Gene Gene information from NCBI Gene database.
Entrez ID 6335
Gene name Sodium voltage-gated channel alpha subunit 9
Gene symbol SCN9A
Synonyms (NCBI Gene)
ETHAFEB3BGEFSP7HSAN2DNE-NANENANav1.7PN1SFNP
Chromosome 2
Chromosome location 2q24.3
Summary This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain d
SNPs SNP information provided by dbSNP.
19
SNP ID Visualize variation Clinical significance Consequence
rs71428908 G>A,C Uncertain-significance, conflicting-interpretations-of-pathogenicity Missense variant, synonymous variant, non coding transcript variant, coding sequence variant, intron variant
rs80356468 T>C Pathogenic Non coding transcript variant, missense variant, coding sequence variant, upstream transcript variant, genic upstream transcript variant
rs80356469 A>G Pathogenic Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs80356470 A>T Conflicting-interpretations-of-pathogenicity Coding sequence variant, non coding transcript variant, 5 prime UTR variant, missense variant
rs121908916 G>A,T Uncertain-significance, pathogenic Non coding transcript variant, stop gained, coding sequence variant, synonymous variant
miRNA miRNA information provided by mirtarbase database.
173
miRTarBase ID miRNA Experiments Reference
MIRT018700 hsa-miR-335-5p Microarray 18185580
MIRT527155 hsa-miR-1323 PAR-CLIP 20371350
MIRT527154 hsa-miR-548o-3p PAR-CLIP 20371350
MIRT527153 hsa-miR-532-3p PAR-CLIP 20371350
MIRT527152 hsa-miR-188-3p PAR-CLIP 20371350
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
USF1 Unknown 8923453
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
36
GO ID Ontology Definition Evidence Reference
GO:0001508 Process Action potential IEA
GO:0001518 Component Voltage-gated sodium channel complex IBA
GO:0001518 Component Voltage-gated sodium channel complex IEA
GO:0005216 Function Monoatomic ion channel activity IEA
GO:0005248 Function Voltage-gated sodium channel activity IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
603415 10597 ENSG00000169432
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q15858
Protein name Sodium channel protein type 9 subunit alpha (Neuroendocrine sodium channel) (hNE-Na) (Peripheral sodium channel 1) (PN1) (Sodium channel protein type IX subunit alpha) (Voltage-gated sodium channel subunit alpha Nav1.7)
Protein function Pore-forming subunit of Nav1.7, a voltage-gated sodium (Nav) channel that directly mediates the depolarizing phase of action potentials in excitable membranes. Navs, also called VGSCs (voltage-gated sodium channels) or VDSCs (voltage-dependent s
PDB 5EK0 , 6J8G , 6J8H , 6J8I , 6J8J , 6N4Q , 6N4R , 6NT3 , 6NT4 , 6VXO , 6W6O , 7K48 , 7W9K , 7W9L , 7W9M , 7W9P , 7W9T , 7XM9 , 7XMF , 7XMG , 7XVE , 7XVF , 8F0P , 8F0Q , 8F0R , 8F0S , 8G1A , 8I5B , 8I5G , 8I5X , 8I5Y , 8J4F , 8S9B , 8S9C , 8THG , 8THH , 8XMM , 8XMN , 8XMO , 8YHZ
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00520 Ion_trans 125 412 Ion transport protein Family
PF11933 Na_trans_cytopl 484 694 Cytoplasmic domain of voltage-gated Na+ ion channel Family
PF00520 Ion_trans 743 978 Ion transport protein Family
PF06512 Na_trans_assoc 982 1187 Sodium ion transport-associated Family
PF00520 Ion_trans 1191 1468 Ion transport protein Family
PF00520 Ion_trans 1514 1771 Ion transport protein Family
Tissue specificity TISSUE SPECIFICITY: Expressed strongly in dorsal root ganglion, with only minor levels elsewhere in the body, smooth muscle cells, MTC cell line and C-cell carcinoma. Also expressed in vagus nerves within the head and neck region (PubMed:31647222). Isofor
Sequence
MAMLPPPGPQSFVHFTKQSLALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLP
FIYGDIPPGMVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISI
KILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGE
FTFLRDPWNWLDFVVIVFAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQ
SVKKLSDVMILTVFCLSVFALIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFR
KYFYYLEGSKDALLCGFSTDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQ
DYWENLYQQTLRAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQAN
IEEAKQKE
LEFQQMLDRLKKEQEEAEAIAAAAAEYTSIRRSRIMGLSESSSETSKLSSKSAKERRNRR
KKKNQKKLSSGEEKGDAEKLSKSESEDSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIR
GSLFSARRSSRTSLFSFKGRGRDIGSETEFADDEHSIFGDNESRRGSLFVPHRPQERRSS
NISQASRSPPMLPVNGKMHSAVDCNGVVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGT
TNQIHKKRRCSSYLLSEDMLNDPNLRQRAMSRAS
ILTNTVEELEESRQKCPPWWYRFAHK
FLIWNCSPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGN
LVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLL
RVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKIN
DDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVL
NLFLALLLSSFSSDNLTA
IEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKI
SREIRQAEDLNTKKENYISNHTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFI
HNPSLTVTVPIAPGESDLENMNAEELSSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEE
AEAEPMNSDEPEACFTDGCVWRFSCCQVNIESGKGKIWWNIRKTCYK
IVEHSWFESFIVL
MILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCW
LDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPS
IMNVLLVCLIFWLIFSIMGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNV
RWKNLKVNFDNVGLGYLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVF
IIFGSFFTLNLFIGVIIDNFNQQKKKLG
GQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRP
GNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTG
ECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRI
LRLVKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFN
FETFGNSMICLFQITTSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYF
VSYIIISFLVVVNMYIAVILENFSVATEEST
EPLSEDDFEMFYEVWEKFDPDATQFIEFS
KLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLR
SQMEERFMSANPSKVSYEPITTTLKRKQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDG
DRDDDLLNKKDMAFDNVNENSSPEKTDATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKG
KDSKESKK
Sequence length 1988
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Taste transduction   Phase 0 - rapid depolarisation
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
5924
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Abnormality of pain sensation Pathogenic rs80356474 RCV001004018
Acute episodes of neuropathic symptoms Pathogenic rs80356474 RCV001004018
Channelopathy-associated congenital insensitivity to pain, autosomal recessive Likely pathogenic; Pathogenic rs1553495048, rs1323162486, rs2106527836, rs2106493110, rs201560701, rs794729216, rs121908908, rs1574856736, rs121908909, rs121908916, rs121908917, rs187558439, rs2468067609, rs2468024864, rs2467868979
View all (9 more)
RCV003448394
RCV001375675
RCV001527654
RCV001528149
RCV002279900
RCV000184036
RCV000006725
RCV000006726
RCV000006727
RCV000006734
RCV000006735
RCV001838994
RCV003229784
RCV003448550
RCV003988766
RCV001535622
RCV003387863
RCV004787893
RCV000680094
RCV000578279
RCV000604892
RCV004788130
RCV004813150
RCV001528173
Generalized epilepsy with febrile seizures plus Likely pathogenic; Pathogenic rs202152511, rs1553473041 RCV001535622
RCV005863204
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Abnormal brainstem MRI signal intensity Uncertain significance rs1553486581 RCV000626832
Acute myeloid leukemia Benign rs58465962 RCV005889290
Autism spectrum disorder Benign; Likely benign rs12478318 RCV003313935
Cervical cancer Benign rs58465962 RCV005889292
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Acid Phosphatase Deficiency Associate 39276275
Ageusia Associate 29978519
Anosmia Associate 29978519, 32420800
Anxiety Associate 38064009
Asthma Associate 36395102
Autism Spectrum Disorder Associate 27956748, 34947986
Autistic Disorder Associate 27956748
Bipolar Disorder Associate 34947986
Bradycardia Associate 35840956
Brain Diseases Associate 31372899