Selected-GenAtlas references	SOURCE	GeneCards	NCBI Gene	Swiss-Prot	Orphanet	Ensembl
	HGNC	UniGene	Nucleotide	OMIM		UCSC

Home Page

FLASH GENE

Symbol

SCN9A

contributors: mct/npt - updated : 27-10-2017

HGNC name	sodium channel, voltage-gated, type IX, alpha subunit
HGNC id	10597

FLASH GENE DNA RNA EXPRESSION PROTEIN DISORDER ANIMAL & CELL MODELS

Corresponding disease	CIEP congenital inability to experience pain/anosmia ETHA erythermalgia, primary GEFSP2 generalized epilepsy with febrile seizures plus, 2 PEXPD paroxysmal extreme pain disorder
Location	2q24.3      Physical location : 167.051.703 - 167.232.497
Synonym name	voltage-gated sodium channel alpha subunit Nav1.7
	sodium channel, voltage-gated, type IX, alpha polypeptide
	neuroendocrine sodium channel
	peripheral sodium channel 1
Synonym symbol(s)	PN1, NE-NA, NENA, Nav1.7

DNA

TYPE	functioning gene
STRUCTURE	116.62 kb     30 Exon(s)

10 Kb 5' upstream gene genomic sequence study

regulatory sequence	Promoter
text structure	a putative SCN9A 5' prime non-coding exon approximately 64,000 nucleotides from the translation start site (Diss 2008)
	; possesses numerous core elements of a TATA-less promoter within a well-defined CpG island (Diss 2008)

MAPPING

cloned

Y

linked

N

status

provisional

RNA

TRANSCRIPTS	type	messenger

identification nb exons type bp product Protein kDa AA specific expression Year Pubmed NM_002977 30 - 9771 NP_002968 - 1977 - Han, Singh (2009) variant 2 - - 9400 isoform 2 - - carcinoma cell line Klugbauer, Chatelier (2008) variant 3 - - 6371 isoform 3 - - carcinoma cell line Klugbauer, Chatelier (2008) variant 4 - - 1585 isoform 4 - - in dorsal root ganglia Raymond, Chatelier (2008) variant 5 - - 1618 isoform 5 - 539 in dorsal root ganglia Raymond, Chatelier (2008)

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 Digestive mouth         Nervous ganglia sensory ganglia dorsal root     Respiratory respiratory tract larynx       Urinary bladder

tissue

System Tissue Tissue level 1 Tissue level 2 Level Pubmed Species Stage Rna symbol Epithelial secretory glandular endocrine   Epithelial sensory

cells

System Cell Pubmed Species Stage Rna symbol nervous brain Nervous neuron

cell lineage

cell lines

fluid/secretion

at STAGE

PROTEIN

PHYSICAL PROPERTIES

STRUCTURE

motifs/domains	4 internal repeats, each with 5 hydrophobic segments (S1, S2, S3, S5, S6)and one positively charged segment (S4)
	a IQ domain

HOMOLOGY

interspecies	homolog to murine Scn9a
	ortholog to rattus Pn1 sodium channel

Homologene

FAMILY

sodium channel family

CATEGORY

transport channel

SUBCELLULAR LOCALIZATION

plasma membrane

basic FUNCTION	mediating the voltage-dependent sodium ion permeability of excitable membranes
	playing a role in pain mechanisms, especially in the development of inflammatory pain
	with SCN2A, and SCN3A, likely account for the tetrodotoxin-sensitive sodium currents in taste receptor cells (Gao 2009)
	essential and non-redundant requirement for nociception
	acting as a critical element of peripheral nociception
	plays an important role in cell migration, endocytosis, and secretion and have a potential role in the aortic progression of intimal hyperplasia after balloon injury (Meguro 2009)
	play a crucial role in pain sensation and in nociception (Chatelier 2008)
	is not only necessary for pain sensation but is also an essential requirement for odour perception

CELLULAR PROCESS

PHYSIOLOGICAL PROCESS

PATHWAY

metabolism

signaling

neurotransmission

a component

beyond the thermosensors, the FGF13c/SCN9A omplex is essential for sustaining the transmission of noxious heat signals

INTERACTION

DNA

RNA

small molecule

protein	interacts with NEDD4 and NEDD4L
	DPYSL2 protein SUMOylation modulates SCN9A channel trafficking
	diverse modifications of DPYSL2 cross-talk to control SCN9A activity
	FGF13 interacted with the sodium channel SCN9A in a heat-facilitated manner (FGF13 increased SCN9A sodium currents and maintained the membrane localization of SCN9A during noxious heat stimulation, enabling the sustained firing of action potentials)

cell & other

REGULATION

ASSOCIATED DISORDERS

corresponding disease(s)

ETHA , CIEP , PEXPD , GEFSP2

Other morbid association(s)

Type Gene Modification Chromosome rearrangement Protein expression Protein Function tumoral     --over   in prostate cancer (Diss 2008) constitutional germinal mutation     loss of function loss-of-function mutations in a single gene, SCN9A, cause a general loss of two major senses—nociception and smell

Susceptibility

Variant & Polymorphism

Candidate gene
Marker
Therapy target	extremely promising target for selective pharmaceutical intervention in the analgesia

ANIMAL & CELL MODELS