ClinVar Miner

List of variants in gene PNKP reported as likely pathogenic for infancy electroclinical syndrome

Included ClinVar conditions (46):

Angelman syndrome; Developmental and epileptic encephalopathy, 2
Autism; Seizures, benign familial infantile, 3; Episodic ataxia, type 9; Developmental and epileptic encephalopathy, 76
Benign familial infantile epilepsy
Benign familial neonatal-infantile seizures 1; Developmental and epileptic encephalopathy, 11; Intellectual disability
Benign familial neonatal-infantile seizures 1; Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11; SCN2A-related generalized epilepsy with febrile seizures plus
Cognitive impairment with or without cerebellar ataxia; Developmental and epileptic encephalopathy, 13; Seizures, benign familial infantile, 5
Cognitive impairment with or without cerebellar ataxia; Developmental and epileptic encephalopathy, 13; Seizures, benign familial infantile, 5; Myoclonus, familial, 2
Developmental and epileptic encephalopathy, 1
Developmental and epileptic encephalopathy, 12
Developmental and epileptic encephalopathy, 13; Seizures, benign familial infantile, 5
Developmental and epileptic encephalopathy, 13; Seizures, benign familial infantile, 5; Myoclonus, familial, 2
Developmental and epileptic encephalopathy, 15
Developmental and epileptic encephalopathy, 1; Autosomal dominant nonsyndromic hearing loss 65; Caused by mutation in the TBC1 domain family, member 24
Developmental and epileptic encephalopathy, 1; Autosomal recessive spinocerebellar ataxia 12
Developmental and epileptic encephalopathy, 1; Congenital disorder of glycosylation
Developmental and epileptic encephalopathy, 1; Developmental and epileptic encephalopathy, 2; Angelman syndrome-like
Developmental and epileptic encephalopathy, 1; Intellectual disability, X-linked, with or without seizures, arx-related
Developmental and epileptic encephalopathy, 1; Intellectual disability, X-linked, with or without seizures, arx-related; Corpus callosum agenesis-abnormal genitalia syndrome; Partington syndrome
Developmental and epileptic encephalopathy, 1; Intellectual disability, X-linked, with or without seizures, arx-related; Corpus callosum agenesis-abnormal genitalia syndrome; X-linked lissencephaly with abnormal genitalia; Partington syndrome
Developmental and epileptic encephalopathy, 2
Developmental and epileptic encephalopathy, 27
Developmental and epileptic encephalopathy, 2; Angelman syndrome-like
Developmental and epileptic encephalopathy, 30
Developmental and epileptic encephalopathy, 40
Developmental and epileptic encephalopathy, 4; West syndrome; Cerebellar vermis hypoplasia
Developmental and epileptic encephalopathy, 5
Developmental and epileptic encephalopathy, 5; Neuronopathy, distal hereditary motor, autosomal dominant 11; Spastic paraplegia 91, autosomal dominant, with or without cerebellar ataxia; Developmental delay with or without epilepsy
Generalized epilepsy with febrile seizures plus, type 1; Developmental and epileptic encephalopathy, 1; Atrial fibrillation, familial, 1; Brugada syndrome 5
Infantile spasms
Intellectual disability, autosomal dominant 6; Developmental and epileptic encephalopathy, 27
Intellectual disability, autosomal dominant 6; West syndrome; Lennox-Gastaut syndrome; GRIN2B-related developmental delay, intellectual disability and autism spectrum disorder
Intellectual disability, autosomal recessive 12; Developmental and epileptic encephalopathy, 15
Seizures, benign familial infantile, 2
Seizures, benign familial infantile, 2; Episodic kinesigenic dyskinesia 1
Seizures, benign familial infantile, 2; Episodic kinesigenic dyskinesia 1; Infantile convulsions and choreoathetosis
Seizures, benign familial infantile, 3
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11; Episodic ataxia, type 9
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11; Episodic ataxia, type 9; Complex neurodevelopmental disorder
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 1; Autism spectrum disorder; SCN2A-related generalized epilepsy with febrile seizures plus; West syndrome; Myoclonic-astatic epilepsy; Non-syndromic intellectual disability; Lennox-Gastaut syndrome; Continuous spikes and waves during sleep
Seizures, benign familial infantile, 3; SCN2A-related generalized epilepsy with febrile seizures plus
Seizures, benign familial infantile, 5
West syndrome
West syndrome; Early infantile epileptic encephalopathy with suppression bursts
West syndrome; Lennox-Gastaut syndrome
West syndrome; Tubulinopathy-associated dysgyria

Minimum submission review status:		Collection method:
Minimum conflict level: Report conflict between different conditions
Gene type: Distinguish antisense genes from sense genes
Show significances as they were submitted (without aggregation into standard terms)
		ClinVar version:

Total variants: 16

Download table as spreadsheet

HGVS	dbSNP	gnomAD frequency
NM_007254.4(PNKP):c.968C>T (p.Thr323Met)	rs372148913	0.00005
NM_007254.4(PNKP):c.636+1G>T	rs1247055716	0.00004
NM_007254.4(PNKP):c.1387-2A>G	rs766419491	0.00002
NM_007254.4(PNKP):c.865+1G>A	rs762003634	0.00002
NM_007254.4(PNKP):c.1188+1G>A	rs1057518102	0.00001
NM_007254.4(PNKP):c.1298+1_1298+10del	rs1568658916	0.00001
NM_007254.4(PNKP):c.1126+1G>C
NM_007254.4(PNKP):c.1296_1298+13del
NM_007254.4(PNKP):c.1298+1G>A	rs149614720
NM_007254.4(PNKP):c.1385G>C (p.Arg462Pro)	rs376854895
NM_007254.4(PNKP):c.1386+1G>C	rs1057520630
NM_007254.4(PNKP):c.152-2A>C
NM_007254.4(PNKP):c.199-2A>G	rs1391913873
NM_007254.4(PNKP):c.636+1G>C	rs1247055716
NM_007254.4(PNKP):c.744+1G>C
NM_007254.4(PNKP):c.865+1G>T

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