1000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del1000 g.(2047989_2088712)del1000 - - TSC2_003476 ~1kb intragenic deletion; cDNA probe E0.7 PubMed: European TSC consortium, 1993 - - Germline - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(1000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del1000 g.(2047989_2088712)del1000 - - TSC2_003476 ~1kb intragenic deletion PubMed: Jones, 1997 - - De novo - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(1000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del1000 g.(2047989_2088712)del1000 1kb deletion - TSC2_003476 deletion 1kb found using cDNA probe 4.9E0.7 PubMed: European TSC consortium, 1993 - - Germline - - - - - Rosemary Ekong
+/+ _1_42_ c.(-106_*102)del(1000) r.0? p.0? - - - deletion, large deletion, large - - pathogenic (dominant) g.(2097990_2138713)del(1000) g.(2047989_2088712)del(1000) - - TSC2_003476 ~1kb intragenic deletion - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(10000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(10000) - - - TSC2_004310 ~10kb intragenic deletion; variant in more than one affected PubMed: Jones 1997 - - Germline yes - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(10000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(10000) - - - TSC2_004310 >10kb deletion (cDNA probe 1A1); variant in more than one affected unpublished - - Germline yes - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(10000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del10000 g.(2047989_2088712)del10000 - - TSC2_003530 ~10kb intragenic deletion PubMed: Jones, 1997 - - Germline - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(10000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del10000 g.(2047989_2088712)del10000 - - TSC2_003530 >10kb deletion (cDNA probe 1A1) originally vd Ouweland - - Germline - - - - - Rosemary Ekong
+/+ _1_42_ c.(-106_*102)del(10000) r.0? p.0? - - - deletion, large deletion, large - - pathogenic (dominant) g.(2097990_2138713)del(10000) g.(2047989_2088712)del(10000) - - TSC2_003530 ~10kb intragenic deletion - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(2500) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(2500) - 2.5kb - TSC2_004313 2.5kb deletion found with cDNA probe 1A1 unpublished - - Germline ? - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(2500) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del2500 g.(2047989_2088712)del2500 2.5kb - TSC2_003533 2.5kb deletion found with cDNA probe 1A1 originally vd Ouweland - - Germline - - - - - Rosemary Ekong
+/+ _1_42_ c.(-106_*102)del(2500) r.0? p.0? - - - deletion, large deletion, large - - pathogenic (dominant) g.(2097990_2138713)del(2500) g.(2047989_2088712)del(2500) - - TSC2_003533 2.5kb deletion - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(3000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(3000) - - - TSC2_004311 ~3kb intragenic deletion; cDNA probes used PubMed: European TSC consortium 1993 - - Germline ? - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(3000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del3000 g.(2047989_2088712)del3000 - - TSC2_003531 ~3kb intragenic deletion; cDNA probes used PubMed: European TSC consortium, 1993 - - Germline - - - - - Rosemary Ekong
+/+ _1_42_ c.(-106_*102)del(3000) r.0? p.0? - - - deletion, large deletion, large - - pathogenic (dominant) g.(2097990_2138713)del(3000) g.(2047989_2088712)del(3000) - - TSC2_003531 ~3kb intragenic deletion - - - SUMMARY record - - - - - Rosemary Ekong
+/. _1_42_ c.(-106_*102)del(4000) r.0? p.0? - - - - - - - pathogenic g.(2097990_2138713)del(4000) - - - TSC2_004312 ~4kb intragenic deletion reported as ~5kb deletion in text; identified using cDNA probe E0.7 PubMed: European TSC consortium 1993 - - Germline ? - - - - 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.