ClinVar Miner

Variants with conflicting interpretations studied for Epileptic encephalopathy

Coded as:
Minimum review status of the submission for Epileptic encephalopathy: Y axis 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 Variants with at least 2 submissions 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 kind of conflict
950 34 0 22 13 1 7 39

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 association
pathogenic 0 4 4 1 1 1
likely pathogenic 9 0 0 0 0 0
uncertain significance 1 2 0 11 5 0
likely benign 0 0 1 0 5 0
benign 0 0 0 4 0 0

Condition to condition summary #

Total conditions: 131
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
not specified 0 3 0 7 8 0 1 16
Early infantile epileptic encephalopathy 12 0 4 0 5 5 0 0 10
not provided 0 24 0 6 1 0 3 9
History of neurodevelopmental disorder 0 2 0 2 4 0 0 6
Early infantile epileptic encephalopathy 10 0 2 0 1 2 0 0 3
Inborn genetic diseases 0 1 0 0 2 0 1 3
Early infantile epileptic encephalopathy 11 0 1 0 1 0 0 1 2
Early infantile epileptic encephalopathy 7 0 1 0 1 0 0 1 2
Epileptic encephalopathy, early infantile, 24 0 0 0 2 0 0 0 2
Wilson disease 0 1 0 1 1 0 1 2
1p13.3 deletion syndrome 0 0 0 1 0 0 0 1
Abnormality of the eye 0 0 0 1 0 0 0 1
Acrodysostosis 2, with or without hormone resistance 0 0 0 0 0 0 1 1
Adams-Oliver syndrome 5 0 0 0 1 0 0 0 1
Aortic aneurysm, familial thoracic 4 0 0 0 0 0 0 1 1
Arrhythmogenic right ventricular dysplasia, familial, 13 0 0 0 0 0 0 1 1
Ataxia-telangiectasia-like disorder 1 0 0 0 1 0 0 0 1
Autism spectrum disorder 0 0 0 1 0 1 1 1
Autism spectrum disorder; Epilepsy 0 0 0 1 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
Autistic disorder of childhood onset 0 0 0 1 0 0 1 1
Autistic disorder of childhood onset; Schizophrenia 0 0 0 1 0 0 0 1
Behavioral abnormality; Low-set ears; Prominent nasal bridge; Underdeveloped nasal alae; Intellectual disability, mild; Postnatal microcephaly 0 0 0 0 0 0 1 1
Behavioral abnormality; Moderate global developmental delay 0 0 0 0 0 0 1 1
Benign familial neonatal seizures 1 0 0 0 1 0 0 0 1
Bethlem myopathy 1 0 0 0 0 0 0 1 1
Biotin-thiamine-responsive basal ganglia disease 0 0 0 0 0 0 1 1
Biotinidase deficiency 0 0 0 0 0 0 1 1
Birk-Barel Intellectual Disability Dysmorphism Syndrome 0 0 0 0 0 0 1 1
Breast-ovarian cancer, familial 1 0 0 0 1 0 0 1 1
Brown-Vialetto-Van Laere syndrome 1 0 0 0 0 0 0 1 1
CHARGE association 0 0 0 0 0 0 1 1
Cerebral cavernous malformation 0 0 0 1 0 0 0 1
Charcot-Marie-Tooth disease 0 0 0 1 0 0 1 1
Charcot-Marie-Tooth disease type 2K 0 0 0 0 0 0 1 1
Charcot-Marie-Tooth disease, demyelinating, type 1b 0 0 0 1 0 0 0 1
Collagen VI-related myopathy 0 0 0 0 0 0 1 1
Combined oxidative phosphorylation deficiency 14 0 0 0 0 0 0 1 1
Combined oxidative phosphorylation deficiency 31 0 0 0 1 0 0 0 1
Cone/cone-rod dystrophy 0 0 0 1 0 0 0 1
Congenital contractural arachnodactyly 0 0 0 0 0 0 1 1
Cornelia de Lange syndrome 1 0 0 0 1 0 0 0 1
Currarino triad 0 0 0 1 0 0 0 1
Cystinuria 0 0 0 1 0 0 0 1
Dilated Cardiomyopathy, Dominant 0 0 0 0 0 0 1 1
Dilated cardiomyopathy 1G 0 0 0 1 0 0 0 1
Duchenne muscular dystrophy 0 0 0 1 0 0 1 1
Ductal breast carcinoma 0 0 0 0 0 0 1 1
Early infantile epileptic encephalopathy 0 5 0 1 0 0 1 1
Early infantile epileptic encephalopathy 2 0 0 0 1 0 0 0 1
Early infantile epileptic encephalopathy 2; Angelman syndrome-like 0 1 0 1 0 0 0 1
Ehlers-Danlos syndrome, classic type 0 0 0 0 0 0 1 1
Epilepsy, childhood absence 2; Familial febrile seizures 8 0 0 0 1 0 0 0 1
Epilepsy, progressive myoclonic 3 0 0 0 0 0 0 1 1
Epileptic encephalopathy, early infantile, 1; Spinocerebellar ataxia, autosomal recessive 12 0 0 0 1 0 0 0 1
Epileptic encephalopathy, early infantile, 26 0 4 0 0 0 0 1 1
Epileptic encephalopathy, early infantile, 48 0 0 0 1 0 0 0 1
Failure to thrive in infancy; Attention deficit hyperactivity disorder 0 0 0 0 0 0 1 1
Familial adenomatous polyposis 1 0 0 0 1 0 0 0 1
Familial cancer of breast 0 0 0 1 0 0 1 1
Familial colorectal cancer 0 0 0 0 0 0 1 1
Familial hypercholesterolemia 0 0 0 1 0 0 1 1
Familial hypokalemia-hypomagnesemia 0 0 0 1 0 0 0 1
Fanconi anemia 0 0 0 0 0 0 1 1
Fanconi anemia, complementation group A 0 0 0 1 0 0 0 1
Galactosylceramide beta-galactosidase deficiency 0 0 0 0 0 0 1 1
Glioma 0 0 0 1 0 0 0 1
Global developmental delay; Hypoplasia of the corpus callosum; Abnormality of the cerebral white matter; Periventricular leukomalacia; Delayed myelination; Muscular hypotonia 0 0 0 1 0 0 0 1
Global developmental delay; Seizures; Intellectual disability 0 0 0 1 0 0 0 1
Hereditary Paraganglioma-Pheochromocytoma Syndromes 0 0 0 0 0 0 1 1
Hereditary breast and ovarian cancer syndrome 0 0 0 1 0 0 0 1
Hereditary cancer-predisposing syndrome 0 0 0 1 0 0 0 1
Hereditary nonpolyposis colon cancer 0 0 0 1 0 0 1 1
Hereditary pancreatitis 0 0 0 0 0 0 1 1
Hereditary sensory and autonomic neuropathy type IIA; Generalized epilepsy with febrile seizures plus, type 7 0 0 0 0 0 0 1 1
Hereditary sensory and autonomic neuropathy type IIB 0 0 0 0 0 0 1 1
Hypertrophic cardiomyopathy 0 0 0 0 0 0 1 1
Idiopathic fibrosing alveolitis, chronic form; Dyskeratosis congenita, autosomal dominant, 2 0 0 0 0 0 0 1 1
Infantile nephronophthisis 0 0 0 1 0 0 0 1
Intellectual disability, mild 0 0 0 0 0 0 1 1
Intestinal malrotation 0 0 0 1 0 0 1 1
Joubert syndrome 20; Meckel syndrome, type 11 0 0 0 0 0 0 1 1
Juvenile polyposis syndrome 0 0 0 0 0 0 1 1
Leber congenital amaurosis 0 0 0 1 0 0 0 1
Left ventricular noncompaction cardiomyopathy 0 0 0 0 0 0 1 1
Limb-girdle muscular dystrophy, type 2A 0 0 0 1 0 0 0 1
Majeed syndrome 0 0 0 1 0 0 0 1
Melanoma, cutaneous malignant, susceptibility to, 10 0 0 0 0 0 0 1 1
Mental retardation, autosomal dominant 18 0 0 0 1 0 0 0 1
Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis 0 0 0 0 0 0 1 1
Mitochondrial complex I deficiency 0 0 0 0 0 0 1 1
Myofibrillar myopathy, filamin C-related; Myopathy, distal, 4; Cardiomyopathy, familial hypertrophic, 26; Dilated Cardiomyopathy, Dominant 0 0 0 0 0 0 1 1
Myopathy, distal, 1 0 0 0 0 0 0 1 1
Myosclerosis 0 0 0 0 0 0 1 1
Myosin storage myopathy 0 0 0 0 0 0 1 1
Nemaline myopathy 6 0 0 0 1 0 0 0 1
Nephronophthisis 0 0 0 0 0 0 1 1
Neuroblastoma 3 0 0 0 0 0 0 1 1
Neurodevelopmental disorder 0 0 0 0 0 0 1 1
Neurofibromatosis, type 2 0 0 0 0 0 0 1 1
Neuronopathy, distal hereditary motor, type viia; Myasthenic syndrome, congenital, 20, presynaptic 0 0 0 0 0 0 1 1
Neuropathy, hereditary motor and sensory, Okinawa type; Spastic paraplegia 57, autosomal recessive 0 0 0 0 0 0 1 1
Parkinson disease 2 0 0 0 1 0 0 0 1
Pediatric metastatic thyroid tumour 0 0 0 1 0 0 0 1
Peripheral neuropathy 0 0 0 0 0 0 1 1
Pitt-Hopkins syndrome 0 0 0 1 0 0 0 1
Primary ciliary dyskinesia 0 0 0 1 0 0 1 1
Primary hyperoxaluria, type I 0 0 0 0 0 0 1 1
Progressive familial heart block type 1B 0 0 0 0 0 0 1 1
Progressive myoclonus epilepsy with ataxia 0 0 0 1 0 0 0 1
Renal transitional cell carcinoma 0 0 0 1 0 0 0 1
Retinal dystrophy 0 0 0 1 0 0 0 1
Retinitis pigmentosa 0 0 0 1 0 0 0 1
Robin sequence; Intellectual disability, mild; Bilateral conductive hearing impairment; Abnormality of esophagus physiology 0 0 0 1 0 0 0 1
Scapuloperoneal myopathy 0 0 0 0 0 0 1 1
Schizophrenia 0 0 0 1 0 0 0 1
Seizures; Delayed speech and language development; Intellectual disability; Generalized hypotonia; Difficulty walking; Epileptic encephalopathy 0 0 0 1 0 0 0 1
Seizures; Intellectual disability 0 1 0 1 0 0 0 1
Seizures; Narrow nasal bridge; Mandibular prognathia; Delayed speech and language development; Intrauterine growth retardation 0 0 0 0 0 0 1 1
Spastic paraplegia 0 0 0 0 0 0 1 1
Spastic paraplegia 11, autosomal recessive 0 0 0 0 0 0 1 1
Spastic paraplegia 30, autosomal recessive; Hereditary sensory and autonomic neuropathy type IIC; Mental retardation, autosomal dominant 9 0 0 0 0 0 0 1 1
Spinal muscular atrophy, distal, autosomal recessive, 5 0 0 0 0 0 0 1 1
Spinocerebellar ataxia 27 0 0 0 1 0 0 0 1
Stargardt disease 1 0 0 0 1 0 0 0 1
Thoracic aortic aneurysm and aortic dissection 0 0 0 1 0 0 1 1
Treacher Collins syndrome 1 0 0 0 1 0 0 0 1
Usher syndrome 0 0 0 1 0 0 0 1
Visceral myopathy 0 0 0 1 0 0 0 1
not provided; not provided 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 39
Download table as spreadsheet
HGVS dbSNP
NM_000053.4(ATP7B):c.1995G>A (p.Met665Ile) rs72552259
NM_000053.4(ATP7B):c.3007G>A (p.Ala1003Thr) rs201497300
NM_000702.4(ATP1A2):c.1777C>T (p.Arg593Trp) rs886039530
NM_001036.5(RYR3):c.4991G>C (p.Gly1664Ala) rs762176717
NM_001036.5(RYR3):c.6125A>G (p.Asn2042Ser) rs116926961
NM_001036.5(RYR3):c.9799C>T (p.Pro3267Ser) rs182972491
NM_001040142.2(SCN2A):c.2687C>T (p.Ala896Val) rs1057519526
NM_001040142.2(SCN2A):c.3947C>T (p.Ala1316Val) rs796053130
NM_001040142.2(SCN2A):c.5645G>A (p.Arg1882Gln) rs794727444
NM_001278512.2(AP3B2):c.1182G>A (p.Lys394=) rs1057519269
NM_001323289.2(CDKL5):c.587C>T (p.Ser196Leu) rs267608501
NM_004104.5(FASN):c.2155G>A (p.Glu719Lys) rs12946178
NM_004104.5(FASN):c.5103G>A (p.Ser1701=) rs752285807
NM_004975.4(KCNB1):c.1105T>C (p.Trp369Arg) rs1569017174
NM_004975.4(KCNB1):c.935G>A (p.Arg312His) rs1555889127
NM_007254.4(PNKP):c.-50G>C rs3739166
NM_007254.4(PNKP):c.1127-8C>T rs3739203
NM_007254.4(PNKP):c.1189-10del rs3739205
NM_007254.4(PNKP):c.1320C>T (p.Ala440=) rs565533397
NM_007254.4(PNKP):c.1385G>C (p.Arg462Pro) rs376854895
NM_007254.4(PNKP):c.1387-11G>A rs200785744
NM_007254.4(PNKP):c.1433T>G (p.Val478Gly) rs3739206
NM_007254.4(PNKP):c.579-5C>T rs767753048
NM_007254.4(PNKP):c.579G>A (p.Arg193=) rs145904995
NM_007254.4(PNKP):c.586T>A (p.Tyr196Asn) rs3739186
NM_007254.4(PNKP):c.627G>A (p.Glu209=) rs532550120
NM_007254.4(PNKP):c.636+7G>A rs3739187
NM_007254.4(PNKP):c.783G>A (p.Pro261=) rs145307985
NM_007254.4(PNKP):c.831G>A (p.Thr277=) rs148491228
NM_007254.4(PNKP):c.939T>C (p.Phe313=) rs149731642
NM_014191.4(SCN8A):c.4423G>A (p.Gly1475Arg) rs796053216
NM_021072.4(HCN1):c.1172G>A (p.Gly391Asp) rs1057519547
NM_021072.4(HCN1):c.459G>C (p.Met153Ile) rs1057519548
NM_138982.4(MAPK10):c.1111-6C>T rs13103861
NM_138982.4(MAPK10):c.960G>A (p.Ala320=) rs55663953
NM_172107.3(KCNQ2):c.1742G>A (p.Arg581Gln) rs118192235
NM_172107.4(KCNQ2):c.802C>T (p.Leu268Phe) rs1057516094
NM_172107.4(KCNQ2):c.901G>A (p.Gly301Ser) rs1057516099
Single allele

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