ClinVar Miner

Variants with conflicting interpretations studied for Epileptic encephalopathy

Coded as:
Minimum review status of the submission for Epileptic encephalopathy: Collection method of the submission for Epileptic encephalopathy:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
3735 414 0 87 69 1 8 160

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All conditions
Epileptic encephalopathy pathogenic likely pathogenic uncertain significance likely benign benign protective other
pathogenic 0 5 3 1 1 1 1
likely pathogenic 10 0 5 0 0 0 0
uncertain significance 1 0 0 21 1 0 0
likely benign 0 0 40 0 9 0 0
benign 0 0 8 65 0 0 0

Condition to condition summary #

Total conditions: 48
Download table as spreadsheet
Condition Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
not provided 0 148 0 63 25 1 7 91
not specified 0 189 0 3 39 0 2 43
FASN-related condition 0 46 0 16 3 0 0 19
RYR3-related condition 0 39 0 14 1 0 0 15
Epileptic encephalopathy 4299 7 0 2 1 0 0 3
GABBR2-related condition 0 12 0 3 0 0 0 3
See cases 0 4 0 2 0 0 1 2
Seizure 0 1 0 2 0 0 1 2
16p13.11 recurrent microdeletion syndrome 0 0 0 1 0 0 0 1
1p13.3 deletion syndrome 0 0 0 1 0 0 0 1
ATAD3 gene cluster related condition 0 0 0 0 0 0 1 1
Abnormal bleeding 0 0 0 1 0 0 0 1
Anophthalmia-microphthalmia syndrome 0 0 0 1 0 0 0 1
Arthrogryphosis 0 0 0 0 0 0 1 1
Atypical behavior; Low-set ears; Prominent nasal bridge; Underdeveloped nasal alae; Intellectual disability, mild; Secondary microcephaly 0 0 0 0 0 0 1 1
Atypical behavior; Moderate global developmental delay 0 0 0 0 0 0 1 1
Autistic behavior; Absent speech 0 0 0 0 0 0 1 1
Autistic behavior; Moderate global developmental delay 0 0 0 1 0 0 0 1
Autistic behavior; Severe global developmental delay 0 0 0 1 0 0 0 1
Cardiovascular phenotype 0 0 0 0 0 0 1 1
Deep venous thrombosis 0 0 0 1 0 0 0 1
Delayed speech and language development 0 0 0 1 0 0 0 1
Flexion contracture 0 2 0 0 1 0 0 1
Focal-onset seizure 0 0 0 1 0 0 0 1
Gingival bleeding; Impaired epinephrine-induced platelet aggregation; Impaired collagen-induced platelet aggregation; Impaired arachidonic acid-induced platelet aggregation; Impaired ristocetin-induced platelet aggregation; Impaired thrombin-induced platelet aggregation; Impaired thromboxane A2 agonist-induced platelet aggregation 0 0 0 1 0 0 0 1
Global developmental delay 0 1 0 0 0 0 1 1
Global developmental delay; Seizure; Hypotelorism; Short philtrum; Infantile muscular hypotonia 0 0 0 0 0 0 1 1
Growth abnormality 0 0 0 0 0 0 1 1
Inherited Immunodeficiency Diseases 0 0 0 1 0 0 0 1
Intellectual disability, mild 0 0 0 0 0 0 1 1
Internal malformations 0 0 0 0 0 0 1 1
KCNQ2-Related Disorders 0 1 0 1 0 0 0 1
MKS1-related condition 0 0 0 0 0 0 1 1
Marfanoid habitus and intellectual disability 0 0 0 1 0 0 0 1
Muscle dystrophy 0 0 0 1 0 0 0 1
Myoclonic absence seizure 0 0 0 1 0 0 0 1
Neurodevelopmental delay 0 0 0 1 0 0 0 1
PPFIA3-related disorder 0 0 0 1 0 0 0 1
Pediatric metastatic thyroid tumour 0 0 0 1 0 0 0 1
Primary amenorrhea 0 0 0 0 0 0 1 1
Renal transitional cell carcinoma 0 0 0 1 0 0 0 1
SLC4A10-related neurodevelopmental disorder 0 0 0 1 0 0 0 1
Silver Russell Syndrome-related disorder 0 0 0 0 0 0 1 1
Spastic paraplegia 0 0 0 1 0 0 1 1
Spinocerebellar ataxia, X-linked 0 0 0 0 0 1 0 1
TAX1BP3-related arrhythmogenic right ventricular cardiomyopathy 0 0 0 1 0 0 0 1
Tobacco addiction, susceptibility to; Neurodevelopmental disorder with poor language and loss of hand skills; Developmental and epileptic encephalopathy, 59 0 2 0 0 1 0 0 1
ZNF331 deletion 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 160
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_007254.4(PNKP):c.1189-10del rs3739205 0.02593
NM_005458.8(GABBR2):c.2661-20C>T rs56377484 0.01890
NM_001036.6(RYR3):c.14110G>A (p.Glu4704Lys) rs182257230 0.00733
NM_004104.5(FASN):c.2815G>A (p.Glu939Lys) rs142371324 0.00581
NM_004104.5(FASN):c.3306C>G (p.Ala1102=) rs34179714 0.00556
NM_004104.5(FASN):c.2155G>A (p.Glu719Lys) rs12946178 0.00551
NM_001036.6(RYR3):c.9759C>T (p.Asp3253=) rs55650127 0.00531
NM_001036.6(RYR3):c.11289C>T (p.Thr3763=) rs138744371 0.00493
NM_004104.5(FASN):c.1436G>T (p.Gly479Val) rs149982597 0.00458
NM_004104.5(FASN):c.6374G>A (p.Arg2125Gln) rs145866788 0.00359
NM_001036.6(RYR3):c.9254C>G (p.Pro3085Arg) rs61996335 0.00307
NM_001036.6(RYR3):c.4701G>A (p.Ala1567=) rs115119086 0.00288
NM_001036.6(RYR3):c.8555G>A (p.Arg2852His) rs150799181 0.00265
NM_001036.6(RYR3):c.4473C>T (p.Asp1491=) rs61996324 0.00260
NM_001036.6(RYR3):c.9873C>G (p.Leu3291=) rs147149598 0.00253
NM_004104.5(FASN):c.6118G>T (p.Ala2040Ser) rs150748779 0.00243
NM_004104.5(FASN):c.5259G>A (p.Leu1753=) rs75603975 0.00207
NM_001036.6(RYR3):c.7490A>G (p.Asn2497Ser) rs61996331 0.00195
NM_001036.6(RYR3):c.1788+10G>C rs146892882 0.00189
NM_001036.6(RYR3):c.4821T>C (p.Tyr1607=) rs200740143 0.00180
NM_004104.5(FASN):c.7169T>G (p.Leu2390Arg) rs138021210 0.00170
NM_001036.6(RYR3):c.10921A>G (p.Met3641Val) rs146201205 0.00168
NM_001036.6(RYR3):c.10698G>A (p.Thr3566=) rs200309704 0.00163
NM_001036.6(RYR3):c.11196G>A (p.Thr3732=) rs148918638 0.00155
NM_001036.6(RYR3):c.11464-8C>A rs200401387 0.00152
NM_001036.6(RYR3):c.6617A>C (p.Asn2206Thr) rs181264765 0.00150
NM_000053.4(ATP7B):c.1995G>A (p.Met665Ile) rs72552259 0.00149
NM_004104.5(FASN):c.3974C>T (p.Pro1325Leu) rs150915750 0.00142
NM_001036.6(RYR3):c.7827C>G (p.Ser2609=) rs149242033 0.00139
NM_001036.6(RYR3):c.2486G>A (p.Arg829His) rs199500216 0.00128
NM_004104.5(FASN):c.5412T>A (p.Ser1804Arg) rs140221463 0.00128
NM_001036.6(RYR3):c.5484A>G (p.Ala1828=) rs187371252 0.00127
NM_004104.5(FASN):c.3555C>G (p.Ala1185=) rs142613672 0.00110
NM_001036.6(RYR3):c.2214G>A (p.Ser738=) rs201215774 0.00105
NM_001036.6(RYR3):c.6698G>A (p.Arg2233Gln) rs199648816 0.00104
NM_001036.6(RYR3):c.9831-8G>C rs377437662 0.00098
NM_001036.6(RYR3):c.4296C>T (p.Gly1432=) rs61749016 0.00089
NM_001036.6(RYR3):c.13938A>G (p.Leu4646=) rs199645058 0.00086
NM_001036.6(RYR3):c.5393G>A (p.Arg1798Gln) rs148818748 0.00080
NM_005458.8(GABBR2):c.1473C>T (p.Leu491=) rs144313756 0.00080
NM_004104.5(FASN):c.4896C>T (p.Phe1632=) rs138021448 0.00078
NM_004104.5(FASN):c.6477C>T (p.Ser2159=) rs146570982 0.00073
NM_001036.6(RYR3):c.8481C>T (p.Tyr2827=) rs188257094 0.00068
NM_001036.6(RYR3):c.2770A>G (p.Thr924Ala) rs199638420 0.00063
NM_001036.6(RYR3):c.11536G>A (p.Val3846Ile) rs187632363 0.00056
NM_001036.6(RYR3):c.7249A>G (p.Ile2417Val) rs200294137 0.00055
NM_001036.6(RYR3):c.3348C>T (p.Ala1116=) rs189409991 0.00051
NM_004104.5(FASN):c.7378G>A (p.Ala2460Thr) rs149224679 0.00051
NM_001036.6(RYR3):c.621G>A (p.Thr207=) rs370200639 0.00048
NM_005458.8(GABBR2):c.51A>G (p.Pro17=) rs893078508 0.00045
NM_004104.5(FASN):c.591C>T (p.Ser197=) rs141843553 0.00044
NM_004104.5(FASN):c.2757G>A (p.Leu919=) rs147904451 0.00040
NM_001036.6(RYR3):c.8236A>G (p.Ile2746Val) rs201914506 0.00039
NM_001036.6(RYR3):c.10556C>G (p.Thr3519Arg) rs377288128 0.00036
NM_004104.5(FASN):c.2120C>T (p.Pro707Leu) rs144627566 0.00036
NM_004104.5(FASN):c.694C>T (p.Leu232=) rs143618212 0.00034
NM_005458.8(GABBR2):c.894C>T (p.Asn298=) rs532040816 0.00034
NM_004104.5(FASN):c.1411G>A (p.Ala471Thr) rs145247848 0.00031
NM_005458.8(GABBR2):c.1938G>A (p.Glu646=) rs79484588 0.00029
NM_004104.5(FASN):c.1840C>T (p.His614Tyr) rs140698052 0.00028
NM_001036.6(RYR3):c.5078C>T (p.Thr1693Met) rs370691735 0.00027
NM_001036.6(RYR3):c.5978T>C (p.Ile1993Thr) rs200006806 0.00027
NM_005458.8(GABBR2):c.1662C>T (p.Thr554=) rs144905072 0.00026
NM_005458.8(GABBR2):c.1767G>A (p.Lys589=) rs150053493 0.00026
NM_001036.6(RYR3):c.17A>G (p.Glu6Gly) rs562147027 0.00024
NM_004104.5(FASN):c.6146G>A (p.Arg2049Gln) rs373838349 0.00022
NM_001036.6(RYR3):c.5799A>T (p.Lys1933Asn) rs199507912 0.00021
NM_001036.6(RYR3):c.6806C>T (p.Thr2269Met) rs201082522 0.00021
NM_004104.5(FASN):c.1230G>A (p.Pro410=) rs376870564 0.00021
NM_004104.5(FASN):c.3829C>G (p.Pro1277Ala) rs764159372 0.00021
NM_005458.8(GABBR2):c.330C>T (p.Asn110=) rs139594158 0.00021
NM_001036.6(RYR3):c.12778A>G (p.Ile4260Val) rs372580668 0.00019
NM_001036.6(RYR3):c.9830+5G>A rs373984848 0.00019
NM_004104.5(FASN):c.1384G>A (p.Ala462Thr) rs141275719 0.00019
NM_001036.6(RYR3):c.13363G>A (p.Glu4455Lys) rs770667248 0.00017
NM_004104.5(FASN):c.5001C>T (p.Pro1667=) rs368052188 0.00016
NM_005458.8(GABBR2):c.1364C>A (p.Thr455Asn) rs373607825 0.00016
NM_005458.8(GABBR2):c.1921A>G (p.Ile641Val) rs565513030 0.00016
NM_004104.5(FASN):c.5285C>T (p.Thr1762Met) rs140375571 0.00015
NM_004104.5(FASN):c.5049C>T (p.Ala1683=) rs150176506 0.00014
NM_005458.8(GABBR2):c.1977C>T (p.Ile659=) rs140073399 0.00014
NM_005458.8(GABBR2):c.2318C>T (p.Thr773Met) rs138346207 0.00014
NM_005458.8(GABBR2):c.884C>T (p.Thr295Met) rs200422079 0.00014
NM_004104.5(FASN):c.966C>T (p.Ile322=) rs200366210 0.00013
NM_005458.8(GABBR2):c.663C>T (p.Gly221=) rs371998319 0.00013
NM_153033.5(KCTD7):c.362G>T (p.Arg121Leu) rs199624315 0.00013
NM_001036.6(RYR3):c.923G>A (p.Arg308Gln) rs201830013 0.00012
NM_001036.6(RYR3):c.13877C>T (p.Ala4626Val) rs202096363 0.00011
NM_004104.5(FASN):c.1328G>A (p.Arg443Gln) rs199956437 0.00009
NM_004104.5(FASN):c.48G>A (p.Ser16=) rs766051789 0.00009
NM_004104.5(FASN):c.4128G>A (p.Ala1376=) rs201599707 0.00008
NM_004104.5(FASN):c.6235A>G (p.Ile2079Val) rs753756949 0.00008
NM_005458.8(GABBR2):c.1212C>T (p.Asn404=) rs140891913 0.00008
NM_001036.6(RYR3):c.7040C>T (p.Ser2347Leu) rs781065862 0.00007
NM_001036.6(RYR3):c.13207C>T (p.Leu4403=) rs369324246 0.00006
NM_001036.6(RYR3):c.4521C>T (p.Phe1507=) rs201164828 0.00006
NM_003359.4(UGDH):c.950G>A (p.Arg317Gln) rs775162839 0.00006
NM_004104.5(FASN):c.1147G>A (p.Val383Ile) rs764001564 0.00006
NM_001036.6(RYR3):c.4183A>G (p.Ile1395Val) rs571025757 0.00005
NM_001036.6(RYR3):c.7852G>A (p.Val2618Ile) rs369629619 0.00005
NM_004104.5(FASN):c.3856G>A (p.Glu1286Lys) rs776776391 0.00005
NM_005458.8(GABBR2):c.399C>T (p.Gly133=) rs754203594 0.00005
NM_001036.6(RYR3):c.3334G>A (p.Val1112Ile) rs757239023 0.00004
NM_001036.6(RYR3):c.3419G>A (p.Arg1140His) rs774751337 0.00004
NM_001037.5(SCN1B):c.265C>T (p.Arg89Cys) rs766910280 0.00004
NM_005458.8(GABBR2):c.1177C>G (p.His393Asp) rs768482972 0.00004
NM_005458.8(GABBR2):c.56C>T (p.Pro19Leu) rs1054346747 0.00004
NM_005458.8(GABBR2):c.613G>A (p.Val205Ile) rs146801036 0.00004
NM_005458.8(GABBR2):c.882C>T (p.His294=) rs200727904 0.00004
NM_004104.5(FASN):c.5103G>A (p.Ser1701=) rs752285807 0.00003
NM_004104.5(FASN):c.5423G>A (p.Arg1808Gln) rs151134760 0.00003
NM_005458.8(GABBR2):c.1896G>A (p.Pro632=) rs373578537 0.00003
NM_005458.8(GABBR2):c.2542+6del rs774664411 0.00003
NM_005458.8(GABBR2):c.630+4C>T rs758380768 0.00003
NM_005458.8(GABBR2):c.664G>A (p.Glu222Lys) rs750467268 0.00003
NM_000053.4(ATP7B):c.3007G>A (p.Ala1003Thr) rs201497300 0.00002
NM_001036.6(RYR3):c.2599A>G (p.Lys867Glu) rs752228470 0.00002
NM_001036.6(RYR3):c.5356G>A (p.Gly1786Ser) rs759581452 0.00002
NM_004104.5(FASN):c.4654C>T (p.Arg1552Cys) rs762427627 0.00002
NM_004104.5(FASN):c.102G>A (p.Thr34=) rs748255121 0.00001
NM_004104.5(FASN):c.1984G>A (p.Val662Met) rs372061454 0.00001
NM_004104.5(FASN):c.4195A>G (p.Thr1399Ala) rs764626319 0.00001
NM_004104.5(FASN):c.6531C>T (p.Arg2177=) rs1160132362 0.00001
NM_005458.8(GABBR2):c.1641G>C (p.Lys547Asn) rs1228267111 0.00001
NM_005458.8(GABBR2):c.1924C>T (p.Arg642Cys) rs756391068 0.00001
NM_005458.8(GABBR2):c.1925G>T (p.Arg642Leu) rs781275870 0.00001
NM_005458.8(GABBR2):c.2412+3A>G rs74429712 0.00001
NM_005458.8(GABBR2):c.599C>T (p.Thr200Met) rs146370047 0.00001
NC_000009.11:g.(?_101470679)_(101611374_?)dup
NM_000702.4(ATP1A2):c.1777C>T (p.Arg593Trp) rs886039530
NM_001036.6(RYR3):c.11G>C (p.Gly4Ala) rs375998723
NM_001036.6(RYR3):c.6125A>G (p.Asn2042Ser) rs116926961
NM_001036.6(RYR3):c.9812G>A (p.Arg3271His) rs187608290
NM_001040142.2(SCN2A):c.3947C>T (p.Ala1316Val) rs796053130
NM_001040142.2(SCN2A):c.5645G>A (p.Arg1882Gln) rs794727444
NM_001165963.4(SCN1A):c.4036T>C (p.Ser1346Pro) rs1553525337
NM_001330260.2(SCN8A):c.4423G>A (p.Gly1475Arg) rs796053216
NM_004104.5(FASN):c.3286G>A (p.Gly1096Arg) rs62642478
NM_004104.5(FASN):c.3874G>A (p.Val1292Ile) rs773063554
NM_004104.5(FASN):c.820C>T (p.Arg274Cys) rs562846615
NM_004104.5(FASN):c.894+8C>A rs759051221
NM_004975.4(KCNB1):c.916C>T (p.Arg306Cys) rs1555889130
NM_004975.4(KCNB1):c.968C>T (p.Thr323Ile) rs1569017257
NM_005458.8(GABBR2):c.113G>A (p.Gly38Glu) rs1830934754
NM_005458.8(GABBR2):c.23G>A (p.Gly8Glu) rs950352036
NM_005458.8(GABBR2):c.2542+4A>G rs1830429438
NM_005458.8(GABBR2):c.25C>G (p.Gln9Glu) rs1026022583
NM_005458.8(GABBR2):c.2737A>G (p.Ser913Gly) rs1830289381
NM_005458.8(GABBR2):c.339G>T (p.Gly113=) rs766579887
NM_005458.8(GABBR2):c.33GCC[7] (p.Pro20dup) rs751111546
NM_005458.8(GABBR2):c.422T>C (p.Ile141Thr) rs1588236381
NM_005458.8(GABBR2):c.58C>T (p.Pro20Ser) rs1430262254
NM_005859.5(PURA):c.98del (p.Gly33fs)
NM_007325.5(GRIA3):c.2327C>T (p.Thr776Met) rs780680047
NM_017646.6(TRIT1):c.334del (p.Arg112fs) rs536000212
NM_020988.3(GNAO1):c.118G>C (p.Gly40Arg) rs886041715
NM_031844.3(HNRNPU):c.651_660del (p.Gly218fs) rs779453109
NM_172107.4(KCNQ2):c.1742G>A (p.Arg581Gln) rs118192235
NM_172107.4(KCNQ2):c.2126dup (p.Val710fs) rs1555850842
Single allele

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