GeneBe

SCN1A-AS1

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

Basic information

Region (hg38): 2:165957188-166390771

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.

  • Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7 (43 variants)
  • Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A (26 variants)
  • not provided (15 variants)
  • Channelopathy-associated congenital insensitivity to pain, autosomal recessive (10 variants)
  • Primary erythromelalgia (4 variants)
  • Early infantile epileptic encephalopathy with suppression bursts (3 variants)
  • Inborn genetic diseases (3 variants)
  • Paroxysmal extreme pain disorder (3 variants)
  • not specified (1 variants)
  • Abnormality of pain sensation;Acute episodes of neuropathic symptoms (1 variants)
  • Generalized epilepsy with febrile seizures plus, type 7 (1 variants)
  • Pain insensitivity (1 variants)
  • SCN9A-related peripheral neuropathies associated with increased pain (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)
1
clinvar
4
clinvar
 5
splice region
4
1
7
1
 13
non coding
80
clinvar
47
clinvar
1347
clinvar
646
clinvar
67
clinvar
 2187
Total 81 47 1351 646 67

Highest pathogenic variant AF is 0.0000197

Variants in SCN1A-AS1

This is a list of pathogenic ClinVar variants found in the SCN1A-AS1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
2-165989256-G-A Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Jan 12, 2018)331855
2-165989284-G-A Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Benign/Likely benign (May 14, 2021)331856
2-165989293-A-G Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Benign/Likely benign (May 24, 2021)331857
2-165989295-C-T Migraine, familial hemiplegic, 3 • Epilepsy • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Jan 13, 2018)331858
2-165989372-GA-G Familial hemiplegic migraine • Epilepsy Conflicting classifications of pathogenicity (Oct 01, 2022)331859
2-165989381-A-T Migraine, familial hemiplegic, 3 • Epilepsy • Generalized epilepsy with febrile seizures plus, type 2 Conflicting classifications of pathogenicity (Nov 01, 2023)331860
2-165989450-C-T Migraine, familial hemiplegic, 3 • Epilepsy • Generalized epilepsy with febrile seizures plus, type 2 Conflicting classifications of pathogenicity (Jan 12, 2018)331861
2-165989451-G-A Generalized epilepsy with febrile seizures plus, type 2 • Migraine, familial hemiplegic, 3 Uncertain significance (Apr 28, 2017)893817
2-165989495-A-G Likely benign (May 19, 2021)1325975
2-165989506-G-A Migraine, familial hemiplegic, 3 • Epilepsy • Generalized epilepsy with febrile seizures plus, type 2 Benign (May 14, 2021)331862
2-165989552-T-C Migraine, familial hemiplegic, 3 • Epilepsy • Generalized epilepsy with febrile seizures plus, type 2 Benign/Likely benign (May 14, 2021)331863
2-165989592-G-A Migraine, familial hemiplegic, 3 • Epilepsy • Generalized epilepsy with febrile seizures plus, type 2 Benign/Likely benign (May 23, 2021)331864
2-165989763-C-T Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Jan 13, 2018)331865
2-165989879-T-A Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Jan 12, 2018)894730
2-165989920-C-T Generalized epilepsy with febrile seizures plus, type 2 • Migraine, familial hemiplegic, 3 Uncertain significance (Jan 12, 2018)894731
2-165989948-C-T Generalized epilepsy with febrile seizures plus, type 2 • Migraine, familial hemiplegic, 3 Uncertain significance (Jan 13, 2018)892748
2-165990021-C-T Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Benign/Likely benign (Jan 12, 2018)331866
2-165990093-T-C Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Jan 13, 2018)892749
2-165990101-C-G Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Mar 30, 2018)892750
2-165990120-A-C Generalized epilepsy with febrile seizures plus, type 2 • Migraine, familial hemiplegic, 3 Uncertain significance (Jan 13, 2018)893545
2-165990124-A-G Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Jan 12, 2018)331867
2-165990214-T-A Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Likely benign (Apr 27, 2017)331868
2-165990220-A-G Epilepsy • Migraine, familial hemiplegic, 3 • Generalized epilepsy with febrile seizures plus, type 2 Benign/Likely benign (Jan 12, 2018)331869
2-165990268-A-G Migraine, familial hemiplegic, 3 • Epilepsy • Generalized epilepsy with febrile seizures plus, type 2 Uncertain significance (Jan 12, 2018)331870
2-165990319-G-A Generalized epilepsy with febrile seizures plus, type 2 • Migraine, familial hemiplegic, 3 Uncertain significance (Mar 30, 2018)893842

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP