{"query":"pediatric refractory seizures developmental delay microcephaly","kind":"text","recognisedAs":"Clinical semantic query","results":[{"kind":"gene","id":"SCN1A","route":"/gene/SCN1A/","label":"SCN1A","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"SCN2A","route":"/gene/SCN2A/","label":"SCN2A","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"CDKL5","route":"/gene/CDKL5/","label":"CDKL5","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"MECP2","route":"/gene/MECP2/","label":"MECP2","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"PLA2G6","route":"/gene/PLA2G6/","label":"PLA2G6","description":"98% match · Seizure, Global developmental delay · Saudi founder allele","source":"ECP Clinical AI"},{"kind":"gene","id":"KCNQ2","route":"/gene/KCNQ2/","label":"KCNQ2","description":"81% match · Seizure, Global developmental delay","source":"ECP Clinical AI"},{"kind":"phenotype","id":"HP:0001250","route":"/phenotype/HP%3A0001250/","label":"Seizure","description":"HP:0001250 · 85% match · Nervous system","source":"Human Phenotype Ontology"},{"kind":"phenotype","id":"HP:0001263","route":"/phenotype/HP%3A0001263/","label":"Global developmental delay","description":"HP:0001263 · 82% match · Nervous system","source":"Human Phenotype Ontology"},{"kind":"phenotype","id":"HP:0000252","route":"/phenotype/HP%3A0000252/","label":"Microcephaly","description":"HP:0000252 · 73% match · Nervous system","source":"Human Phenotype Ontology"}],"semantic":{"query":"pediatric refractory seizures developmental delay microcephaly","isNaturalLanguage":true,"matchedPhenotypes":[{"id":"HP:0001250","label":"Seizure","similarity":0.854,"matchedTokens":["Seizure","seizures","refractory seizures"],"category":"Nervous system","definition":"A paroxysmal event of motor, sensory, autonomic, or cognitive dysfunction caused by excessive cortical neuronal discharge.","route":"/phenotype/HP%3A0001250/"},{"id":"HP:0001263","label":"Global developmental delay","similarity":0.816,"matchedTokens":["developmental delay","developmental","delay"],"category":"Nervous system","definition":"A delay in the achievement of motor, cognitive, speech, or social developmental milestones across multiple domains in children under five.","route":"/phenotype/HP%3A0001263/"},{"id":"HP:0000252","label":"Microcephaly","similarity":0.727,"matchedTokens":["Microcephaly","microcephaly"],"category":"Nervous system","definition":"Head circumference more than 2 standard deviations below the mean for age and sex.","route":"/phenotype/HP%3A0000252/"}],"candidateGenes":[{"symbol":"SCN1A","geneId":"ENSG00000144285","score":0.98,"matchedPhenotypes":["Seizure","Global developmental delay","Microcephaly"],"omimDiseases":["Dravet syndrome (OMIM:607208)","Familial febrile seizures 3A (OMIM:604403)","Developmental and epileptic encephalopathy 6B"],"inheritance":"Autosomal dominant / De novo","founderEnriched":false,"reasoning":"Sodium voltage-gated channel alpha subunit 1; accounts for 3 of 3 identified phenotypes (Seizure, Global developmental delay, Microcephaly). Associated with Dravet syndrome (OMIM:607208).","route":"/gene/SCN1A/"},{"symbol":"SCN2A","geneId":"ENSG00000136531","score":0.98,"matchedPhenotypes":["Seizure","Global developmental delay","Microcephaly"],"omimDiseases":["Developmental and epileptic encephalopathy 11 (OMIM:613721)","Benign familial neonatal-infantile seizures 5 (OMIM:607745)"],"inheritance":"Autosomal dominant / De novo","founderEnriched":false,"reasoning":"Sodium voltage-gated channel alpha subunit 2; accounts for 3 of 3 identified phenotypes (Seizure, Global developmental delay, Microcephaly). Associated with Developmental and epileptic encephalopathy 11 (OMIM:613721).","route":"/gene/SCN2A/"},{"symbol":"CDKL5","geneId":"ENSG00000008018","score":0.98,"matchedPhenotypes":["Seizure","Global developmental delay","Microcephaly"],"omimDiseases":["Developmental and epileptic encephalopathy 2 (OMIM:300672)","Early infantile epileptic encephalopathy"],"inheritance":"X-linked dominant","founderEnriched":false,"reasoning":"Cyclin-dependent kinase-like 5; accounts for 3 of 3 identified phenotypes (Seizure, Global developmental delay, Microcephaly). Associated with Developmental and epileptic encephalopathy 2 (OMIM:300672).","route":"/gene/CDKL5/"},{"symbol":"MECP2","geneId":"ENSG00000169057","score":0.98,"matchedPhenotypes":["Seizure","Global developmental delay","Microcephaly"],"omimDiseases":["Rett syndrome (OMIM:312750)","Encephalopathy neonatal severe (OMIM:300673)"],"inheritance":"X-linked dominant","founderEnriched":false,"reasoning":"Methyl-CpG binding protein 2; accounts for 3 of 3 identified phenotypes (Seizure, Global developmental delay, Microcephaly). Associated with Rett syndrome (OMIM:312750).","route":"/gene/MECP2/"},{"symbol":"PLA2G6","geneId":"ENSG00000184381","score":0.98,"matchedPhenotypes":["Seizure","Global developmental delay"],"omimDiseases":["Infantile neuroaxonal dystrophy 1 (INAD1, OMIM:256600)","Parkinson disease 14 (OMIM:612953)"],"inheritance":"Autosomal recessive","founderEnriched":true,"founderAlleleNote":"High-prevalence Saudi founder allele c.2221C>T (p.Arg741Trp). Enriched in regional cohorts with infantile onset neuroaxonal dystrophy.","reasoning":"Phospholipase A2 group VI; accounts for 2 of 3 identified phenotypes (Seizure, Global developmental delay). Associated with Infantile neuroaxonal dystrophy 1 (INAD1, OMIM:256600). High-prevalence Saudi founder allele c.2221C>T (p.Arg741Trp). Enriched in regional cohorts with infantile onset neuroaxonal dystrophy.","route":"/gene/PLA2G6/"},{"symbol":"KCNQ2","geneId":"ENSG00000075043","score":0.807,"matchedPhenotypes":["Seizure","Global developmental delay"],"omimDiseases":["Developmental and epileptic encephalopathy 7 (OMIM:608831)","Benign familial neonatal seizures 1 (OMIM:121200)"],"inheritance":"Autosomal dominant / De novo","founderEnriched":false,"reasoning":"Potassium voltage-gated channel subfamily Q member 2; accounts for 2 of 3 identified phenotypes (Seizure, Global developmental delay). Associated with Developmental and epileptic encephalopathy 7 (OMIM:608831).","route":"/gene/KCNQ2/"}],"clinicalReasoning":"Clinical NLP resolved 3 clinical features: Seizure (HP:0001250), Global developmental delay (HP:0001263), Microcephaly (HP:0000252). Semantic phenotype-to-gene prioritization highlights SCN1A, SCN2A, CDKL5, MECP2 based on syndromic convergence and OMIM disease co-occurrence.","suggestedTargets":[{"kind":"gene","id":"SCN1A","route":"/gene/SCN1A/","label":"SCN1A","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"SCN2A","route":"/gene/SCN2A/","label":"SCN2A","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"CDKL5","route":"/gene/CDKL5/","label":"CDKL5","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"MECP2","route":"/gene/MECP2/","label":"MECP2","description":"98% match · Seizure, Global developmental delay, Microcephaly","source":"ECP Clinical AI"},{"kind":"gene","id":"PLA2G6","route":"/gene/PLA2G6/","label":"PLA2G6","description":"98% match · Seizure, Global developmental delay · Saudi founder allele","source":"ECP Clinical AI"},{"kind":"gene","id":"KCNQ2","route":"/gene/KCNQ2/","label":"KCNQ2","description":"81% match · Seizure, Global developmental delay","source":"ECP Clinical AI"},{"kind":"phenotype","id":"HP:0001250","route":"/phenotype/HP%3A0001250/","label":"Seizure","description":"HP:0001250 · 85% match · Nervous system","source":"Human Phenotype Ontology"},{"kind":"phenotype","id":"HP:0001263","route":"/phenotype/HP%3A0001263/","label":"Global developmental delay","description":"HP:0001263 · 82% match · Nervous system","source":"Human Phenotype Ontology"},{"kind":"phenotype","id":"HP:0000252","route":"/phenotype/HP%3A0000252/","label":"Microcephaly","description":"HP:0000252 · 73% match · Nervous system","source":"Human Phenotype Ontology"}]}}