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SCN1A-AS1

SCN1A and SCN9A antisense RNA 1, the group of Antisense RNAs

Basic information

Links

ENSG00000236107 ∙ NCBI:101929680 ∙ ∙ HGNC:54069 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCN1A-AS1 gene.

  • Early infantile epileptic encephalopathy with suppression bursts (2388 variants)
  • not provided (1678 variants)
  • Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7 (979 variants)
  • Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A (910 variants)
  • Severe myoclonic epilepsy in infancy (642 variants)
  • Inborn genetic diseases (533 variants)
  • not specified (304 variants)
  • Generalized epilepsy with febrile seizures plus, type 2 (292 variants)
  • Paroxysmal extreme pain disorder (228 variants)
  • Channelopathy-associated congenital insensitivity to pain, autosomal recessive (216 variants)
  • Primary erythromelalgia (213 variants)
  • Migraine, familial hemiplegic, 3 (138 variants)
  • Small fiber neuropathy (99 variants)
  • Inherited Erythromelalgia (86 variants)
  • Epilepsy (64 variants)
  • Seizure (38 variants)
  • Developmental and epileptic encephalopathy 6B (29 variants)
  • Generalized epilepsy with febrile seizures plus, type 7 (26 variants)
  • Generalized epilepsy with febrile seizures plus, type 1 (25 variants)
  • Congenital Indifference to Pain (24 variants)
  • Generalized epilepsy with febrile seizures plus (18 variants)
  • SCN1A-related condition (18 variants)
  • Neuropathy, hereditary sensory and autonomic, type 2A (14 variants)
  • Febrile seizures, familial (14 variants)
  • 6 conditions (14 variants)
  • Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2 (14 variants)
  • Autosomal dominant epilepsy (13 variants)
  • See cases (9 variants)
  • Familial hemiplegic migraine (9 variants)
  • Intellectual disability (8 variants)
  • Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B (8 variants)
  • Primary erythromelalgia;Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (8 variants)
  • Developmental and epileptic encephalopathy, 6 (7 variants)
  • Childhood epilepsy with centrotemporal spikes (7 variants)
  • Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy (5 variants)
  • Generalized epilepsy with febrile seizures plus, type 2;Severe myoclonic epilepsy in infancy (5 variants)
  • Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2;Severe myoclonic epilepsy in infancy (5 variants)
  • Generalized epilepsy (4 variants)
  • Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy;Developmental and epileptic encephalopathy 6B;Generalized epilepsy with febrile seizures plus, type 2 (4 variants)
  • SCN1A Seizure Disorders (4 variants)
  • Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Primary erythromelalgia;Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder (4 variants)
  • Epileptic encephalopathy (4 variants)
  • SCN9A-related condition (4 variants)
  • Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy;Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2 (3 variants)
  • Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Primary erythromelalgia (3 variants)
  • SCN1A-related conditions (3 variants)
  • Focal epilepsy (3 variants)
  • Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3 (3 variants)
  • Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2 (3 variants)
  • Developmental and epileptic encephalopathy, 1 (3 variants)
  • Microcephaly (2 variants)
  • SUDDEN INFANT DEATH SYNDROME (2 variants)
  • Severe myoclonic epilepsy in infancy;Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2 (2 variants)
  • Charcot-Marie-Tooth disease (2 variants)
  • Autism (2 variants)
  • Sudden unexplained death in childhood (2 variants)
  • 11 conditions (2 variants)
  • Febrile seizures, familial, 3b (2 variants)
  • Primary erythromelalgia;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (2 variants)
  • Febrile seizures, familial, 3a (2 variants)
  • Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy (2 variants)
  • Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2 (2 variants)
  • Pain insensitivity (2 variants)
  • Migraine, familial hemiplegic, 3;Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2 (2 variants)
  • Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy (2 variants)
  • West syndrome (2 variants)
  • 7 conditions (1 variants)
  • Severe myoclonic epilepsy in infancy;Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B (1 variants)
  • Myoclonic encephalopathy (1 variants)
  • SCN9A-related disorders (1 variants)
  • SCN1A-related channelopathy (1 variants)
  • Severe myoclonic epilepsy in infancy;Early infantile epileptic encephalopathy with suppression bursts;Generalized epilepsy with febrile seizures plus;Familial hemiplegic migraine (1 variants)
  • Primary generalized epilepsy (1 variants)
  • Global developmental delay;Seizure (1 variants)
  • Seizure;Global developmental delay (1 variants)
  • Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Generalized epilepsy with febrile seizures plus, type 7;Primary erythromelalgia;Severe myoclonic epilepsy in infancy (1 variants)
  • Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3;Developmental and epileptic encephalopathy 6B (1 variants)
  • Abnormality of pain sensation;Acute episodes of neuropathic symptoms (1 variants)
  • Focal-onset seizure (1 variants)
  • myoclonic epilepsy (1 variants)
  • Neuropathy, hereditary sensory and autonomic, type IId (1 variants)
  • Severe myoclonic epilepsy in infancy;Developmental and epileptic encephalopathy 6B (1 variants)
  • Neuropathy, hereditary sensory and autonomic, type 2A;Primary erythromelalgia;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (1 variants)
  • Generalized epilepsy with febrile seizures plus;Primary erythromelalgia;Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (1 variants)
  • carbamazepine response - Dosage (1 variants)
  • Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 7;Primary erythromelalgia (1 variants)
  • Severe myoclonic epilepsy in infancy;Developmental and epileptic encephalopathy 6B;Generalized epilepsy with febrile seizures plus, type 2 (1 variants)
  • Primary erythromelalgia;Generalized epilepsy with febrile seizures plus;Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (1 variants)
  • Neurodevelopmental disorder (1 variants)
  • Intellectual disability;Obesity;Seizure (1 variants)
  • pharmacoresistant multifocal epilepsy (1 variants)
  • Epilepsy;Severe myoclonic epilepsy in infancy (1 variants)
  • Primary erythromelalgia;Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Generalized epilepsy with febrile seizures plus (1 variants)
  • SCN9A-related peripheral neuropathies associated with increased pain (1 variants)
  • SCN1A-Related Disorders (1 variants)
  • Febrile seizure (within the age range of 3 months to 6 years) (1 variants)
  • Global developmental delay;Seizure;Autism (1 variants)
  • Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy;Febrile seizures, familial, 1;Generalized epilepsy with febrile seizures plus, type 2 (1 variants)
  • Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3 (1 variants)
  • Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Generalized epilepsy with febrile seizures plus;Primary erythromelalgia (1 variants)
  • Autosomal dominant SCN1A-related disorder (1 variants)
  • Primary erythromelalgia;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder (1 variants)
  • Autism;Focal-onset seizure;Microcephaly (1 variants)
  • Developmental and epileptic encephalopathy, 76 (1 variants)
  • Developmental and epileptic encephalopathy 6B;Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2;Severe myoclonic epilepsy in infancy (1 variants)
  • Generalized non-motor (absence) seizure;Abnormal brainstem MRI signal intensity (1 variants)
  • Febrile seizures, familial, 1 (1 variants)
  • Seizure;Bilateral tonic-clonic seizure;Generalized non-motor (absence) seizure (1 variants)
  • Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B;Migraine, familial hemiplegic, 3 (1 variants)
  • Generalized epilepsy with febrile seizures plus, type 2;Severe myoclonic epilepsy in infancy;Migraine, familial hemiplegic, 3;Developmental and epileptic encephalopathy 6B (1 variants)
  • Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B (1 variants)
  • Primary erythromelalgia;Paroxysmal extreme pain disorder;Generalized epilepsy with febrile seizures plus, type 7;Severe myoclonic epilepsy in infancy;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (1 variants)
  • Delayed speech and language development;Seizure (1 variants)
  • Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy (1 variants)
  • Seizure;Intellectual disability, mild (1 variants)
  • Focal impaired awareness seizure (1 variants)
  • Severe myoclonic epilepsy in infancy;Acute encephalopathy (1 variants)
  • Hypoglycemia;Seizure;Global developmental delay (1 variants)
  • Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B;Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy (1 variants)
  • Primary erythromelalgia;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Paroxysmal extreme pain disorder (1 variants)
  • Severe myoclonic epilepsy in infancy;Developmental and epileptic encephalopathy 6B;Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2 (1 variants)
  • Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2;Severe myoclonic epilepsy in infancy;Developmental and epileptic encephalopathy 6B (1 variants)
  • Macrocephaly and epileptic encephalopathy (1 variants)
  • Autism spectrum disorder (1 variants)
  • Seizure;Intellectual disability (1 variants)
  • Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Primary erythromelalgia;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (1 variants)
  • Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Primary erythromelalgia (1 variants)
  • Generalized epilepsy with febrile seizures plus, type 2;Developmental and epileptic encephalopathy 6B;Severe myoclonic epilepsy in infancy;Migraine, familial hemiplegic, 3 (1 variants)
  • Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 7;Primary erythromelalgia;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive (1 variants)
  • Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Primary erythromelalgia;Paroxysmal extreme pain disorder;Neuropathy, hereditary sensory and autonomic, type 2A (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCN1A-AS1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
0
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
15
clinvar
1
clinvar
18
clinvar
9
clinvar
 43
splice region
?
    Intron variants in splice region, excluding donor/acceptor (+/-2bp)
 0
non coding
?
    UTR, intron and other, non coding variants
1158
clinvar
640
clinvar
2437
clinvar
1501
clinvar
214
clinvar
 5950
Total 1173 641 2455 1510 214

Highest pathogenic variant AF is 0.0000263

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP