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FLASH GENE

Symbol

SCN1A

contributors: mct - updated : 03-02-2017

HGNC name	sodium channel, voltage-gated, type I, alpha subunit
HGNC id	10585

FLASH GENE DNA RNA EXPRESSION PROTEIN DISORDER ANIMAL & CELL MODELS

Corresponding disease	DEL2Q24 chromosome 2 interstitial deletion, including sub-band 2q24.3 GEFSP2 generalized epilepsy with febrile seizures plus, 2 SMEI2 severe myoclonic epilepsy in infancy 2
Location	2q24.3      Physical location : 166.845.670 - 166.930.149
Synonym name	sodium channel, brain type 1, alpha subunit
	sodium channel, voltage-gated, type I, alpha polypeptide
Synonym symbol(s)	SCN1, NAC1, HBSCI, Nav1.1, SMEI, EIEE6, FEB3, FEB3A, FHM3, GEFSP2

DNA

TYPE	functioning gene
SPECIAL FEATURE	component of a cluster
text	SCN1A-SCN2A-SCN3A gene cluster
STRUCTURE	84.48 kb     26 Exon(s)

10 Kb 5' upstream gene genomic sequence study

motif

repetitive sequence

MAPPING

cloned

Y

linked

N

status

provisional

Map	cen - SCN9A - SCN1A - D2S2330 - D2S2384 - D2S2363 - D2S2195 - D2S111 - SCN2A2 - D2S124 - SCN3A - D2S382 - D2S2157 - qter
Authors	PMID: 11254445

RNA

TRANSCRIPTS	type	messenger

identification nb exons type bp product Protein kDa AA specific expression Year Pubmed variant 1 - - 4809 isoform 1 - - - 2007 17436242 SCN1A exon 5 splicing NOVA2-mediated modulation of SCN1A exon 5 splicing epilepsy is worse in patients with the AA genotype, therefore requiring higher doses of antiepileptic medication to effectively control the seizures NM_001165963 29 - 8612 NP_001159435 229 2009 - 2007 17436242 NM_001165964 28 - 8441 NP_001159436 226 1981 - 2007 17436242 NM_006920 26 - 8100 NP_008851 227.6 1998 - 2007 17436242 NM_001202435 28 - 8426 NP_001189364 - 2009 - 2007 17436242 NM_001353948 27 - 8433 NP_001340877 - 2009 - 2007 17436242 NM_001353949 27 - 8301 NP_001340878 - 1998 - 2007 17436242 NM_001353950 28 - 8393 NP_001340879 - 1998 - 2007 17436242 NM_001353951 27 - 8400 NP_001340880 - 1998 - 2007 17436242 NM_001353952 28 - 8492 NP_001340881 - 1998 - 2007 17436242 NM_001353954 28 - 8449 NP_001340883 - 1997 - 2007 17436242 NM_001353955 27 - 8397 NP_001340884 - 1997 - 2007 17436242 NM_001353957 27 - 8349 NP_001340886 - 1981 - 2007 17436242 NM_001353958 28 - 8342 NP_001340887 - 1982 - 2007 17436242 NM_001353960 27 - 8438 NP_001340889 - 1980 - 2007 17436242 NM_001353961 28 - 8508 NP_001340890 - 1195 - 2007 17436242

EXPRESSION

Type	restricted

expressed in	(based on citations)
organ(s)	System Organ level 1 Organ level 2 Organ level 3 Organ level 4 Level Pubmed Species Stage Rna symbol Nervous brain limbic system hippocampus     Mus musculus Visual eye

tissue

System Tissue Tissue level 1 Tissue level 2 Level Pubmed Species Stage Rna symbol Muscular striatum skeletal

cells

System Cell Pubmed Species Stage Rna symbol Nervous neuron Mus musculus

cell lineage

cell lines

fluid/secretion

at STAGE

PROTEIN

PHYSICAL PROPERTIES		Hydrophobic
STRUCTURE

motifs/domains	four domains of homology, each with six alpha helical membrane spanning segments
	two cytoplasmic loops

mono polymer

monomer

HOMOLOGY

interspecies

homolog to murine Scn1a

intraspecies

homolog to SCN8A

Homologene

FAMILY

sodium channel family

CATEGORY

transport channel

SUBCELLULAR LOCALIZATION	plasma membrane
	intracellular
	intracellular,nucleus,nucleoplasm,nuclear bodies

basic FUNCTION	mediating the voltage-dependent sodium ion permeability of excitable membranes
	having a slope conductance (17 pS) similar to channels found in native mammalian neurons
	is the primary voltage-gated Na(+) channel in several classes of GABAergic interneurons, and its reduced activity leads to reduced excitability and decreased GABAergic tone
	in axon initial segments of bipolar cells augment input to magnocellular visual pathways in the primate retina
	plays a critical role in the initiation of action potential in the central nervous system

CELLULAR PROCESS

PHYSIOLOGICAL PROCESS

electron transport

PATHWAY

metabolism

signaling

a component

protein constituent of membrane

INTERACTION

DNA

RNA

small molecule

protein	interacting with NOVA2 (specific regulatory role of NOVA2 in controlling a clinically significant alternative splicing of SCN1A)
	potential involvement of RACK1 in negatively regulating SCN1A transcription via interaction with the silencer
	RER1 controls the assembly and transport of SCN1A, SCN8A, the principal sodium channels responsible for recurrent firing, in Purkinje cell (PC)

cell & other

REGULATION

ASSOCIATED DISORDERS

corresponding disease(s)

GEFSP2 , SMEI2 , DEL2Q24

Other morbid association(s)

Type Gene Modification Chromosome rearrangement Protein expression Protein Function constitutional germinal mutation       sporadic autistic disorder constitutional       loss of function may disrupt information processing in Dravet syndrom via a dysregulation of brain rhythms constitutional       loss of function dysfunction in SCN1A is increasingly being linked to neuropsychiatric abnormalities, social deficits and cognitive disabilities

Susceptibility

to Rasmussen encephalitis to Dravet syndrome to autism spectrum disorder

Variant & Polymorphism other	R1575C mutation identified in a patient with Rasmussen encephalitis
	putative disease-associated haplotype in two patients affected with Dravet syndrome

Candidate gene

Marker

Therapy target

ANIMAL & CELL MODELS

	mice with Scn1a haploinsufficiency display hyperactivity, stereotyped behaviors, social interaction deficits, and impaired context-dependent spatial memory
	Scn1a+/- mice exhibit hyperactivity, increased anxiety, and increased stereotyped behaviors, which are phenocopies of autistic traits in Dravet sdr