ClinVar Miner

Variants from Génétique des Maladies du Développement, Hospices Civils de Lyon

Location: France — Primary collection method: clinical testing
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If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells.

pathogenic likely pathogenic uncertain significance likely benign benign total
138 104 48 5 1 295

Gene and significance breakdown #

Total genes and gene combinations: 131
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign total
KCNQ2 10 5 0 0 0 15
SCN2A 7 6 1 1 0 15
GRIN2A 5 3 5 0 0 13
KCNT1 4 4 2 0 0 10
CDKL5 5 3 0 0 0 8
SYNGAP1 8 0 0 0 0 8
CHD2 1 4 2 0 0 7
ATP1A3 2 2 2 0 0 6
SCN1A 6 0 0 0 0 6
STXBP1 4 2 0 0 0 6
KMT2D 3 2 0 0 0 5
LOC102724058, SCN1A 3 2 1 0 0 5
MECP2 2 0 3 0 0 5
PCDH19 4 1 0 0 0 5
SCN8A 2 2 1 0 0 5
EHMT1 1 2 1 0 0 4
GNAO1 3 1 0 0 0 4
PRRT2 3 1 0 0 0 4
SLC6A1 0 3 1 0 0 4
ADNP 3 0 0 0 0 3
ARHGEF9 1 2 0 0 0 3
ARID1B 2 1 0 0 0 3
GRIN2B 2 0 1 0 0 3
IQSEC2 2 1 0 0 0 3
KDM5C 1 2 0 0 0 3
SCN1B 0 0 3 0 0 3
SETD5 2 1 0 0 0 3
SLC2A1 2 1 0 0 0 3
SNHG14, UBE3A 2 1 0 0 0 3
WDR45 1 2 0 0 0 3
ARMCX5-GPRASP2, GPRASP1 0 0 2 0 0 2
ATP1A2 2 0 0 0 0 2
CACNA1A 1 1 0 0 0 2
CASK 0 2 0 0 0 2
CNKSR2 0 1 1 0 0 2
DEPDC5 0 0 2 0 0 2
DNMT3A 0 2 0 0 0 2
EEF1A2 1 1 0 0 0 2
EMC1 1 1 0 0 0 2
FOXP1 0 2 0 0 0 2
GABRA1 2 0 0 0 0 2
GABRB3 0 1 1 0 0 2
IL1RAPL1 1 0 1 0 0 2
KANSL1 2 0 0 0 0 2
KCNB1 1 1 0 0 0 2
MED12 0 0 2 0 0 2
MED13L 1 1 0 0 0 2
NR2F1 0 2 0 0 0 2
NSD1 1 1 0 0 0 2
POGZ 1 1 0 0 0 2
RPS6KA3 1 1 0 0 0 2
SATB2 1 1 0 0 0 2
SMARCA4 0 2 0 0 0 2
TRIO 0 1 1 0 0 2
TRIP12 1 1 0 0 0 2
TUBA1A 0 1 1 0 0 2
ACTB 0 1 0 0 0 1
AIFM1, RAB33A 0 0 0 0 1 1
ALDH4A1 0 1 0 0 0 1
ALG13 0 0 1 0 0 1
ANKRD11 1 0 0 0 0 1
ASXL3 1 0 0 0 0 1
BRPF1 1 0 0 0 0 1
CDKL5, RS1 0 1 0 0 0 1
CHD4 0 0 1 0 0 1
CHD7 1 0 0 0 0 1
CHRNA2 0 1 0 0 0 1
CREBBP 0 1 0 0 0 1
CUX2 0 1 0 0 0 1
DCX 1 0 0 0 0 1
DMD 0 0 1 0 0 1
DYRK1A 1 0 0 0 0 1
FARS2 0 1 0 0 0 1
FGF12 0 1 0 0 0 1
FLNA, LOC107988032 0 0 1 0 0 1
FOXG1 0 1 0 0 0 1
FOXP2 0 0 1 0 0 1
GABRG2 0 0 0 1 0 1
GATAD2B 1 0 0 0 0 1
GH-LCR, SCN4A 0 0 0 1 0 1
GRIN1 0 1 0 0 0 1
GRIN2D 0 0 1 0 0 1
GRM1 1 0 0 0 0 1
HDAC8 0 0 1 0 0 1
HIVEP2 1 0 0 0 0 1
HNRNPU 1 0 0 0 0 1
KAT6A 1 0 0 0 0 1
KAT6B 1 0 0 0 0 1
KCNA2 1 0 0 0 0 1
KCNC1 0 1 0 0 0 1
KCND3 0 1 0 0 0 1
KCNQ3 0 1 0 0 0 1
KDM6A 0 1 0 0 0 1
KMT2A 0 1 0 0 0 1
MBD5 0 1 0 0 0 1
MEA1, PPP2R5D 1 0 0 0 0 1
MEF2C 0 1 0 0 0 1
NEDD4L 0 0 1 0 0 1
NEXMIF 1 0 0 0 0 1
NFIX 1 0 0 0 0 1
NHLRC1 1 0 0 0 0 1
PACS1 1 0 0 0 0 1
PDHA1 1 0 0 0 0 1
PHF21A 0 0 1 0 0 1
PIGA 0 1 0 0 0 1
PLAA 1 0 0 0 0 1
PNPO 1 0 0 0 0 1
PPP3CA 1 0 0 0 0 1
PQBP1 1 0 0 0 0 1
PTCHD1 0 0 1 0 0 1
SEMA5A 0 0 1 0 0 1
SETBP1 1 0 0 0 0 1
SHANK2 0 0 1 0 0 1
SHANK3 1 0 0 0 0 1
SIK1 0 0 0 1 0 1
SLC1A1, SPATA6L 0 0 0 1 0 1
SLC35A2 0 1 0 0 0 1
SLC9A6 1 0 0 0 0 1
SMC1A 0 0 1 0 0 1
SMC3 0 1 0 0 0 1
SMS 0 1 0 0 0 1
SON 1 0 0 0 0 1
SOX11 0 1 0 0 0 1
SOX5 0 1 0 0 0 1
STAMBP 0 0 1 0 0 1
STX1B 1 0 0 0 0 1
TCF20 1 0 0 0 0 1
TCF4 1 0 0 0 0 1
USP9X 0 1 0 0 0 1
WWOX 0 1 0 0 0 1
ZDHHC9 0 1 0 0 0 1

Condition and significance breakdown #

Total conditions: 143
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Condition pathogenic likely pathogenic uncertain significance likely benign benign total
Epilepsy, focal, with speech disorder and with or without mental retardation 5 3 4 0 0 12
Generalized epilepsy with febrile seizures plus, type 2 7 2 0 0 0 9
Intellectual disability 1 1 5 0 1 8
Mental retardation, autosomal dominant 5 8 0 0 0 0 8
Benign familial neonatal seizures 1 6 1 0 0 0 7
Early infantile epileptic encephalopathy 14 3 3 1 0 0 7
Early infantile epileptic encephalopathy 2 4 3 0 0 0 7
Early infantile epileptic encephalopathy 4 5 2 0 0 0 7
Epileptic encephalopathy, childhood-onset 1 4 2 0 0 7
Alternating hemiplegia of childhood 2 2 2 2 0 0 6
Early infantile epileptic encephalopathy 11 3 2 0 1 0 6
Early infantile epileptic encephalopathy 7 3 3 0 0 0 6
Early infantile epileptic encephalopathy 9 4 1 0 0 0 5
Seizures 3 0 0 2 0 5
Benign familial neonatal-infantile seizures; Early infantile epileptic encephalopathy 11 1 2 1 0 0 4
Early infantile epileptic encephalopathy 13 2 1 1 0 0 4
Kabuki syndrome 1 3 1 0 0 0 4
Kleefstra syndrome 1 1 2 1 0 0 4
Myoclonic-atonic epilepsy 0 3 1 0 0 4
Angelman syndrome 2 1 0 0 0 3
Benign familial neonatal-infantile seizures 2 1 0 0 0 3
Coffin-Siris syndrome 1 2 1 0 0 0 3
Early infantile epileptic encephalopathy 17 2 1 0 0 0 3
Early infantile epileptic encephalopathy 8 1 2 0 0 0 3
Epilepsy, nocturnal frontal lobe, 5 1 1 1 0 0 3
Helsmoortel-Van der Aa Syndrome 3 0 0 0 0 3
Mental retardation, X-linked 1 2 1 0 0 0 3
Mental retardation, autosomal dominant 23 2 1 0 0 0 3
Mental retardation, syndromic, Claes-Jensen type, X-linked 1 2 0 0 0 3
Neurodegeneration with brain iron accumulation 5 1 2 0 0 0 3
Rett syndrome 1 0 2 0 0 3
Seizures, benign familial infantile, 2 2 1 0 0 0 3
Severe myoclonic epilepsy in infancy 2 0 1 0 0 3
Acute myeloid leukemia; Tatton-Brown-rahman syndrome 0 2 0 0 0 2
Bosch-Boonstra-Schaaf optic atrophy syndrome 0 2 0 0 0 2
Chromosome 2q32-q33 deletion syndrome 1 1 0 0 0 2
Coffin-Lowry syndrome; Mental retardation, X-linked 19 1 1 0 0 0 2
Dystonia 10 2 0 0 0 0 2
Epilepsy, familial focal, with variable foci 1 0 0 2 0 0 2
Epileptic encephalopathy 1 1 0 0 0 2
Epileptic encephalopathy, early infantile, 26 1 1 0 0 0 2
Epileptic encephalopathy, early infantile, 27 1 0 1 0 0 2
Epileptic encephalopathy, early infantile, 42 1 1 0 0 0 2
Epileptic encephalopathy, early infantile, 43 0 1 1 0 0 2
GLUT1 deficiency syndrome 2 1 1 0 0 0 2
Generalized epilepsy with febrile seizures plus, type 1 0 0 2 0 0 2
Global developmental delay; Cerebellar atrophy 1 1 0 0 0 2
KBG syndrome 2 0 0 0 0 2
Koolen-de Vries syndrome 2 0 0 0 0 2
Lissencephaly 3 0 1 1 0 0 2
MENTAL RETARDATION, AUTOSOMAL DOMINANT 49 1 1 0 0 0 2
Mental retardation 21, X-linked 1 0 1 0 0 2
Mental retardation with language impairment and with or without autistic features 0 2 0 0 0 2
Polymicrogyria 2 0 0 0 0 2
Rhabdoid tumor predisposition syndrome 2; Mental retardation, autosomal dominant 16 0 2 0 0 0 2
Seizures; Intellectual disability 1 1 0 0 0 2
Sotos syndrome 1; Acute myeloid leukemia 1 1 0 0 0 2
Transposition of the great arteries, dextro-looped 1; Mental retardation and distinctive facial features with or without cardiac defects 1 1 0 0 0 2
White-sutton syndrome 1 1 0 0 0 2
X-linked mental retardation with marfanoid habitus syndrome; FG syndrome 1; Ohdo syndrome, X-linked 0 0 2 0 0 2
22q13.3 deletion syndrome; Schizophrenia 15 1 0 0 0 0 1
Autism 17 0 0 1 0 0 1
Autism, susceptibility to, X-linked 4 0 0 1 0 0 1
Bainbridge-Ropers syndrome 1 0 0 0 0 1
Baraitser-Winter syndrome 1; Juvenile-onset dystonia 0 1 0 0 0 1
Becker muscular dystrophy; Duchenne muscular dystrophy; Dilated cardiomyopathy 3B 0 0 1 0 0 1
Benign familial neonatal seizures 1; Early infantile epileptic encephalopathy 7 0 1 0 0 0 1
Benign familial neonatal seizures 2 0 1 0 0 0 1
CHARGE association; Kallmann syndrome 5 1 0 0 0 0 1
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIm 0 1 0 0 0 1
Cardiac valvular dysplasia, X-linked; FG syndrome 2; Periventricular nodular heterotopia 1; Intestinal pseudoobstruction neuronal chronic idiopathic X-linked; Melnick-Needles syndrome; Oto-palato-digital syndrome, type I; Oto-palato-digital syndrome, type II; Terminal osseous dysplasia; Frontometaphyseal dysplasia 1 0 0 1 0 0 1
Christianson syndrome 1 0 0 0 0 1
Cognitive impairment with or without cerebellar ataxia; Early infantile epileptic encephalopathy 13; Seizures, benign familial infantile, 5 0 1 0 0 0 1
Combined oxidative phosphorylation deficiency 14 0 1 0 0 0 1
Congenital muscular hypertrophy-cerebral syndrome 0 0 1 0 0 1
Cornelia de Lange syndrome 3 0 1 0 0 0 1
Cornelia de Lange syndrome 5 0 0 1 0 0 1
Deafness, autosomal recessive 28 0 1 0 0 0 1
Deficiency of pyrroline-5-carboxylate reductase 0 1 0 0 0 1
Dicarboxylic aminoaciduria; Schizophrenia 18 0 0 0 1 0 1
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 67 0 1 0 0 0 1
Epilepsy, juvenile myoclonic 5; Epileptic encephalopathy, early infantile, 19 1 0 0 0 0 1
Epilepsy, nocturnal frontal lobe, type 4 0 1 0 0 0 1
Epilepsy, progressive myoclonic 7 0 1 0 0 0 1
Epileptic encephalopathy, early infantile, 19 1 0 0 0 0 1
Epileptic encephalopathy, early infantile, 28 0 1 0 0 0 1
Epileptic encephalopathy, early infantile, 32 1 0 0 0 0 1
Epileptic encephalopathy, early infantile, 33 1 0 0 0 0 1
Epileptic encephalopathy, early infantile, 36 0 0 1 0 0 1
Epileptic encephalopathy, early infantile, 46 0 0 1 0 0 1
Epileptic encephalopathy, early infantile, 47 0 1 0 0 0 1
Epileptic encephalopathy, early infantile, 54 1 0 0 0 0 1
Familial temporal lobe epilepsy 1 0 0 1 0 0 1
Focal seizures 0 0 0 1 0 1
Generalized epilepsy with febrile seizures plus, type 1; Brugada syndrome 5; Atrial fibrillation, familial, 13; Epileptic encephalopathy, early infantile, 52 0 0 1 0 0 1
Generalized epilepsy with febrile seizures plus, type 9 1 0 0 0 0 1
Intellectual developmental disorder with dysmorphic facies and ptosis 1 0 0 0 0 1
Kabuki syndrome 2 0 1 0 0 0 1
Lafora disease 1 0 0 0 0 1
Lamb-shaffer syndrome 0 1 0 0 0 1
Lissencephaly, X-linked 1 0 0 0 0 1
Marshall-Smith syndrome; Sotos syndrome 2 1 0 0 0 0 1
Mental retardation and microcephaly with pontine and cerebellar hypoplasia 0 1 0 0 0 1
Mental retardation and microcephaly with pontine and cerebellar hypoplasia; FG syndrome 4 0 1 0 0 0 1
Mental retardation, X-linked 98 1 0 0 0 0 1
Mental retardation, X-linked 99; Mental retardation, X-linked 99, syndromic, female-restricted 0 1 0 0 0 1
Mental retardation, X-linked, syndromic, Raymond type 0 1 0 0 0 1
Mental retardation, autosomal dominant 1 0 1 0 0 0 1
Mental retardation, autosomal dominant 18 1 0 0 0 0 1
Mental retardation, autosomal dominant 26 0 1 0 0 0 1
Mental retardation, autosomal dominant 27 0 1 0 0 0 1
Mental retardation, autosomal dominant 32 1 0 0 0 0 1
Mental retardation, autosomal dominant 35 1 0 0 0 0 1
Mental retardation, autosomal dominant 38; Epileptic encephalopathy, early infantile, 33 0 1 0 0 0 1
Mental retardation, autosomal dominant 43 1 0 0 0 0 1
Mental retardation, autosomal dominant 44 0 0 1 0 0 1
Mental retardation, autosomal dominant 6; Epileptic encephalopathy, early infantile, 27 1 0 0 0 0 1
Mental retardation, autosomal dominant 7 1 0 0 0 0 1
Mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations 0 1 0 0 0 1
Microcephaly-capillary malformation syndrome 0 0 1 0 0 1
Multiple congenital anomalies-hypotonia-seizures syndrome 2 0 1 0 0 0 1
NEURODEVELOPMENTAL DISORDER WITH PROGRESSIVE MICROCEPHALY, SPASTICITY, AND BRAIN ANOMALIES 1 0 0 0 0 1
Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant; NEURODEVELOPMENTAL DISORDER WITH OR WITHOUT HYPERKINETIC MOVEMENTS AND SEIZURES, AUTOSOMAL RECESSIVE 0 1 0 0 0 1
Nicolaides-Baraitser syndrome 0 1 0 0 0 1
Periventricular nodular heterotopia 7 0 0 1 0 0 1
Pitt-Hopkins syndrome; Corneal dystrophy, Fuchs endothelial, 3 1 0 0 0 0 1
Pyridoxal 5'-phosphate-dependent epilepsy 1 0 0 0 0 1
Pyruvate dehydrogenase E1-alpha deficiency 1 0 0 0 0 1
Renpenning syndrome 1 1 0 0 0 0 1
Rett syndrome, congenital variant 0 1 0 0 0 1
Rubinstein-Taybi syndrome 1 0 1 0 0 0 1
Schinzel-Giedion syndrome; Mental retardation, autosomal dominant 29 1 0 0 0 0 1
Schuurs-hoeijmakers syndrome 1 0 0 0 0 1
Severe neonatal-onset encephalopathy with microcephaly 0 0 1 0 0 1
Severe neonatal-onset encephalopathy with microcephaly; MECP2 duplication syndrome; Mental retardation, X-linked, syndromic 13; Rett syndrome 1 0 0 0 0 1
Sifrim-Hitz-Weiss syndrome 0 0 1 0 0 1
Smith-Magenis syndrome 0 1 0 0 0 1
Speech-language disorder 1 0 0 1 0 0 1
Spinocerebellar ataxia, autosomal recessive 13 1 0 0 0 0 1
Stomatin-deficient cryohydrocytosis with neurologic defects; Dystonia 9; GLUT1 deficiency syndrome 1; GLUT1 deficiency syndrome 2; Epilepsy, idiopathic generalized, susceptibility to, 12 1 0 0 0 0 1
Wiedemann-Steiner syndrome 0 1 0 0 0 1
Wilms tumor 1; Simpson-Golabi-Behmel syndrome 0 0 1 0 0 1
ZTTK syndrome 1 0 0 0 0 1

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