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Q15858

- SCN9A_HUMAN

UniProt

Q15858 - SCN9A_HUMAN

Protein

Sodium channel protein type 9 subunit alpha

Gene

SCN9A

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 135 (01 Oct 2014)
      Sequence version 3 (05 Apr 2011)
      Previous versions | rss
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    Functioni

    Mediates 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 through which Na+ ions may pass in accordance with their electrochemical gradient. It is a tetrodotoxin-sensitive Na+ channel isoform. Plays a role in pain mechanisms, especially in the development of inflammatory pain By similarity.By similarity

    GO - Molecular functioni

    1. sodium ion binding Source: Ensembl
    2. voltage-gated sodium channel activity Source: RefGenome

    GO - Biological processi

    1. behavioral response to pain Source: Ensembl
    2. inflammatory response Source: Ensembl
    3. membrane depolarization during action potential Source: RefGenome
    4. neuronal action potential Source: RefGenome
    5. post-embryonic development Source: Ensembl
    6. response to toxic substance Source: Ensembl
    7. sodium ion transmembrane transport Source: RefGenome
    8. sodium ion transport Source: ProtInc

    Keywords - Molecular functioni

    Ion channel, Sodium channel, Voltage-gated channel

    Keywords - Biological processi

    Ion transport, Sodium transport, Transport

    Keywords - Ligandi

    Sodium

    Enzyme and pathway databases

    ReactomeiREACT_22266. Interaction between L1 and Ankyrins.

    Protein family/group databases

    TCDBi1.A.1.10.5. the voltage-gated ion channel (vic) superfamily.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sodium channel protein type 9 subunit alpha
    Alternative name(s):
    Neuroendocrine sodium channel
    Short name:
    hNE-Na
    Peripheral sodium channel 1
    Short name:
    PN1
    Sodium channel protein type IX subunit alpha
    Voltage-gated sodium channel subunit alpha Nav1.7
    Gene namesi
    Name:SCN9A
    Synonyms:NENA
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:10597. SCN9A.

    Subcellular locationi

    Membrane; Multi-pass membrane protein
    Note: In neurite terminals.By similarity

    GO - Cellular componenti

    1. plasma membrane Source: RefGenome
    2. voltage-gated sodium channel complex Source: Ensembl

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Primary erythermalgia (PERYTHM) [MIM:133020]: Autosomal dominant disease characterized by recurrent episodes of severe pain associated with redness and warmth in the feet or hands.6 Publications
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti10 – 101Q → R in PERYTHM; causes a hyperpolarizing shift of -5.3 mV for the midpoint of activation which is smaller than that seen in other mutations causing early-onset erythromelalgia mutations; also causes a faster rate of activation and slower deactivation compared to wild-type; expression of the mutant protein induced hyperexcitability in dorsal root ganglion neurons but the increase is smaller than that produced by Thr-859. 1 Publication
    VAR_064595
    Natural varianti216 – 2161F → S in PERYTHM; hyperpolarizes the voltage dependence of activation by 11 mV, accelerates activation, slows deactivation and enhances the response to slow, small depolarizations. 1 Publication
    VAR_064598
    Natural varianti241 – 2411S → T in PERYTHM. 1 Publication
    VAR_032014
    Natural varianti395 – 3951N → K in PERYTHM. 1 Publication
    VAR_064600
    Natural varianti406 – 4061E → K in PERYTHM.
    VAR_064601
    Natural varianti859 – 8591I → T in PERYTHM; sporadic; activated at more negative potentials; slower inactivation kinetics than wild-type channels. 2 Publications
    VAR_019947
    Natural varianti869 – 8691L → F in PERYTHM; causes a hyperpolarizing shift in channel activation, a depolarizing shift of inactivation and an 18-fold increase in deactivation time compared to wild-type; the mean ramp current amplitude in response to slow depolarization is higher in the mutant channels. 2 Publications
    VAR_064609
    Natural varianti869 – 8691L → H in PERYTHM; activated at more negative potentials; slower inactivation kinetics than wild-type channels. 1 Publication
    VAR_019948
    Natural varianti1460 – 14601F → V in PERYTHM; produces a hyperpolarizing shift in channel activation and a depolarizing shift in steady-state activation. 1 Publication
    VAR_032019
    Congenital indifference to pain autosomal recessive (CIPAR) [MIM:243000]: A disorder characterized by congenital inability to perceive any form of pain, in any part of the body. All other sensory modalities are preserved and the peripheral and central nervous systems are apparently intact. Patients perceive the sensations of touch, warm and cold temperature, proprioception, tickle and pressure, but not painful stimuli. There is no evidence of a motor or sensory neuropathy, either axonal or demyelinating.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti907 – 9071R → Q in CIPAR; significant reduction in membrane localization of the mutant protein compared to the wild-type; complete loss of function of the sodium channel. 1 Publication
    VAR_064610
    Natural varianti1381 – 13855Missing in CIPAR; significant reduction in membrane localization of the mutant protein compared to the wild-type; complete loss of function of the sodium channel.
    VAR_064614
    Paroxysmal extreme pain disorder (PEPD) [MIM:167400]: Autosomal dominant paroxysmal disorder of pain and autonomic dysfunction. The distinctive features are paroxysmal episodes of burning pain in the rectal, ocular, and mandibular areas accompanied by autonomic manifestations such as skin flushing.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti1007 – 10071R → C in PEPD. 1 Publication
    Corresponds to variant rs121908910 [ dbSNP | Ensembl ].
    VAR_032015
    Natural varianti1309 – 13091V → D in PEPD. 1 Publication
    VAR_032016
    Natural varianti1309 – 13091V → F in PEPD. 1 Publication
    VAR_032017
    Natural varianti1310 – 13101V → F in PEPD. 1 Publication
    VAR_032018
    Natural varianti1472 – 14721I → T in PEPD; reduction in fast inactivation leading to persistent sodium current. 1 Publication
    VAR_032020
    Natural varianti1473 – 14731F → V in PEPD. 1 Publication
    VAR_032021
    Natural varianti1475 – 14751T → I in PEPD; reduction in fast inactivation leading to persistent sodium current. 1 Publication
    VAR_032022
    Natural varianti1638 – 16381M → K in PEPD; reduction in fast inactivation leading to persistent sodium current. 1 Publication
    VAR_032023
    Generalized epilepsy with febrile seizures plus 7 (GEFS+7) [MIM:613863]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti641 – 6411N → Y in GEFS+7. 1 Publication
    VAR_064604
    Natural varianti666 – 6661K → R in GEFS+7; also found in a patient with severe myoclonic epilepsy in infancy. 1 Publication
    Corresponds to variant rs121908919 [ dbSNP | Ensembl ].
    VAR_064605
    Febrile seizures, familial, 3B (FEB3B) [MIM:613863]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti62 – 621I → V in FEB3B. 1 Publication
    VAR_064596
    Natural varianti149 – 1491P → Q in FEB3B. 1 Publication
    VAR_064597

    Keywords - Diseasei

    Disease mutation, Epilepsy

    Organism-specific databases

    MIMi133020. phenotype.
    167400. phenotype.
    243000. phenotype.
    613863. phenotype.
    Orphaneti88642. Channelopathy-associated congenital insensitivity to pain.
    33069. Dravet syndrome.
    1956. Erythromelalgia.
    36387. Generalized epilepsy with febrile seizures-plus context.
    970. Hereditary sensory and autonomic neuropathy type 2.
    46348. Paroxysmal extreme pain disorder.
    90026. Primary erythermalgia.
    306577. Sodium channelopathy-related small fiber neuropathy.
    PharmGKBiPA35010.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 19881988Sodium channel protein type 9 subunit alphaPRO_0000048502Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi209 – 2091N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi283 – 2831N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi1352 – 13521N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi1366 – 13661N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi1375 – 13751N-linked (GlcNAc...)Sequence Analysis
    Modified residuei1490 – 14901Phosphoserine; by PKCBy similarity

    Post-translational modificationi

    Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4 By similarity.By similarity
    Phosphorylation at Ser-1490 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.By similarity

    Keywords - PTMi

    Glycoprotein, Phosphoprotein, Ubl conjugation

    Proteomic databases

    PaxDbiQ15858.
    PRIDEiQ15858.

    PTM databases

    PhosphoSiteiQ15858.

    Expressioni

    Tissue specificityi

    Expressed strongly in dorsal root ganglion, with only minor levels elsewhere in the body, smooth muscle cells, MTC cell line and C-cell carcinoma. Isoform 1 is expressed preferentially in the central and peripheral nervous system. Isoform 2 is expressed preferentially in the dorsal root ganglion.4 Publications

    Gene expression databases

    ArrayExpressiQ15858.
    BgeeiQ15858.
    CleanExiHS_SCN9A.
    GenevestigatoriQ15858.

    Organism-specific databases

    HPAiCAB013679.

    Interactioni

    Subunit structurei

    The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large polypeptide. Interacts with NEDD4 and NEDD4L By similarity.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ15858.
    SMRiQ15858. Positions 1761-1916.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei122 – 14524Helical; Name=S1 of repeat ISequence AnalysisAdd
    BLAST
    Transmembranei154 – 17320Helical; Name=S2 of repeat ISequence AnalysisAdd
    BLAST
    Transmembranei187 – 20519Helical; Name=S3 of repeat ISequence AnalysisAdd
    BLAST
    Transmembranei212 – 23120Helical; Voltage-sensor; Name=S4 of repeat ISequence AnalysisAdd
    BLAST
    Transmembranei248 – 27124Helical; Name=S5 of repeat ISequence AnalysisAdd
    BLAST
    Transmembranei379 – 40426Helical; Name=S6 of repeat ISequence AnalysisAdd
    BLAST
    Transmembranei739 – 76325Helical; Name=S1 of repeat IISequence AnalysisAdd
    BLAST
    Transmembranei775 – 79824Helical; Name=S2 of repeat IISequence AnalysisAdd
    BLAST
    Transmembranei807 – 82620Helical; Name=S3 of repeat IISequence AnalysisAdd
    BLAST
    Transmembranei833 – 85220Helical; Voltage-sensor; Name=S4 of repeat IISequence AnalysisAdd
    BLAST
    Transmembranei869 – 88921Helical; Name=S5 of repeat IISequence AnalysisAdd
    BLAST
    Transmembranei943 – 96826Helical; Name=S6 of repeat IISequence AnalysisAdd
    BLAST
    Transmembranei1188 – 121124Helical; Name=S1 of repeat IIISequence AnalysisAdd
    BLAST
    Transmembranei1225 – 125026Helical; Name=S2 of repeat IIISequence AnalysisAdd
    BLAST
    Transmembranei1257 – 127822Helical; Name=S3 of repeat IIISequence AnalysisAdd
    BLAST
    Transmembranei1283 – 130422Helical; Voltage-sensor; Name=S4 of repeat IIISequence AnalysisAdd
    BLAST
    Transmembranei1324 – 135128Helical; Name=S5 of repeat IIISequence AnalysisAdd
    BLAST
    Transmembranei1431 – 145727Helical; Name=S6 of repeat IIISequence AnalysisAdd
    BLAST
    Transmembranei1511 – 153424Helical; Name=S1 of repeat IVSequence AnalysisAdd
    BLAST
    Transmembranei1546 – 156924Helical; Name=S2 of repeat IVSequence AnalysisAdd
    BLAST
    Transmembranei1576 – 159924Helical; Name=S3 of repeat IVSequence AnalysisAdd
    BLAST
    Transmembranei1610 – 163122Helical; Voltage-sensor; Name=S4 of repeat IVSequence AnalysisAdd
    BLAST
    Transmembranei1647 – 166923Helical; Name=S5 of repeat IVSequence AnalysisAdd
    BLAST
    Transmembranei1736 – 176025Helical; Name=S6 of repeat IVSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati121 – 405285IAdd
    BLAST
    Repeati738 – 969232IIAdd
    BLAST
    Repeati1187 – 1458272IIIAdd
    BLAST
    Repeati1510 – 1761252IVAdd
    BLAST
    Domaini1889 – 191830IQAdd
    BLAST

    Domaini

    The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1,S2,S3,S5,S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.

    Sequence similaritiesi

    Contains 1 IQ domain.Curated

    Keywords - Domaini

    Repeat, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG1226.
    HOVERGENiHBG053100.
    KOiK04841.
    OrthoDBiEOG7DJSK9.
    PhylomeDBiQ15858.
    TreeFamiTF323985.

    Family and domain databases

    Gene3Di1.20.120.350. 4 hits.
    InterProiIPR027359. Channel_four-helix_dom.
    IPR024583. DUF3451.
    IPR005821. Ion_trans_dom.
    IPR000048. IQ_motif_EF-hand-BS.
    IPR001696. Na_channel_asu.
    IPR010526. Na_trans_assoc.
    IPR028803. SCN9A.
    [Graphical view]
    PANTHERiPTHR10037:SF28. PTHR10037:SF28. 1 hit.
    PfamiPF11933. DUF3451. 1 hit.
    PF00520. Ion_trans. 4 hits.
    PF06512. Na_trans_assoc. 1 hit.
    [Graphical view]
    PRINTSiPR00170. NACHANNEL.
    SMARTiSM00015. IQ. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q15858-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MAMLPPPGPQ SFVHFTKQSL ALIEQRIAER KSKEPKEEKK DDDEEAPKPS     50
    SDLEAGKQLP FIYGDIPPGM VSEPLEDLDP YYADKKTFIV LNKGKTIFRF 100
    NATPALYMLS PFSPLRRISI KILVHSLFSM LIMCTILTNC IFMTMNNPPD 150
    WTKNVEYTFT GIYTFESLVK ILARGFCVGE FTFLRDPWNW LDFVVIVFAY 200
    LTEFVNLGNV SALRTFRVLR ALKTISVIPG LKTIVGALIQ SVKKLSDVMI 250
    LTVFCLSVFA LIGLQLFMGN LKHKCFRNSL ENNETLESIM NTLESEEDFR 300
    KYFYYLEGSK DALLCGFSTD SGQCPEGYTC VKIGRNPDYG YTSFDTFSWA 350
    FLALFRLMTQ DYWENLYQQT LRAAGKTYMI FFVVVIFLGS FYLINLILAV 400
    VAMAYEEQNQ ANIEEAKQKE LEFQQMLDRL KKEQEEAEAI AAAAAEYTSI 450
    RRSRIMGLSE SSSETSKLSS KSAKERRNRR KKKNQKKLSS GEEKGDAEKL 500
    SKSESEDSIR RKSFHLGVEG HRRAHEKRLS TPNQSPLSIR GSLFSARRSS 550
    RTSLFSFKGR GRDIGSETEF ADDEHSIFGD NESRRGSLFV PHRPQERRSS 600
    NISQASRSPP MLPVNGKMHS AVDCNGVVSL VDGRSALMLP NGQLLPEVII 650
    DKATSDDSGT TNQIHKKRRC SSYLLSEDML NDPNLRQRAM SRASILTNTV 700
    EELEESRQKC PPWWYRFAHK FLIWNCSPYW IKFKKCIYFI VMDPFVDLAI 750
    TICIVLNTLF MAMEHHPMTE EFKNVLAIGN LVFTGIFAAE MVLKLIAMDP 800
    YEYFQVGWNI FDSLIVTLSL VELFLADVEG LSVLRSFRLL RVFKLAKSWP 850
    TLNMLIKIIG NSVGALGNLT LVLAIIVFIF AVVGMQLFGK SYKECVCKIN 900
    DDCTLPRWHM NDFFHSFLIV FRVLCGEWIE TMWDCMEVAG QAMCLIVYMM 950
    VMVIGNLVVL NLFLALLLSS FSSDNLTAIE EDPDANNLQI AVTRIKKGIN 1000
    YVKQTLREFI LKAFSKKPKI SREIRQAEDL NTKKENYISN HTLAEMSKGH 1050
    NFLKEKDKIS GFGSSVDKHL MEDSDGQSFI HNPSLTVTVP IAPGESDLEN 1100
    MNAEELSSDS DSEYSKVRLN RSSSSECSTV DNPLPGEGEE AEAEPMNSDE 1150
    PEACFTDGCV WRFSCCQVNI ESGKGKIWWN IRKTCYKIVE HSWFESFIVL 1200
    MILLSSGALA FEDIYIERKK TIKIILEYAD KIFTYIFILE MLLKWIAYGY 1250
    KTYFTNAWCW LDFLIVDVSL VTLVANTLGY SDLGPIKSLR TLRALRPLRA 1300
    LSRFEGMRVV VNALIGAIPS IMNVLLVCLI FWLIFSIMGV NLFAGKFYEC 1350
    INTTDGSRFP ASQVPNRSEC FALMNVSQNV RWKNLKVNFD NVGLGYLSLL 1400
    QVATFKGWTI IMYAAVDSVN VDKQPKYEYS LYMYIYFVVF IIFGSFFTLN 1450
    LFIGVIIDNF NQQKKKLGGQ DIFMTEEQKK YYNAMKKLGS KKPQKPIPRP 1500
    GNKIQGCIFD LVTNQAFDIS IMVLICLNMV TMMVEKEGQS QHMTEVLYWI 1550
    NVVFIILFTG ECVLKLISLR HYYFTVGWNI FDFVVVIISI VGMFLADLIE 1600
    TYFVSPTLFR VIRLARIGRI LRLVKGAKGI RTLLFALMMS LPALFNIGLL 1650
    LFLVMFIYAI FGMSNFAYVK KEDGINDMFN FETFGNSMIC LFQITTSAGW 1700
    DGLLAPILNS KPPDCDPKKV HPGSSVEGDC GNPSVGIFYF VSYIIISFLV 1750
    VVNMYIAVIL ENFSVATEES TEPLSEDDFE MFYEVWEKFD PDATQFIEFS 1800
    KLSDFAAALD PPLLIAKPNK VQLIAMDLPM VSGDRIHCLD ILFAFTKRVL 1850
    GESGEMDSLR SQMEERFMSA NPSKVSYEPI TTTLKRKQED VSATVIQRAY 1900
    RRYRLRQNVK NISSIYIKDG DRDDDLLNKK DMAFDNVNEN SSPEKTDATS 1950
    STTSPPSYDS VTKPDKEKYE QDRTEKEDKG KDSKESKK 1988
    Length:1,988
    Mass (Da):226,372
    Last modified:April 5, 2011 - v3
    Checksum:i1BAEB8F32EBF5438
    GO
    Isoform 2 (identifier: Q15858-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         200-229: YLTEFVNLGNVSALRTFRVLRALKTISVIP → YVTEFVDLGNVSALRTFRVLRALKTISVIP

    Show »
    Length:1,988
    Mass (Da):226,359
    Checksum:i8C9066AD56148C02
    GO
    Isoform 3 (identifier: Q15858-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         648-658: Missing.

    Show »
    Length:1,977
    Mass (Da):225,227
    Checksum:i8B2BD5CF665F11A8
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti201 – 2011L → V in AAT85835. (PubMed:15302875)Curated
    Sequence conflicti201 – 2011L → V in AAT85833. (PubMed:15302875)Curated
    Sequence conflicti206 – 2061N → D in AAT85835. (PubMed:15302875)Curated
    Sequence conflicti206 – 2061N → D in AAT85833. (PubMed:15302875)Curated
    Sequence conflicti267 – 2671F → S in AAT85834. (PubMed:15302875)Curated
    Sequence conflicti301 – 3011K → R in AAT85835. (PubMed:15302875)Curated
    Sequence conflicti309 – 3091S → P in AAT85834. (PubMed:15302875)Curated
    Sequence conflicti420 – 4201E → G in AAT85834. (PubMed:15302875)Curated
    Sequence conflicti430 – 4301L → P in AAT85834. (PubMed:15302875)Curated
    Sequence conflicti501 – 5011S → P in AAT85835. (PubMed:15302875)Curated
    Sequence conflicti610 – 6101P → T in AAT85835. (PubMed:15302875)Curated
    Sequence conflicti642 – 6421G → R in AAT85835. (PubMed:15302875)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti10 – 101Q → R in PERYTHM; causes a hyperpolarizing shift of -5.3 mV for the midpoint of activation which is smaller than that seen in other mutations causing early-onset erythromelalgia mutations; also causes a faster rate of activation and slower deactivation compared to wild-type; expression of the mutant protein induced hyperexcitability in dorsal root ganglion neurons but the increase is smaller than that produced by Thr-859. 1 Publication
    VAR_064595
    Natural varianti62 – 621I → V in FEB3B. 1 Publication
    VAR_064596
    Natural varianti149 – 1491P → Q in FEB3B. 1 Publication
    VAR_064597
    Natural varianti216 – 2161F → S in PERYTHM; hyperpolarizes the voltage dependence of activation by 11 mV, accelerates activation, slows deactivation and enhances the response to slow, small depolarizations. 1 Publication
    VAR_064598
    Natural varianti228 – 2281I → M.1 Publication
    Corresponds to variant rs71428908 [ dbSNP | Ensembl ].
    VAR_064599
    Natural varianti241 – 2411S → T in PERYTHM. 1 Publication
    VAR_032014
    Natural varianti395 – 3951N → K in PERYTHM. 1 Publication
    VAR_064600
    Natural varianti406 – 4061E → K in PERYTHM.
    VAR_064601
    Natural varianti490 – 4901S → N.1 Publication
    Corresponds to variant rs58022607 [ dbSNP | Ensembl ].
    VAR_064602
    Natural varianti519 – 5191E → K.1 Publication
    Corresponds to variant rs187453572 [ dbSNP | Ensembl ].
    VAR_064603
    Natural varianti641 – 6411N → Y in GEFS+7. 1 Publication
    VAR_064604
    Natural varianti666 – 6661K → R in GEFS+7; also found in a patient with severe myoclonic epilepsy in infancy. 1 Publication
    Corresponds to variant rs121908919 [ dbSNP | Ensembl ].
    VAR_064605
    Natural varianti695 – 6951I → M.1 Publication
    VAR_064606
    Natural varianti710 – 7101C → Y Found in a patient with severe myoclonic epilepsy in infancy. 1 Publication
    VAR_064607
    Natural varianti750 – 7501I → V.1 Publication
    Corresponds to variant rs182650126 [ dbSNP | Ensembl ].
    VAR_064608
    Natural varianti859 – 8591I → T in PERYTHM; sporadic; activated at more negative potentials; slower inactivation kinetics than wild-type channels. 2 Publications
    VAR_019947
    Natural varianti869 – 8691L → F in PERYTHM; causes a hyperpolarizing shift in channel activation, a depolarizing shift of inactivation and an 18-fold increase in deactivation time compared to wild-type; the mean ramp current amplitude in response to slow depolarization is higher in the mutant channels. 2 Publications
    VAR_064609
    Natural varianti869 – 8691L → H in PERYTHM; activated at more negative potentials; slower inactivation kinetics than wild-type channels. 1 Publication
    VAR_019948
    Natural varianti907 – 9071R → Q in CIPAR; significant reduction in membrane localization of the mutant protein compared to the wild-type; complete loss of function of the sodium channel. 1 Publication
    VAR_064610
    Natural varianti932 – 9321M → L.
    Corresponds to variant rs12478318 [ dbSNP | Ensembl ].
    VAR_030444
    Natural varianti943 – 9431M → L.
    Corresponds to variant rs12478318 [ dbSNP | Ensembl ].
    VAR_055646
    Natural varianti1007 – 10071R → C in PEPD. 1 Publication
    Corresponds to variant rs121908910 [ dbSNP | Ensembl ].
    VAR_032015
    Natural varianti1134 – 11341L → F.1 Publication
    Corresponds to variant rs200160858 [ dbSNP | Ensembl ].
    VAR_064611
    Natural varianti1161 – 11611W → R.3 Publications
    Corresponds to variant rs6746030 [ dbSNP | Ensembl ].
    VAR_019949
    Natural varianti1171 – 11711E → Q Found in a patient with severe myoclonic epilepsy in infancy. 1 Publication
    VAR_064612
    Natural varianti1278 – 12781L → V.1 Publication
    Corresponds to variant rs180922748 [ dbSNP | Ensembl ].
    VAR_064613
    Natural varianti1309 – 13091V → D in PEPD. 1 Publication
    VAR_032016
    Natural varianti1309 – 13091V → F in PEPD. 1 Publication
    VAR_032017
    Natural varianti1310 – 13101V → F in PEPD. 1 Publication
    VAR_032018
    Natural varianti1381 – 13855Missing in CIPAR; significant reduction in membrane localization of the mutant protein compared to the wild-type; complete loss of function of the sodium channel.
    VAR_064614
    Natural varianti1460 – 14601F → V in PERYTHM; produces a hyperpolarizing shift in channel activation and a depolarizing shift in steady-state activation. 1 Publication
    VAR_032019
    Natural varianti1472 – 14721I → T in PEPD; reduction in fast inactivation leading to persistent sodium current. 1 Publication
    VAR_032020
    Natural varianti1473 – 14731F → V in PEPD. 1 Publication
    VAR_032021
    Natural varianti1475 – 14751T → I in PEPD; reduction in fast inactivation leading to persistent sodium current. 1 Publication
    VAR_032022
    Natural varianti1638 – 16381M → K in PEPD; reduction in fast inactivation leading to persistent sodium current. 1 Publication
    VAR_032023
    Natural varianti1919 – 19191D → G.
    Corresponds to variant rs3750904 [ dbSNP | Ensembl ].
    VAR_019950

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei200 – 22930YLTEF…ISVIP → YVTEFVDLGNVSALRTFRVL RALKTISVIP in isoform 2. 1 PublicationVSP_012028Add
    BLAST
    Alternative sequencei648 – 65811Missing in isoform 3. 3 PublicationsVSP_012029Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82835 mRNA. Translation: CAA58042.1.
    DQ857292 mRNA. Translation: ABI51981.1.
    AC074101 Genomic DNA. No translation available.
    AC107082 Genomic DNA. No translation available.
    AC108146 Genomic DNA. No translation available.
    AY682084 mRNA. Translation: AAT85833.1.
    AY682085 mRNA. Translation: AAT85834.1.
    AY682086 mRNA. Translation: AAT85835.1.
    AJ310882 mRNA. Translation: CAC84550.1.
    AJ310883 mRNA. Translation: CAC84551.1.
    AJ310897 mRNA. Translation: CAC84537.1.
    AJ580918 Genomic DNA. Translation: CAE45644.1.
    AJ580919 Genomic DNA. Translation: CAE45645.1.
    CCDSiCCDS46441.1. [Q15858-3]
    PIRiS54771.
    RefSeqiNP_002968.1. NM_002977.3.
    XP_005246814.1. XM_005246757.1. [Q15858-1]
    UniGeneiHs.439145.

    Genome annotation databases

    EnsembliENST00000409435; ENSP00000386330; ENSG00000169432. [Q15858-1]
    ENST00000409672; ENSP00000386306; ENSG00000169432. [Q15858-3]
    ENST00000454569; ENSP00000413212; ENSG00000169432.
    GeneIDi6335.
    KEGGihsa:6335.
    UCSCiuc010fpl.3. human. [Q15858-3]

    Polymorphism databases

    DMDMi327478559.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Web resourcesi

    Wikipedia

    SCN9A entry

    Protein Spotlight

    Silent pain - Issue 102 of February 2009

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82835 mRNA. Translation: CAA58042.1 .
    DQ857292 mRNA. Translation: ABI51981.1 .
    AC074101 Genomic DNA. No translation available.
    AC107082 Genomic DNA. No translation available.
    AC108146 Genomic DNA. No translation available.
    AY682084 mRNA. Translation: AAT85833.1 .
    AY682085 mRNA. Translation: AAT85834.1 .
    AY682086 mRNA. Translation: AAT85835.1 .
    AJ310882 mRNA. Translation: CAC84550.1 .
    AJ310883 mRNA. Translation: CAC84551.1 .
    AJ310897 mRNA. Translation: CAC84537.1 .
    AJ580918 Genomic DNA. Translation: CAE45644.1 .
    AJ580919 Genomic DNA. Translation: CAE45645.1 .
    CCDSi CCDS46441.1. [Q15858-3 ]
    PIRi S54771.
    RefSeqi NP_002968.1. NM_002977.3.
    XP_005246814.1. XM_005246757.1. [Q15858-1 ]
    UniGenei Hs.439145.

    3D structure databases

    ProteinModelPortali Q15858.
    SMRi Q15858. Positions 1761-1916.
    ModBasei Search...
    MobiDBi Search...

    Chemistry

    BindingDBi Q15858.
    ChEMBLi CHEMBL4296.
    DrugBanki DB00555. Lamotrigine.
    DB00281. Lidocaine.
    GuidetoPHARMACOLOGYi 584.

    Protein family/group databases

    TCDBi 1.A.1.10.5. the voltage-gated ion channel (vic) superfamily.

    PTM databases

    PhosphoSitei Q15858.

    Polymorphism databases

    DMDMi 327478559.

    Proteomic databases

    PaxDbi Q15858.
    PRIDEi Q15858.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000409435 ; ENSP00000386330 ; ENSG00000169432 . [Q15858-1 ]
    ENST00000409672 ; ENSP00000386306 ; ENSG00000169432 . [Q15858-3 ]
    ENST00000454569 ; ENSP00000413212 ; ENSG00000169432 .
    GeneIDi 6335.
    KEGGi hsa:6335.
    UCSCi uc010fpl.3. human. [Q15858-3 ]

    Organism-specific databases

    CTDi 6335.
    GeneCardsi GC02M167051.
    GeneReviewsi SCN9A.
    HGNCi HGNC:10597. SCN9A.
    HPAi CAB013679.
    MIMi 133020. phenotype.
    167400. phenotype.
    243000. phenotype.
    603415. gene.
    613863. phenotype.
    neXtProti NX_Q15858.
    Orphaneti 88642. Channelopathy-associated congenital insensitivity to pain.
    33069. Dravet syndrome.
    1956. Erythromelalgia.
    36387. Generalized epilepsy with febrile seizures-plus context.
    970. Hereditary sensory and autonomic neuropathy type 2.
    46348. Paroxysmal extreme pain disorder.
    90026. Primary erythermalgia.
    306577. Sodium channelopathy-related small fiber neuropathy.
    PharmGKBi PA35010.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1226.
    HOVERGENi HBG053100.
    KOi K04841.
    OrthoDBi EOG7DJSK9.
    PhylomeDBi Q15858.
    TreeFami TF323985.

    Enzyme and pathway databases

    Reactomei REACT_22266. Interaction between L1 and Ankyrins.

    Miscellaneous databases

    GeneWikii Nav1.7.
    GenomeRNAii 6335.
    NextBioi 24600.
    PROi Q15858.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q15858.
    Bgeei Q15858.
    CleanExi HS_SCN9A.
    Genevestigatori Q15858.

    Family and domain databases

    Gene3Di 1.20.120.350. 4 hits.
    InterProi IPR027359. Channel_four-helix_dom.
    IPR024583. DUF3451.
    IPR005821. Ion_trans_dom.
    IPR000048. IQ_motif_EF-hand-BS.
    IPR001696. Na_channel_asu.
    IPR010526. Na_trans_assoc.
    IPR028803. SCN9A.
    [Graphical view ]
    PANTHERi PTHR10037:SF28. PTHR10037:SF28. 1 hit.
    Pfami PF11933. DUF3451. 1 hit.
    PF00520. Ion_trans. 4 hits.
    PF06512. Na_trans_assoc. 1 hit.
    [Graphical view ]
    PRINTSi PR00170. NACHANNEL.
    SMARTi SM00015. IQ. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Structure and functional expression of a new member of the tetrodotoxin-sensitive voltage-activated sodium channel family from human neuroendocrine cells."
      Klugbauer N., Lacinova L., Flockerzi V., Hofmann F.
      EMBO J. 14:1084-1090(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION IN VOLTAGE-EVOKED DEPOLARIZATION, TISSUE SPECIFICITY, VARIANT ARG-1161.
      Tissue: Thyroid.
    2. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), INVOLVEMENT IN CONGENITAL INSENSITIVITY TO PAIN, CHARACTERIZATION, VARIANT ARG-1161.
    3. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
      Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
      , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
      Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "Expression of alternatively spliced sodium channel alpha-subunit genes: unique splicing patterns are observed in dorsal root ganglia."
      Raymond C.K., Castle J.C., Garrett-Engele P.W., Armour C.D., Kan Z.G., Tsinoremas N.T., Johnson J.M.
      J. Biol. Chem. 279:46234-46241(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 136-674 (ISOFORMS 1; 2 AND 3), TISSUE SPECIFICITY.
      Tissue: Spinal ganglion.
    5. "Upregulation of voltage-gated Na+ channel expression and metastatic potential in human breast cancer: correlative studies on cell lines and biopsy tissues."
      Diss J.K.J., Fraser S.P., Coombes R.C., Djamgoz M.B.A.
      Submitted (APR-2001) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 150-264 AND 1340-1400.
    6. "Mutations in SCN9A, encoding a sodium channel alpha subunit, in patients with primary erythermalgia."
      Yang Y., Wang Y., Li S., Xu Z., Li H., Ma L., Fan J., Bu D., Liu B., Fan Z., Wu G., Jin J., Ding B., Zhu X., Shen Y.
      J. Med. Genet. 41:171-174(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 840-958, VARIANTS PERYTHM THR-859 AND HIS-869.
    7. Cited for: TISSUE SPECIFICITY.
    8. "Voltage-gated sodium channel expressed in cultured human smooth muscle cells: involvement of SCN9A."
      Jo T., Nagata T., Iida H., Imuta H., Iwasawa K., Ma J., Hara K., Omata M., Nagai R., Takizawa H., Nagase T., Nakajima T.
      FEBS Lett. 567:339-343(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN VOLTAGE-EVOKED DEPOLARIZATION, TISSUE SPECIFICITY.
    9. "Electrophysiological properties of mutant Nav1.7 sodium channels in a painful inherited neuropathy."
      Cummins T.R., Dib-Hajj S.D., Waxman S.G.
      J. Neurosci. 24:8232-8236(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION OF VARIANTS PERYTHM THR-859 AND HIS-869.
    10. "Autosomal dominant erythermalgia associated with a novel mutation in the voltage-gated sodium channel alpha subunit Nav1.7."
      Michiels J.J., te Morsche R.H.M., Jansen J.B.M.J., Drenth J.P.H.
      Arch. Neurol. 62:1587-1590(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT PERYTHM THR-241.
    11. "Gain-of-function mutation in Nav1.7 in familial erythromelalgia induces bursting of sensory neurons."
      Dib-Hajj S.D., Rush A.M., Cummins T.R., Hisama F.M., Novella S., Tyrrell L., Marshall L., Waxman S.G.
      Brain 128:1847-1854(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT PERYTHM VAL-1460, CHARACTERIZATION OF VARIANT PERYTHM VAL-1460.
    12. "SCN9A mutations define primary erythermalgia as a neuropathic disorder of voltage gated sodium channels."
      Drenth J.P., te Morsche R.H., Guillet G., Taieb A., Kirby R.L., Jansen J.B.
      J. Invest. Dermatol. 124:1333-1338(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS PERYTHM SER-216; LYS-395; THR-859 AND PHE-869, VARIANT ARG-1161.
    13. "Sporadic onset of erythermalgia: a gain-of-function mutation in Nav1.7."
      Han C., Rush A.M., Dib-Hajj S.D., Li S., Xu Z., Wang Y., Tyrrell L., Wang X., Yang Y., Waxman S.G.
      Ann. Neurol. 59:553-558(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT PERYTHM PHE-869, CHARACTERIZATION OF VARIANT PERYTHM PHE-869.
    14. "Inherited erythermalgia: limb pain from an S4 charge-neutral Na channelopathy."
      Choi J.S., Dib-Hajj S.D., Waxman S.G.
      Neurology 67:1563-1567(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION OF VARIANT PERYTHM SER-216.
    15. "SCN9A mutations in paroxysmal extreme pain disorder: allelic variants underlie distinct channel defects and phenotypes."
      Fertleman C.R., Baker M.D., Parker K.A., Moffatt S., Elmslie F.V., Abrahamsen B., Ostman J., Klugbauer N., Wood J.N., Gardiner R.M., Rees M.
      Neuron 52:767-774(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS PEPD CYS-1007; PHE-1309; ASP-1309; PHE-1310; THR-1472; VAL-1473; ILE-1475 AND LYS-1638, CHARACTERIZATION OF VARIANTS PEPD THR-1472; ILE-1475 AND LYS-1638.
    16. "A single sodium channel mutation produces hyper- or hypoexcitability in different types of neurons."
      Rush A.M., Dib-Hajj S.D., Liu S., Cummins T.R., Black J.A., Waxman S.G.
      Proc. Natl. Acad. Sci. U.S.A. 103:8245-8250(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION OF VARIANT PERYTHM HIS-869.
    17. "Early- and late-onset inherited erythromelalgia: genotype-phenotype correlation."
      Han C., Dib-Hajj S.D., Lin Z., Li Y., Eastman E.M., Tyrrell L., Cao X., Yang Y., Waxman S.G.
      Brain 132:1711-1722(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT PERYTHM ARG-10, CHARACTERIZATION OF VARIANTS PERYTHM ARG-10 AND THR-859.
    18. "A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome."
      Singh N.A., Pappas C., Dahle E.J., Claes L.R., Pruess T.H., De Jonghe P., Thompson J., Dixon M., Gurnett C., Peiffer A., White H.S., Filloux F., Leppert M.F.
      PLoS Genet. 5:E1000649-E1000649(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS GEFS+7 TYR-641 AND ARG-666, VARIANTS FEB3B VAL-62 AND GLN-149, VARIANTS MET-228; ASN-490; LYS-519; MET-695; TYR-710; VAL-750; PHE-1134; GLN-1171 AND VAL-1278.
    19. "Congenital insensitivity to pain: novel SCN9A missense and in-frame deletion mutations."
      Cox J.J., Sheynin J., Shorer Z., Reimann F., Nicholas A.K., Zubovic L., Baralle M., Wraige E., Manor E., Levy J., Woods C.G., Parvari R.
      Hum. Mutat. 31:E1670-E1686(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS CIPAR GLN-907 AND 1381-ARG--LEU-1385 DEL, CHARACTERIZATION OF VARIANTS CIPAR GLN-907 AND 1381-ARG--LEU-1385 DEL.

    Entry informationi

    Entry nameiSCN9A_HUMAN
    AccessioniPrimary (citable) accession number: Q15858
    Secondary accession number(s): A1BUH5
    , Q6B4R9, Q6B4S0, Q6B4S1, Q70HX1, Q70HX2, Q8WTU1, Q8WWN4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 23, 2004
    Last sequence update: April 5, 2011
    Last modified: October 1, 2014
    This is version 135 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. Protein Spotlight
      Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3