AutismKB 2.0

Evidence Details for SCN1A


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Basic Information Top
Gene Symbol:SCN1A ( FEB3,FEB3A,GEFSP2,HBSCI,NAC1,Nav1.1,SCN1,SMEI )
Gene Full Name: sodium channel, voltage-gated, type I, alpha subunit
Band: 2q24.3
Quick LinksEntrez ID:6323; OMIM: 182389; Uniprot ID:SCN1A_HUMAN; ENSEMBL ID: ENSG00000144285; HGNC ID: 10585
Relate to Another Database: SFARIGene; denovo-db
Sequences Top
>SCN1A|6323|nucleotide
ATGGAGCAAACAGTGCTTGTACCACCAGGACCTGACAGCTTCAACTTCTTCACCAGAGAATCTCTTGCGGCTATTGAAAGACGCATTGCAGAAGAAAAGGCAAAG
AATCCCAAACCAGACAAAAAAGATGACGACGAAAATGGCCCAAAGCCAAATAGTGACTTGGAAGCTGGAAAGAACCTTCCATTTATTTATGGAGACATTCCTCCA
GAGATGGTGTCAGAGCCCCTGGAGGACCTGGACCCCTACTATATCAATAAGAAAACTTTTATAGTATTGAATAAAGGGAAGGCCATCTTCCGGTTCAGTGCCACC
TCTGCCCTGTACATTTTAACTCCCTTCAATCCTCTTAGGAAAATAGCTATTAAGATTTTGGTACATTCATTATTCAGCATGCTAATTATGTGCACTATTTTGACA
AACTGTGTGTTTATGACAATGAGTAACCCTCCTGATTGGACAAAGAATGTAGAATACACCTTCACAGGAATATATACTTTTGAATCACTTATAAAAATTATTGCA
AGGGGATTCTGTTTAGAAGATTTTACTTTCCTTCGGGATCCATGGAACTGGCTCGATTTCACTGTCATTACATTTGCGTACGTCACAGAGTTTGTGGACCTGGGC
AATGTCTCGGCATTGAGAACATTCAGAGTTCTCCGAGCATTGAAGACGATTTCAGTCATTCCAGGCCTGAAAACCATTGTGGGAGCCCTGATCCAGTCTGTGAAG
AAGCTCTCAGATGTAATGATCCTGACTGTGTTCTGTCTGAGCGTATTTGCTCTAATTGGGCTGCAGCTGTTCATGGGCAACCTGAGGAATAAATGTATACAATGG
CCTCCCACCAATGCTTCCTTGGAGGAACATAGTATAGAAAAGAATATAACTGTGAATTATAATGGTACACTTATAAATGAAACTGTCTTTGAGTTTGACTGGAAG
TCATATATTCAAGATTCAAGATATCATTATTTCCTGGAGGGTTTTTTAGATGCACTACTATGTGGAAATAGCTCTGATGCAGGCCAATGTCCAGAGGGATATATG
TGTGTGAAAGCTGGTAGAAATCCCAATTATGGCTACACAAGCTTTGATACCTTCAGTTGGGCTTTTTTGTCCTTGTTTCGACTAATGACTCAGGACTTCTGGGAA
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>SCN1A|6323|protein
MEQTVLVPPGPDSFNFFTRESLAAIERRIAEEKAKNPKPDKKDDDENGPKPNSDLEAGKNLPFIYGDIPPEMVSEPLEDLDPYYINKKTFIVLNKGKAIFRFSAT
SALYILTPFNPLRKIAIKILVHSLFSMLIMCTILTNCVFMTMSNPPDWTKNVEYTFTGIYTFESLIKIIARGFCLEDFTFLRDPWNWLDFTVITFAYVTEFVDLG
NVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLRNKCIQWPPTNASLEEHSIEKNITVNYNGTLINETVFEFDWK
SYIQDSRYHYFLEGFLDALLCGNSSDAGQCPEGYMCVKAGRNPNYGYTSFDTFSWAFLSLFRLMTQDFWENLYQLTLRAAGKTYMIFFVLVIFLGSFYLINLILA
VVAMAYEEQNQATLEEAEQKEAEFQQMIEQLKKQQEAAQQAATATASEHSREPSAAGRLSDSSSEASKLSSKSAKERRNRRKKRKQKEQSGGEEKDEDEFQKSES
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Evidence summary Top

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Evidences Syndromic Gene GWAS CNV Linkage Association Expression NGS de novo NGS Mosaic NGS Other Low-Scale Gene Studies Total
Score (No. of Studies) Yes 0 (0) 0 (0) 0 (0) 0 (0) 2 (2) 0 (4) 0 (0) 1 (3) 1 (1) 20 (10)
Syndromic Autism Gene Top
Abbreviations: AD, autosomal dominant; AR, autosomal recessive; ASD, autism spectrum disorder; ID, intellectual disability; XL, X linked.
InheritanceAD
OMIMDravet syndrome (607208)
DescriptionSevere myoclonic epilepsy of infancy (Dravet syndrome); ASD or autistic features have been reported repeatedly
Reference(s)16893627; -; 16122630; 16122630; 17030758; 19400878; 19764027; 21620773;
LevelLevel 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
Genome-Wide Association Studies(By Ethnic Group) Top
CNV Studies Top
Linkage Studies Top
Low Scale Association Studies (by Ethnic Group) Top
Large Scale Expression Studies Top
Microarray Studies: 2
Reference Source Tissue #Subjects
(% Women)		 ADI-R ADOS Endo- pheno Diagnosis Normal Controls
(% Women)		 Fold Change Up/ Down P/Q value
Garbett, 2008_1 Unknown superior temporal gyrus (STG) 6
(33.33%)		---autism 6
(33.33%)		 -1.23807 Down 0.00323535
  • Platform: Affymetrix Human Genome 133 plus 2 microarrays
  • ProbeSet: 1555246_a_at
  • RefSeq_ID/ EST: -
  • GEO_ID: -
  • Statistic Method: pairwise/groupwise two-tailed t-test between the RMA intensities of AUT and CONT samples
Voineagu, 2011_1 Unknown 16 frontal cortex(BA9) and 13 temporal cortex(BA41 16
(25.00%)		-autism 16
(6.25%)		 0.863716 Down 26.4019
  • Platform: Illumina Ref8 v3 microarrays
  • ProbeSet: ILMN_1741059
  • RefSeq_ID/ EST: -
  • GEO_ID: GSE28521
  • Statistic Method: SAM package and unless otherwise specified the significance threshold was FDR,0.05 and fold changes.1.3.
Proteomics Studies:0
Reference Source Tissue Platform #Subjects
(% Women)		 ADI-R ADOS Diagnosis Normal Controls(% Women)
No Evidence.
NGS de novo Mutation Studies Top
Reference Case Number Family Number de novo Number Title
O'Roak BJ, 2011 - 20 21 Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.
O'Roak BJ, 2012 2446 - 46 Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.
De Rubeis S, 2014 2270 - 1702 Synaptic, transcriptional and chromatin genes disrupted in autism
C Yuen RK, 2017 1625 - 237 Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.
NGS Mosaic SNV Studies Top
NGS Other Studies Top
Reference Source Platform ADI-R ADOS Diagnosis Family Affected Validation Method
Total Simplex Multiplex
Toma C, 2014 - Illumina HiSeq 2000--ASD 10 - - 21 -
Li J, 2014 - Illumina HiSeq 2000ASD - - - 25 -
Alvarez-Mora MI, 2016 - Illumina MiSeqASD - - - 44 Sanger sequencing
Low Scale Gene Studies Top

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  (e.g. CHD8)

Syndromic Genes

Non-syndromic Genes

AutismKB Statistics

  • Studies: 1,036
  • Genes: 1,379
  • CNVs/SVs: 5,420
  • SNVs/Indels: 11,669
  • de novo Mutations: 5,669
  • Mosaics: 789
  • Linkage Regions: 172
  • Paper Collected: 6/30/2018
  • Last Update: 8/26/2018


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