TSC2 — 10567 ClinVar variants

All ClinVar germline TSC2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 4565 flagged for review →

965 Pathogenic · 105 Pathogenic/Likely pathogenic · 243 Likely pathogenic · 1500 Conflicting · 220 Benign · 999 Benign/Likely benign · 2257 Likely benign · 4278 Uncertain significance

Full TSC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 4565

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors agree, ClinVar conflicts 726

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification. · showing the 150 best-reviewed of 726

Predicted LoF vs a conflicting call 26

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 2053

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 2053

Predictors split 1749

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 1749

All TSC2 variants

Pathogenic 965

Showing the top 300 by review status; the full set is in the sitemap.

Pathogenic/Likely pathogenic 105

Likely pathogenic 243

Conflicting classifications of pathogenicity 1500

Showing the top 300 by review status; the full set is in the sitemap.

Benign 220

Benign/Likely benign 999

Showing the top 300 by review status; the full set is in the sitemap.

  • p.Ile1702= Multiple submitters hereditary neoplastic syndrome
  • p.Ser1799= Multiple submitters hereditary neoplastic syndrome
  • c.1119+12dup Multiple submitters lymphangioleiomyomatosis
  • c.1119+6G>C Multiple submitters lymphangioleiomyomatosis
  • c.1120-12C>T Multiple submitters tuberous sclerosis 2
  • c.1120-16G>A Multiple submitters tuberous sclerosis 2
  • c.1120-17C>T Multiple submitters tuberous sclerosis 2
  • c.1257+10C>G Multiple submitters tuberous sclerosis 2
  • c.1257+11del Multiple submitters tuberous sclerosis
  • c.1257+14C>T Multiple submitters tuberous sclerosis 2
  • c.1361+16T>G Multiple submitters tuberous sclerosis 2
  • c.1361+18G>C Multiple submitters tuberous sclerosis 2
  • c.1361+20C>G Multiple submitters tuberous sclerosis 2
  • c.1361+8del Multiple submitters tuberous sclerosis 2
  • c.1362-10C>T Multiple submitters hereditary neoplastic syndrome
  • c.1362-4G>A Multiple submitters hereditary neoplastic syndrome
  • c.1362-5C>T Multiple submitters hereditary neoplastic syndrome
  • c.138+20C>G Multiple submitters tuberous sclerosis 2
  • c.139-6C>T Multiple submitters tuberous sclerosis
  • c.1443+15G>A Multiple submitters tuberous sclerosis 2
  • c.1443+18C>T Multiple submitters lymphangioleiomyomatosis
  • c.1599+8C>A Multiple submitters tuberous sclerosis 2
  • c.1599+9C>T Multiple submitters tuberous sclerosis 2
  • c.1716+15C>T Multiple submitters tuberous sclerosis 2
  • c.1717-12CT[3] Multiple submitters hereditary neoplastic syndrome
  • c.1717-14T>C Multiple submitters lymphangioleiomyomatosis
  • c.1717-15G>A Multiple submitters tuberous sclerosis
  • c.1717-15G>T Multiple submitters tuberous sclerosis
  • c.1717-16C>T Multiple submitters lymphangioleiomyomatosis
  • c.1717-30G>A Multiple submitters tuberous sclerosis
  • c.1717-6C>T Multiple submitters tuberous sclerosis 2
  • c.1839+10C>T Multiple submitters tuberous sclerosis 2
  • c.1839+20G>A Multiple submitters tuberous sclerosis 2
  • c.1839+20G>C Multiple submitters tuberous sclerosis 2
  • c.1840-11C>G Multiple submitters tuberous sclerosis
  • c.1840-14C>T Multiple submitters tuberous sclerosis
  • c.1946+14C>T Multiple submitters tuberous sclerosis 2
  • c.1946+20C>T Multiple submitters tuberous sclerosis 2
  • c.1946+6C>T Multiple submitters tuberous sclerosis 2
  • c.1946+7G>A Multiple submitters tuberous sclerosis 2
  • c.1947-3C>T Multiple submitters tuberous sclerosis 2
  • c.1947-4G>A Multiple submitters hereditary neoplastic syndrome
  • c.1947-9C>T Multiple submitters tuberous sclerosis
  • c.2097+10del Multiple submitters tuberous sclerosis 2
  • c.2097+13G>A Multiple submitters tuberous sclerosis 2
  • c.2097+43A>G Multiple submitters tuberous sclerosis
  • c.2098-13C>T Multiple submitters tuberous sclerosis
  • c.2098-6T>C Multiple submitters tuberous sclerosis 2
  • c.2098-9T>C Multiple submitters tuberous sclerosis
  • c.2220+11C>T Multiple submitters tuberous sclerosis 2
  • c.2220+20del Multiple submitters tuberous sclerosis 2
  • c.2221-19G>A Multiple submitters tuberous sclerosis 2
  • c.2221-8G>C Multiple submitters tuberous sclerosis 2
  • c.2356-4G>A Multiple submitters tuberous sclerosis
  • c.2545+244C>G Multiple submitters tuberous sclerosis 2
  • c.2545+26G>A Multiple submitters tuberous sclerosis 2
  • c.2545+31C>T Multiple submitters tuberous sclerosis 2
  • c.2545+9C>G Multiple submitters tuberous sclerosis 2
  • c.2546-10A>G Multiple submitters tuberous sclerosis
  • c.2546-31G>A Multiple submitters tuberous sclerosis 2
  • c.2546-4G>A Multiple submitters hereditary neoplastic syndrome
  • c.2546-5C>G Multiple submitters hereditary neoplastic syndrome
  • c.2546-5C>T Multiple submitters hereditary neoplastic syndrome
  • c.2546-6C>T Multiple submitters hereditary neoplastic syndrome
  • c.2640-13C>T Multiple submitters hereditary neoplastic syndrome
  • c.2742+13C>T Multiple submitters lymphangioleiomyomatosis
  • c.2743-10A>G Multiple submitters tuberous sclerosis 2
  • c.2743-11C>T Multiple submitters tuberous sclerosis 2
  • c.2743-19G>A Multiple submitters tuberous sclerosis 2
  • c.2743-3C>A Multiple submitters hereditary neoplastic syndrome
  • c.2743-40A>G Multiple submitters tuberous sclerosis
  • c.2743-7C>G Multiple submitters hereditary neoplastic syndrome
  • c.2743-9C>T Multiple submitters hereditary neoplastic syndrome
  • c.2837+11dup Multiple submitters lymphangioleiomyomatosis
  • c.2838-13C>T Multiple submitters tuberous sclerosis 2
  • c.2838-4A>G Multiple submitters lymphangioleiomyomatosis
  • c.2966+19G>T Multiple submitters tuberous sclerosis 2
  • c.2966+20G>T Multiple submitters tuberous sclerosis 2
  • c.2967-13C>T Multiple submitters tuberous sclerosis 2
  • c.2967-16C>T Multiple submitters tuberous sclerosis 2
  • c.2967-6C>T Multiple submitters tuberous sclerosis 2
  • c.3131+8C>T Multiple submitters tuberous sclerosis 2
  • c.3132-15C>T Multiple submitters tuberous sclerosis 2
  • c.3132-16G>A Multiple submitters tuberous sclerosis 2
  • c.3285-19C>T Multiple submitters tuberous sclerosis 2
  • c.336+10A>G Multiple submitters isolated focal cortical dysplasia type II
  • c.336+33G>T Multiple submitters tuberous sclerosis 2
  • c.336+8C>T Multiple submitters tuberous sclerosis 2
  • c.337-3T>C Multiple submitters tuberous sclerosis
  • c.3398-19C>T Multiple submitters tuberous sclerosis 2
  • c.3398-9C>T Multiple submitters tuberous sclerosis 2
  • c.3610+9C>T Multiple submitters lymphangioleiomyomatosis
  • c.3611-10G>A Multiple submitters hereditary neoplastic syndrome
  • c.3611-11C>T Multiple submitters hereditary neoplastic syndrome
  • c.3611-4G>A Multiple submitters tuberous sclerosis 2
  • c.3611-5C>T Multiple submitters tuberous sclerosis
  • c.3814+10A>G Multiple submitters lymphangioleiomyomatosis
  • c.3814+7G>A Multiple submitters tuberous sclerosis 2
  • c.3814+9C>A Multiple submitters tuberous sclerosis 2
  • c.3815-15G>A Multiple submitters tuberous sclerosis
  • c.3815-16C>T Multiple submitters tuberous sclerosis 2
  • c.3815-20C>T Multiple submitters tuberous sclerosis 2
  • c.3815-21G>A Multiple submitters hereditary neoplastic syndrome
  • c.3883+15_3883+16del Multiple submitters hereditary neoplastic syndrome
  • c.3883+8C>G Multiple submitters lymphangioleiomyomatosis
  • c.3884-16G>A Multiple submitters tuberous sclerosis 2
  • c.4005+7G>A Multiple submitters tuberous sclerosis 2
  • c.4006-4C>G Multiple submitters tuberous sclerosis 2
  • c.4006-8C>T Multiple submitters lymphangioleiomyomatosis
  • c.4493+16_4493+17delinsGT Multiple submitters lymphangioleiomyomatosis
  • c.4493+16C>G Multiple submitters lymphangioleiomyomatosis
  • c.4493+17C>T Multiple submitters lymphangioleiomyomatosis
  • c.4493+18G>A Multiple submitters tuberous sclerosis 2
  • c.4494-12dup Multiple submitters tuberous sclerosis 2
  • c.4569+46C>T Multiple submitters tuberous sclerosis 2
  • c.4569+4G>A Multiple submitters hereditary neoplastic syndrome
  • c.4662+10C>T Multiple submitters tuberous sclerosis 2
  • c.4662+17G>A Multiple submitters lymphangioleiomyomatosis
  • c.4662+18G>A Multiple submitters tuberous sclerosis 2
  • c.4663-12dup Multiple submitters tuberous sclerosis 2
  • c.4663-16_4663-15del Multiple submitters tuberous sclerosis 2
  • c.4663-3C>T Multiple submitters hereditary neoplastic syndrome
  • c.4663-7C>T Multiple submitters tuberous sclerosis
  • c.481+8C>T Multiple submitters tuberous sclerosis 2
  • c.481+9C>T Multiple submitters tuberous sclerosis 2
  • c.482-14C>T Multiple submitters tuberous sclerosis 2
  • c.482-16G>A Multiple submitters tuberous sclerosis 2
  • c.482-20T>A Multiple submitters tuberous sclerosis 2
  • c.482-3C>T Multiple submitters hereditary neoplastic syndrome
  • c.482-4C>T Multiple submitters tuberous sclerosis 2
  • c.4849+13G>A Multiple submitters tuberous sclerosis 2
  • c.4849+4C>T Multiple submitters hereditary neoplastic syndrome
  • c.4850-12G>A Multiple submitters tuberous sclerosis 2
  • c.4850-19C>T Multiple submitters tuberous sclerosis 2
  • c.4850-8A>G Multiple submitters tuberous sclerosis
  • c.4850-9C>T Multiple submitters tuberous sclerosis 2
  • c.4989+15G>A Multiple submitters tuberous sclerosis 2
  • c.4989+20T>A Multiple submitters tuberous sclerosis 2
  • c.4990-11T>C Multiple submitters tuberous sclerosis
  • c.4990-3C>T Multiple submitters hereditary neoplastic syndrome
  • c.4990-5G>T Multiple submitters hereditary neoplastic syndrome
  • c.4990-7C>G Multiple submitters tuberous sclerosis
  • c.4990-7C>T Multiple submitters tuberous sclerosis
  • c.5068+27_5069-47del Multiple submitters hereditary neoplastic syndrome
  • c.5068+27_5069-47dup34 Multiple submitters lymphangioleiomyomatosis
  • c.5069-13C>T Multiple submitters hereditary neoplastic syndrome
  • c.5069-14_5069-12del Multiple submitters tuberous sclerosis
  • c.5069-8C>T Multiple submitters tuberous sclerosis
  • c.5160+7G>C Multiple submitters tuberous sclerosis 2
  • c.5161-10A>C Multiple submitters lymphangioleiomyomatosis
  • c.5161-20C>T Multiple submitters tuberous sclerosis 2
  • c.5161-4C>G Multiple submitters tuberous sclerosis
  • c.5161-8G>A Multiple submitters tuberous sclerosis 2
  • c.5161-8G>C Multiple submitters tuberous sclerosis
  • c.5259+25C>T Multiple submitters polycystic kidney disease 1
  • c.5259+9T>C Multiple submitters isolated focal cortical dysplasia type II
  • c.5260-12C>T Multiple submitters tuberous sclerosis 2
  • c.5260-14G>A Multiple submitters tuberous sclerosis 2
  • c.5260-15C>T Multiple submitters tuberous sclerosis
  • c.5260-9T>C Multiple submitters tuberous sclerosis 2
  • c.599+10G>C Multiple submitters tuberous sclerosis 2
  • c.599+17G>C Multiple submitters tuberous sclerosis 2
  • c.600-15C>T Multiple submitters lymphangioleiomyomatosis
  • c.600-18G>A Multiple submitters tuberous sclerosis 2
  • c.648+9C>T Multiple submitters tuberous sclerosis 2
  • c.649-17G>A Multiple submitters tuberous sclerosis 2
  • c.649-18C>T Multiple submitters tuberous sclerosis 2
  • c.649-20G>A Multiple submitters tuberous sclerosis 2
  • c.649-8T>C Multiple submitters tuberous sclerosis 2
  • c.649-9C>G Multiple submitters tuberous sclerosis 2
  • c.775-12T>C Multiple submitters tuberous sclerosis
  • c.775-17C>T Multiple submitters tuberous sclerosis 2
  • c.775-4G>A Multiple submitters lymphangioleiomyomatosis
  • c.848+276C>G Multiple submitters
  • c.848+7G>A Multiple submitters hereditary neoplastic syndrome
  • c.975+13C>T Multiple submitters hereditary neoplastic syndrome
  • c.975+15G>A Multiple submitters lymphangioleiomyomatosis
  • c.976-16C>T Multiple submitters lymphangioleiomyomatosis
  • c.976-3C>T Multiple submitters hereditary neoplastic syndrome
  • c.-29-10G>C Multiple submitters tuberous sclerosis
  • c.*1G>C Multiple submitters tuberous sclerosis 2
  • c.*35G>A Multiple submitters tuberous sclerosis
  • c.*4C>G Multiple submitters tuberous sclerosis
  • c.*71C>T Multiple submitters tuberous sclerosis
  • p.Ala100= Multiple submitters tuberous sclerosis 2
  • p.Ala1009= Multiple submitters tuberous sclerosis 2
  • p.Ala107= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1108= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1141Thr Multiple submitters hereditary neoplastic syndrome
  • p.Ala1141Val Multiple submitters hereditary neoplastic syndrome
  • p.Ala1153= Multiple submitters tuberous sclerosis
  • p.Ala1163= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1164Ser Multiple submitters hereditary neoplastic syndrome
  • p.Ala1164Thr Multiple submitters hereditary neoplastic syndrome
  • p.Ala1184= Multiple submitters tuberous sclerosis
  • p.Ala1185= Multiple submitters tuberous sclerosis
  • p.Ala1195= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1234= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1237= Multiple submitters tuberous sclerosis 2
  • p.Ala1257Val Multiple submitters lymphangioleiomyomatosis
  • p.Ala1261= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1297= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1323Val Multiple submitters hereditary neoplastic syndrome
  • p.Ala1332= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1349= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1349Thr Multiple submitters hereditary neoplastic syndrome
  • p.Ala1405= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1416= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1429= Multiple submitters hereditary neoplastic syndrome
  • p.Ala145= Multiple submitters hereditary neoplastic syndrome
  • p.Ala145Thr Multiple submitters tuberous sclerosis
  • p.Ala1479= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1479Val Multiple submitters hereditary neoplastic syndrome
  • p.Ala1484= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1486= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1489= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1560= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1622= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1716= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1742= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1759= Multiple submitters hereditary neoplastic syndrome
  • p.Ala1759Thr Multiple submitters hereditary neoplastic syndrome
  • p.Ala1778= Multiple submitters hereditary neoplastic syndrome
  • p.Ala196= Multiple submitters tuberous sclerosis 2
  • p.Ala196Thr Multiple submitters hereditary neoplastic syndrome
  • p.Ala210= Multiple submitters tuberous sclerosis 2
  • p.Ala210Thr Multiple submitters lymphangioleiomyomatosis
  • p.Ala272Thr Multiple submitters tuberous sclerosis 2
  • p.Ala295= Multiple submitters hereditary neoplastic syndrome
  • p.Ala31= Multiple submitters tuberous sclerosis 2
  • p.Ala328= Multiple submitters tuberous sclerosis 2
  • p.Ala42= Multiple submitters hereditary neoplastic syndrome
  • p.Ala431= Multiple submitters hereditary neoplastic syndrome
  • p.Ala431Val Multiple submitters hereditary neoplastic syndrome
  • p.Ala447= Multiple submitters tuberous sclerosis 2
  • p.Ala460Thr Multiple submitters lymphangioleiomyomatosis
  • p.Ala516= Multiple submitters tuberous sclerosis 2
  • p.Ala555= Multiple submitters tuberous sclerosis 2
  • p.Ala583Thr Multiple submitters isolated focal cortical dysplasia type II ⚠
  • p.Ala607= Multiple submitters lymphangioleiomyomatosis
  • p.Ala607Thr Multiple submitters hereditary neoplastic syndrome ⚠
  • p.Ala623= Multiple submitters lymphangioleiomyomatosis
  • p.Ala673Val Multiple submitters hereditary neoplastic syndrome
  • p.Ala675= Multiple submitters hereditary neoplastic syndrome
  • p.Ala678= Multiple submitters hereditary neoplastic syndrome
  • p.Ala68= Multiple submitters hereditary neoplastic syndrome
  • p.Ala736= Multiple submitters tuberous sclerosis 2
  • p.Ala736Val Multiple submitters tuberous sclerosis 2
  • p.Ala77= Multiple submitters tuberous sclerosis 2
  • p.Ala835= Multiple submitters tuberous sclerosis 2
  • p.Ala837= Multiple submitters hereditary neoplastic syndrome
  • p.Ala840= Multiple submitters hereditary neoplastic syndrome
  • p.Ala866= Multiple submitters hereditary neoplastic syndrome
  • p.Ala870= Multiple submitters hereditary neoplastic syndrome
  • p.Ala894= Multiple submitters hereditary neoplastic syndrome
  • p.Ala97= Multiple submitters tuberous sclerosis 2
  • p.Ala972= Multiple submitters tuberous sclerosis 2
  • p.Arg1103= Multiple submitters tuberous sclerosis 2
  • p.Arg1122Cys Multiple submitters hereditary neoplastic syndrome
  • p.Arg1129= Multiple submitters tuberous sclerosis 2
  • p.Arg1138Gln Multiple submitters hereditary neoplastic syndrome
  • p.Arg1159Trp Multiple submitters lymphangioleiomyomatosis
  • p.Arg1174Trp Multiple submitters hereditary neoplastic syndrome
  • p.Arg1268= Multiple submitters tuberous sclerosis 2
  • p.Arg1268His Multiple submitters hereditary neoplastic syndrome
  • p.Arg1329His Multiple submitters lymphangioleiomyomatosis
  • p.Arg1355= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1369= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1409= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1417= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1459= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1470= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1477= Multiple submitters hereditary neoplastic syndrome
  • p.Arg151= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1529= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1570= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1729= Multiple submitters tuberous sclerosis 2
  • p.Arg1749= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1793= Multiple submitters hereditary neoplastic syndrome
  • p.Arg1793Gln Multiple submitters hereditary neoplastic syndrome ⚠
  • p.Arg1795Cys Multiple submitters isolated focal cortical dysplasia type II ⚠
  • p.Arg208Gln Multiple submitters hereditary neoplastic syndrome
  • p.Arg245= Multiple submitters hereditary neoplastic syndrome
  • p.Arg25= Multiple submitters tuberous sclerosis 2
  • p.Arg261Trp Multiple submitters hereditary neoplastic syndrome ⚠
  • p.Arg29= Multiple submitters hereditary neoplastic syndrome
  • p.Arg308= Multiple submitters hereditary neoplastic syndrome
  • p.Arg350= Multiple submitters tuberous sclerosis 2
  • p.Arg367= Multiple submitters tuberous sclerosis
  • p.Arg381= Multiple submitters hereditary neoplastic syndrome
  • p.Arg462= Multiple submitters tuberous sclerosis 2
  • p.Arg477= Multiple submitters tuberous sclerosis 2
  • p.Arg537Cys Multiple submitters hereditary neoplastic syndrome
  • p.Arg611= Multiple submitters hereditary neoplastic syndrome
  • p.Arg622= Multiple submitters tuberous sclerosis 2
  • p.Arg628= Multiple submitters hereditary neoplastic syndrome
  • p.Arg691= Multiple submitters lymphangioleiomyomatosis
  • p.Arg712= Multiple submitters tuberous sclerosis 2
  • p.Arg718= Multiple submitters hereditary neoplastic syndrome
  • p.Arg799= Multiple submitters tuberous sclerosis

Likely benign 2257

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 4278

Showing the top 300 by review status; the full set is in the sitemap.