SCN11A (sodium voltage-gated channel alpha subunit 11)

Gene

• Entrez ID: 11280
• Gene name: Sodium voltage-gated channel alpha subunit 11
• Gene symbol: SCN11A
• Synonyms: FEPS3, HSAN7, NAV1.9, NaN, PN5, SCN12A, SNS-2
• Chromosome: 3
• Chromosome location: 3p22.2
• Summary: Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials i

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs138607170	G>A	Pathogenic	Genic upstream transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs141686175	A>G	Pathogenic, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, missense variant, coding sequence variant
rs148425367	G>A	Conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, synonymous variant, genic downstream transcript variant
rs151155193	C>A,G,T	Likely-benign, likely-pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs483352920	A>G	Pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant
rs483352921	G>C,T	Likely-pathogenic, pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant
rs606231280	A>G	Pathogenic	Missense variant, coding sequence variant, intron variant, genic downstream transcript variant, genic upstream transcript variant
rs1064795711	C>T	Likely-pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant
rs1085307142	A>G	Pathogenic	Intron variant, genic downstream transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs1553633131	G>A	Pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT048261	hsa-miR-196a-5p	CLASH	23622248
MIRT047837	hsa-miR-30c-5p	CLASH	23622248
MIRT1329693	hsa-miR-106a	CLIP-seq
MIRT1329694	hsa-miR-106b	CLIP-seq
MIRT1329695	hsa-miR-1193	CLIP-seq
MIRT1329696	hsa-miR-17	CLIP-seq
MIRT1329697	hsa-miR-192	CLIP-seq
MIRT1329698	hsa-miR-20a	CLIP-seq
MIRT1329699	hsa-miR-20b	CLIP-seq
MIRT1329700	hsa-miR-215	CLIP-seq
MIRT1329701	hsa-miR-2392	CLIP-seq
MIRT1329702	hsa-miR-302a	CLIP-seq
MIRT1329703	hsa-miR-302b	CLIP-seq
MIRT1329704	hsa-miR-302c	CLIP-seq
MIRT1329705	hsa-miR-302d	CLIP-seq
MIRT1329706	hsa-miR-302e	CLIP-seq
MIRT1329707	hsa-miR-3187-3p	CLIP-seq
MIRT1329708	hsa-miR-371-5p	CLIP-seq
MIRT1329709	hsa-miR-371b-5p	CLIP-seq
MIRT1329710	hsa-miR-372	CLIP-seq
MIRT1329711	hsa-miR-373	CLIP-seq
MIRT1329712	hsa-miR-3973	CLIP-seq
MIRT1329713	hsa-miR-4312	CLIP-seq
MIRT1329714	hsa-miR-4435	CLIP-seq
MIRT1329715	hsa-miR-4438	CLIP-seq
MIRT1329716	hsa-miR-4701-5p	CLIP-seq
MIRT1329717	hsa-miR-4731-5p	CLIP-seq
MIRT1329718	hsa-miR-4757-5p	CLIP-seq
MIRT1329719	hsa-miR-4781-3p	CLIP-seq
MIRT1329720	hsa-miR-5095	CLIP-seq
MIRT1329721	hsa-miR-512-3p	CLIP-seq
MIRT1329722	hsa-miR-519d	CLIP-seq
MIRT1329723	hsa-miR-520a-3p	CLIP-seq
MIRT1329724	hsa-miR-520b	CLIP-seq
MIRT1329725	hsa-miR-520c-3p	CLIP-seq
MIRT1329726	hsa-miR-520d-3p	CLIP-seq
MIRT1329727	hsa-miR-520e	CLIP-seq
MIRT1329728	hsa-miR-520g	CLIP-seq
MIRT1329729	hsa-miR-520h	CLIP-seq
MIRT1329730	hsa-miR-548s	CLIP-seq
MIRT1329731	hsa-miR-588	CLIP-seq
MIRT1329732	hsa-miR-640	CLIP-seq
MIRT1329733	hsa-miR-93	CLIP-seq
MIRT2097736	hsa-miR-122	CLIP-seq
MIRT2097737	hsa-miR-1226	CLIP-seq
MIRT2097738	hsa-miR-150	CLIP-seq
MIRT2097739	hsa-miR-1976	CLIP-seq
MIRT2097740	hsa-miR-3135b	CLIP-seq
MIRT2097741	hsa-miR-3652	CLIP-seq
MIRT2097742	hsa-miR-3664-5p	CLIP-seq
MIRT2097743	hsa-miR-4279	CLIP-seq
MIRT2097744	hsa-miR-4430	CLIP-seq
MIRT2097745	hsa-miR-4503	CLIP-seq
MIRT2097746	hsa-miR-4639-3p	CLIP-seq
MIRT2097747	hsa-miR-4722-3p	CLIP-seq
MIRT2097748	hsa-miR-4733-3p	CLIP-seq
MIRT2097749	hsa-miR-564	CLIP-seq
MIRT1329693	hsa-miR-106a	CLIP-seq
MIRT1329694	hsa-miR-106b	CLIP-seq
MIRT2097736	hsa-miR-122	CLIP-seq
MIRT2097737	hsa-miR-1226	CLIP-seq
MIRT2097738	hsa-miR-150	CLIP-seq
MIRT1329696	hsa-miR-17	CLIP-seq
MIRT2322018	hsa-miR-1915	CLIP-seq
MIRT2097739	hsa-miR-1976	CLIP-seq
MIRT1329698	hsa-miR-20a	CLIP-seq
MIRT1329699	hsa-miR-20b	CLIP-seq
MIRT2322019	hsa-miR-24	CLIP-seq
MIRT1329702	hsa-miR-302a	CLIP-seq
MIRT1329703	hsa-miR-302b	CLIP-seq
MIRT1329704	hsa-miR-302c	CLIP-seq
MIRT1329705	hsa-miR-302d	CLIP-seq
MIRT1329706	hsa-miR-302e	CLIP-seq
MIRT2097740	hsa-miR-3135b	CLIP-seq
MIRT2322020	hsa-miR-3199	CLIP-seq
MIRT2097741	hsa-miR-3652	CLIP-seq
MIRT2097742	hsa-miR-3664-5p	CLIP-seq
MIRT1329708	hsa-miR-371-5p	CLIP-seq
MIRT1329709	hsa-miR-371b-5p	CLIP-seq
MIRT1329710	hsa-miR-372	CLIP-seq
MIRT1329711	hsa-miR-373	CLIP-seq
MIRT1329712	hsa-miR-3973	CLIP-seq
MIRT2097743	hsa-miR-4279	CLIP-seq
MIRT2322021	hsa-miR-4284	CLIP-seq
MIRT1329713	hsa-miR-4312	CLIP-seq
MIRT2097744	hsa-miR-4430	CLIP-seq
MIRT1329715	hsa-miR-4438	CLIP-seq
MIRT2097745	hsa-miR-4503	CLIP-seq
MIRT2097746	hsa-miR-4639-3p	CLIP-seq
MIRT2322022	hsa-miR-4713-5p	CLIP-seq
MIRT2097747	hsa-miR-4722-3p	CLIP-seq
MIRT2322023	hsa-miR-4726-3p	CLIP-seq
MIRT1329717	hsa-miR-4731-5p	CLIP-seq
MIRT2097748	hsa-miR-4733-3p	CLIP-seq
MIRT1329718	hsa-miR-4757-5p	CLIP-seq
MIRT2322024	hsa-miR-4772-3p	CLIP-seq
MIRT2322025	hsa-miR-4797-5p	CLIP-seq
MIRT1329720	hsa-miR-5095	CLIP-seq
MIRT1329721	hsa-miR-512-3p	CLIP-seq
MIRT1329722	hsa-miR-519d	CLIP-seq
MIRT1329723	hsa-miR-520a-3p	CLIP-seq
MIRT1329724	hsa-miR-520b	CLIP-seq
MIRT1329725	hsa-miR-520c-3p	CLIP-seq
MIRT1329726	hsa-miR-520d-3p	CLIP-seq
MIRT1329727	hsa-miR-520e	CLIP-seq
MIRT1329728	hsa-miR-520g	CLIP-seq
MIRT1329729	hsa-miR-520h	CLIP-seq
MIRT2322026	hsa-miR-532-3p	CLIP-seq
MIRT2322027	hsa-miR-562	CLIP-seq
MIRT2097749	hsa-miR-564	CLIP-seq
MIRT1329733	hsa-miR-93	CLIP-seq
MIRT1329718	hsa-miR-4757-5p	CLIP-seq
MIRT2458918	hsa-miR-3149	CLIP-seq
MIRT2322020	hsa-miR-3199	CLIP-seq
MIRT2458919	hsa-miR-411	CLIP-seq
MIRT1329715	hsa-miR-4438	CLIP-seq
MIRT2458920	hsa-miR-4735-5p	CLIP-seq
MIRT2458921	hsa-miR-4775	CLIP-seq
MIRT1329720	hsa-miR-5095	CLIP-seq
MIRT2458922	hsa-miR-590-3p	CLIP-seq
MIRT2097736	hsa-miR-122	CLIP-seq
MIRT2097737	hsa-miR-1226	CLIP-seq
MIRT2322019	hsa-miR-24	CLIP-seq
MIRT2097740	hsa-miR-3135b	CLIP-seq
MIRT2458918	hsa-miR-3149	CLIP-seq
MIRT2322020	hsa-miR-3199	CLIP-seq
MIRT2097741	hsa-miR-3652	CLIP-seq
MIRT2458919	hsa-miR-411	CLIP-seq
MIRT2322021	hsa-miR-4284	CLIP-seq
MIRT2097744	hsa-miR-4430	CLIP-seq
MIRT1329715	hsa-miR-4438	CLIP-seq
MIRT2097748	hsa-miR-4733-3p	CLIP-seq
MIRT2458920	hsa-miR-4735-5p	CLIP-seq
MIRT2322024	hsa-miR-4772-3p	CLIP-seq
MIRT2458921	hsa-miR-4775	CLIP-seq
MIRT1329720	hsa-miR-5095	CLIP-seq
MIRT2097749	hsa-miR-564	CLIP-seq
MIRT2458922	hsa-miR-590-3p	CLIP-seq
MIRT2097736	hsa-miR-122	CLIP-seq
MIRT2097737	hsa-miR-1226	CLIP-seq
MIRT2097738	hsa-miR-150	CLIP-seq
MIRT2322018	hsa-miR-1915	CLIP-seq
MIRT2322019	hsa-miR-24	CLIP-seq
MIRT2097740	hsa-miR-3135b	CLIP-seq
MIRT2458918	hsa-miR-3149	CLIP-seq
MIRT2322020	hsa-miR-3199	CLIP-seq
MIRT2097741	hsa-miR-3652	CLIP-seq
MIRT2458919	hsa-miR-411	CLIP-seq
MIRT2322021	hsa-miR-4284	CLIP-seq
MIRT2097744	hsa-miR-4430	CLIP-seq
MIRT1329715	hsa-miR-4438	CLIP-seq
MIRT2097745	hsa-miR-4503	CLIP-seq
MIRT2322022	hsa-miR-4713-5p	CLIP-seq
MIRT2322023	hsa-miR-4726-3p	CLIP-seq
MIRT2097748	hsa-miR-4733-3p	CLIP-seq
MIRT2458920	hsa-miR-4735-5p	CLIP-seq
MIRT2322024	hsa-miR-4772-3p	CLIP-seq
MIRT2458921	hsa-miR-4775	CLIP-seq
MIRT1329720	hsa-miR-5095	CLIP-seq
MIRT2322026	hsa-miR-532-3p	CLIP-seq
MIRT2097749	hsa-miR-564	CLIP-seq
MIRT2458922	hsa-miR-590-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001518	Component	Voltage-gated sodium channel complex	IBA	21873635
GO:0005244	Function	Voltage-gated ion channel activity	IEA
GO:0005248	Function	Voltage-gated sodium channel activity	IBA	21873635
GO:0006814	Process	Sodium ion transport	TAS
GO:0019228	Process	Neuronal action potential	IBA	21873635
GO:0030424	Component	Axon	ISS
GO:0034765	Process	Regulation of ion transmembrane transport	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IBA	21873635
GO:0042493	Process	Response to drug	TAS
GO:0044299	Component	C-fiber	IEA
GO:0051930	Process	Regulation of sensory perception of pain	ISS
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0086010	Process	Membrane depolarization during action potential	IBA	21873635

Other IDs

• MIM: 604385
• HGNC: 10583
• e!Ensembl: ENSG00000168356

Protein

• UniProt ID: Q9UI33
• Protein name: Sodium channel protein type 11 subunit alpha (Peripheral nerve sodium channel 5) (PN5) (Sensory neuron sodium channel 2) (Sodium channel protein type XI subunit alpha) (Voltage-gated sodium channel subunit alpha Nav1.9) (hNaN)
• Protein function: Sodium channel mediating the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel throug
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00520	Ion_trans	128 → 411	Ion transport protein	Family
  PF00520	Ion_trans	576 → 822	Ion transport protein	Family
  PF06512	Na_trans_assoc	826 → 1051	Sodium ion transport-associated	Family
  PF00520	Ion_trans	1055 → 1319	Ion transport protein	Family
  PF00520	Ion_trans	1365 → 1615	Ion transport protein	Family

• Sequence:

  MDDRCYPVIFPDERNFRPFTSDSLAAIEKRIAIQKEKKKSKDQTGEVPQPRPQLDLKASR
  KLPKLYGDIPRELIGKPLEDLDPFYRNHKTFMVLNRKRTIYRFSAKHALFIFGPFNSIRS
  LAIRVSVHSLFSMFIIGTVIINCVFMATGPAKNSNSNNTDIAECVFTGIYIFEALIKILA
  RGFILDEFSFLRDPWNWLDSIVIGIAIVSYIPGITIKLLPLRTFRVFRALKAISVVSRLK
  VIVGALLRSVKKLVNVIILTFFCLSIFALVGQQLFMGSLNLKCISRDCKNISNPEAYDHC
  FEKKENSPEFKMCGIWMGNSACSIQYECKHTKINPDYNYTNFDNFGWSFLAMFRLMTQDS
  WEKLYQQTLRTTGLYSVFFFIVVIFLGSFYLINLTLAVVTMAYEEQNKNVAAEIEAKEKM
  FQEAQQLLKEEKEALVAMGIDRSSLTSLETSYFTPKKRKLFGNKKRKSFFLRESGKDQPP
  GSDSDEDCQKKPQLLEQTKRLSQNLSLDHFDEHGDPLQRQRALSAVSILTITMKEQEKSQ
  EPCLPCGENLASKYLVWNCCPQWLCVKKVLRTVMTDPFTELAITICIIINTVFLAMEHHK
  MEASFEKMLNIGNLVFTSIFIAEMCLKIIALDPYHYFRRGWNIFDSIVALLSFADVMNCV
  LQKRSWPFLRSFRVLRVFKLAKSWPTLNTLIKIIGNSVGALGSLTVVLVIVIFIFSVVGM
  QLFGRSFNSQKSPKLCNPTGPTVSCLRHWHMGDFWHSFLVVFRILCGEWIENMWECMQEA
  NASSSLCVIVFILITVIGKLVVLNLFIALLLNSFSNEERNGNLEGEARKTKVQLALDRFR
  RAFCFVRHTLEHFCHKWCRKQNLPQQKEVAGGCAAQSKDIIPLVMEMKRGSETQEELGIL
  TSVPKTLGVRHDWTWLAPLAEEEDDVEFSGEDNAQRITQPEPEQQAYELHQENKKPTSQR
  VQSVEIDMFSEDEPHLTIQDPRKKSDVTSILSECSTIDLQDGFGWLPEMVPKKQPERCLP
  KGFGCCFPCCSVDKRKPPWVIWWNLRKTCYQIVKHSWFESFIIFVILLSSGALIFEDVHL
  ENQPKIQELLNCTDIIFTHIFILEMVLKWVAFGFGKYFTSAWCCLDFIIVIVSVTTLINL
  MELKSFRTLRALRPLRALSQFEGMKVVVNALIGAIPAILNVLLVCLIFWLVFCILGVYFF
  SGKFGKCINGTDSVINYTIITNKSQCESGNFSWINQKVNFDNVGNAYLALLQVATFKGWM
  DIIYAAVDSTEKEQQPEFESNSLGYIYFVVFIIFGSFFTLNLFIGVIIDNFNQQQKKLGG
  QDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNKCQGLVFDIVTSQIFDIIIISLIILNM
  ISMMAESYNQPKAMKSILDHLNWVFVVIFTLECLIKIFALRQYYFTNGWNLFDCVVVLLS
  IVSTMISTLENQEHIPFPPTLFRIVRLARIGRILRLVRAARGIRTLLFALMMSLPSLFNI
  GLLLFLIMFIYAILGMNWFSKVNPESGIDDIFNFKTFASSMLCLFQISTSAGWDSLLSPM
  LRSKESCNSSSENCHLPGIATSYFVSYIIISFLIVVNMYIAVILENFNTATEESEDPLGE
  DDFDIFYEVWEKFDPEATQFIKYSALSDFADALPEPLRVAKPNKYQFLVMDLPMVSEDRL
  HCMDILFAFTARVLGGSDGLDSMKAMMEEKFMEANPLKKLYEPIVTTTKRKEEERGAAII
  QKAFRKYMMKVTKGDQGDQNDLENGPHSPLQTLCNGDLSSFGVAKGKVHCD

• Sequence length: 1791

Pathways

Reactome:

Phase 0 - rapid depolarisation

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Dysautonomia	Dysautonomia	rs111033171, rs137853022, rs28939712, rs754348901, rs749052963, rs1057517169, rs1057516865, rs763445509, rs767527819, rs781333644, rs1239081703, rs1554696574, rs539544212, rs1201626345, rs774890086, rs1554703061, rs1554703613, rs1319053366, rs1554703851, rs868073099, rs926177767, rs376078668, rs1554695299, rs1554696648, rs1554696934, rs1554699327, rs1554691572, rs1554695846, rs1554697001, rs770668926, rs1554698037, rs759412460, rs1554702142, rs765572951, rs1554702880, rs1554703831, rs760774999, rs1554696650, rs757972943, rs1554703874, rs1554703907, rs571348995
Episodic pain syndrome	EPISODIC PAIN SYNDROME, FAMILIAL, 3, Familial episodic pain syndrome with predominantly lower limb involvement	rs398123010, rs138607170, rs483352921, rs1230622899	24776970, 24207120, 27224030, 24036948, 24813307, 25791876, 28298626
Erythermalgia	Primary Erythermalgia	rs139632595, rs372318863
Erythromelalgia	Primary erythromelalgia	rs80356475, rs80356474, rs80356478, rs80356476, rs80356469, rs80356473, rs1553491169
Hereditary motor and sensory neuropathy	NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VII	rs1555365597, rs387906941, rs207482230, rs587778791, rs587778798, rs587777108, rs587780564, rs587777789, rs1566733927	24813307, 26645915, 25118027, 24036948, 28298626, 27503742, 26746779, 28289907
Hereditary sensory and autonomic neuropathy	Hereditary Sensory Autonomic Neuropathy, Type 5, Hereditary sensory and autonomic neuropathy type 7	rs137852739, rs137852737, rs28940291, rs28940294, rs267607089, rs267607091, rs119482081, rs119482083, rs119482082, rs267607087, rs111033592, rs111033590, rs111033591, rs387906331, rs387906332, rs137852736, rs137852738, rs137852734, rs137852735, rs398122819, rs587778791, rs587778798, rs483352920, rs672601370, rs864621998, rs863224970, rs879253939, rs879254294, rs1057519416, rs1057518748, rs746681765, rs1057519295, rs1064795772, rs1085307142, rs1554716504, rs775437084, rs1554093168, rs1184021143, rs1562435373, rs201871537, rs1478989689, rs1242078669, rs759006806, rs1559030991, rs757480516, rs759333796, rs1594986869, rs1580849841, rs1574706911, rs1574843584, rs1580870705, rs1197928094, rs1951910839, rs1601814238, rs1639043704, rs1799544883
Leukemia	leukemia	rs121909646, rs121913488, rs587776834, rs752746786, rs869312821, rs767454740, rs1554564297, rs11978267, rs4132601
Paroxysmal extreme pain disorder	PAROXYSMAL EXTREME PAIN DISORDER	rs121908911, rs121908912, rs121908913, rs121908914, rs121908915, rs879253994, rs1131691776, rs1553474394
Vasculitis	Vasculitis	rs376785840, rs587777240, rs200930463, rs587777241, rs77563738, rs202134424, rs148936893, rs587777242, rs775440641, rs770689762, rs45511697, rs139750129, rs756881285, rs747774101, rs1568966771, rs766602945, rs1601419986, rs1489114116, rs754904956, rs755007390, rs368615054

Unknown
Disease name	Disease term	dbSNP ID	References
Congenital pain insensitivity	Congenital Pain Insensitivity		24036948
Motor delay	Clumsiness - motor delay
Nervous system diseases	Peripheral Nervous System Diseases
Sodium channelopathy-related small fiber neuropathy	Sodium channelopathy-related small fiber neuropathy