Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999912 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM144700)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:166892788C>TN/A show variant in all transcripts   IGV
HGNC symbol SCN1A
Ensembl transcript ID ENST00000423058
Genbank transcript ID N/A
UniProt peptide P35498
alteration type single base exchange
alteration region CDS
DNA changes c.3199G>A
cDNA.3217G>A
g.37362G>A
AA changes A1067T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1067
frameshift no
known variant Reference ID: rs2298771
databasehomozygous (T/T)heterozygousallele carriers
1000G15877752362
ExAC32206-31645561

known disease mutation at this position, please check HGMD for details (HGMD ID CM144700)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7210.012
-0.640
(flanking)-0.0970.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased37362wt: 0.56 / mu: 0.83wt: ATACAGCAGAAATTG
mu: ATACAACAGAAATTG		 ACAG|caga
Donor marginally increased37364wt: 0.7615 / mu: 0.7799 (marginal change - not scored)wt: ACAGCAGAAATTGGG
mu: ACAACAGAAATTGGG		 AGCA|gaaa
distance from splice site 231
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1067NKKDSCMSNHTAEIGKDLDYLKDV
mutated  not conserved    1067NKKDSCMSNHTTEIGKDLDYLKD
Ptroglodytes  not conserved  ENSPTRG00000012595  1067NKKDSCMSNHTTEIGKDLDYLKD
Mmulatta  not conserved  ENSMMUG00000008407  969NKKDSCMSNHTTEIGKDLDYLKD
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000064329  1067NRKDNCISNHTTEIGKDLDCLKD
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000010095  1057TSVEITKDPSGVYMTE
Drerio  all identical  ENSDARG00000062744  1041SDGKENCLSNH-APVAVDLTK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
10801080CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11461146CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11581161CONFLICTDIGA -> GHRR (in Ref. 2; AAK00217).might get lost (downstream of altered splice site)
12001514REPEATIII.might get lost (downstream of altered splice site)
12141237TRANSMEMHelical; Name=S1 of repeat III; (By similarity).might get lost (downstream of altered splice site)
12511276TRANSMEMHelical; Name=S2 of repeat III; (By similarity).might get lost (downstream of altered splice site)
12831304TRANSMEMHelical; Name=S3 of repeat III; (By similarity).might get lost (downstream of altered splice site)
13091330TRANSMEMHelical; Voltage-sensor; Name=S4 of repeat III; (By similarity).might get lost (downstream of altered splice site)
13501377TRANSMEMHelical; Name=S5 of repeat III; (By similarity).might get lost (downstream of altered splice site)
13781378CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
13921392CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14031403CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
14571483TRANSMEMHelical; Name=S6 of repeat III; (By similarity).might get lost (downstream of altered splice site)
15231821REPEATIV.might get lost (downstream of altered splice site)
15371537CONFLICTF -> L (in Ref. 7; CAA46439/M91803).might get lost (downstream of altered splice site)
15371560TRANSMEMHelical; Name=S1 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
15721595TRANSMEMHelical; Name=S2 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
16021625TRANSMEMHelical; Name=S3 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
16361657TRANSMEMHelical; Voltage-sensor; Name=S4 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
16731695TRANSMEMHelical; Name=S5 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
17621786TRANSMEMHelical; Name=S6 of repeat IV; (By similarity).might get lost (downstream of altered splice site)
17881788CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
19151944DOMAINIQ.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6030 / 6030
position (AA) of stopcodon in wt / mu AA sequence 2010 / 2010
position of stopcodon in wt / mu cDNA 6048 / 6048
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 19 / 19
chromosome 2
strand -1
last intron/exon boundary 4871
theoretical NMD boundary in CDS 4802
length of CDS 6030
coding sequence (CDS) position 3199
cDNA position
(for ins/del: last normal base / first normal base)		 3217
gDNA position
(for ins/del: last normal base / first normal base)		 37362
chromosomal position
(for ins/del: last normal base / first normal base)		 166892788
original gDNA sequence snippet GTTGTATGTCCAATCATACAGCAGAAATTGGGAAAGATCTT
altered gDNA sequence snippet GTTGTATGTCCAATCATACAACAGAAATTGGGAAAGATCTT
original cDNA sequence snippet GTTGTATGTCCAATCATACAGCAGAAATTGGGAAAGATCTT
altered cDNA sequence snippet GTTGTATGTCCAATCATACAACAGAAATTGGGAAAGATCTT
wildtype AA sequence MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK PNSDLEAGKN
LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF RFSATSALYI LTPFNPLRKI
AIKILVHSLF SMLIMCTILT NCVFMTMSNP PDWTKNVEYT FTGIYTFESL IKIIARGFCL
EDFTFLRDPW NWLDFTVITF AYVTEFVDLG NVSALRTFRV LRALKTISVI PGLKTIVGAL
IQSVKKLSDV MILTVFCLSV FALIGLQLFM GNLRNKCIQW PPTNASLEEH SIEKNITVNY
NGTLINETVF EFDWKSYIQD SRYHYFLEGF LDALLCGNSS DAGQCPEGYM CVKAGRNPNY
GYTSFDTFSW AFLSLFRLMT QDFWENLYQL TLRAAGKTYM IFFVLVIFLG SFYLINLILA
VVAMAYEEQN QATLEEAEQK EAEFQQMIEQ LKKQQEAAQQ AATATASEHS REPSAAGRLS
DSSSEASKLS SKSAKERRNR RKKRKQKEQS GGEEKDEDEF QKSESEDSIR RKGFRFSIEG
NRLTYEKRYS SPHQSLLSIR GSLFSPRRNS RTSLFSFRGR AKDVGSENDF ADDEHSTFED
NESRRDSLFV PRRHGERRNS NLSQTSRSSR MLAVFPANGK MHSTVDCNGV VSLVGGPSVP
TSPVGQLLPE VIIDKPATDD NGTTTETEMR KRRSSSFHVS MDFLEDPSQR QRAMSIASIL
TNTVEELEES RQKCPPCWYK FSNIFLIWDC SPYWLKVKHV VNLVVMDPFV DLAITICIVL
NTLFMAMEHY PMTDHFNNVL TVGNLVFTGI FTAEMFLKII AMDPYYYFQE GWNIFDGFIV
TLSLVELGLA NVEGLSVLRS FRLLRVFKLA KSWPTLNMLI KIIGNSVGAL GNLTLVLAII
VFIFAVVGMQ LFGKSYKDCV CKIASDCQLP RWHMNDFFHS FLIVFRVLCG EWIETMWDCM
EVAGQAMCLT VFMMVMVIGN LVVLNLFLAL LLSSFSADNL AATDDDNEMN NLQIAVDRMH
KGVAYVKRKI YEFIQQSFIR KQKILDEIKP LDDLNNKKDS CMSNHTAEIG KDLDYLKDVN
GTTSGIGTGS SVEKYIIDES DYMSFINNPS LTVTVPIAVG ESDFENLNTE DFSSESDLEE
SKEKLNESSS SSEGSTVDIG APVEEQPVVE PEETLEPEAC FTEGCVQRFK CCQINVEEGR
GKQWWNLRRT CFRIVEHNWF ETFIVFMILL SSGALAFEDI YIDQRKTIKT MLEYADKVFT
YIFILEMLLK WVAYGYQTYF TNAWCWLDFL IVDVSLVSLT ANALGYSELG AIKSLRTLRA
LRPLRALSRF EGMRVVVNAL LGAIPSIMNV LLVCLIFWLI FSIMGVNLFA GKFYHCINTT
TGDRFDIEDV NNHTDCLKLI ERNETARWKN VKVNFDNVGF GYLSLLQVAT FKGWMDIMYA
AVDSRNVELQ PKYEESLYMY LYFVIFIIFG SFFTLNLFIG VIIDNFNQQK KKFGGQDIFM
TEEQKKYYNA MKKLGSKKPQ KPIPRPGNKF QGMVFDFVTR QVFDISIMIL ICLNMVTMMV
ETDDQSEYVT TILSRINLVF IVLFTGECVL KLISLRHYYF TIGWNIFDFV VVILSIVGMF
LAELIEKYFV SPTLFRVIRL ARIGRILRLI KGAKGIRTLL FALMMSLPAL FNIGLLLFLV
MFIYAIFGMS NFAYVKREVG IDDMFNFETF GNSMICLFQI TTSAGWDGLL APILNSKPPD
CDPNKVNPGS SVKGDCGNPS VGIFFFVSYI IISFLVVVNM YIAVILENFS VATEESAEPL
SEDDFEMFYE VWEKFDPDAT QFMEFEKLSQ FAAALEPPLN LPQPNKLQLI AMDLPMVSGD
RIHCLDILFA FTKRVLGESG EMDALRIQME ERFMASNPSK VSYQPITTTL KRKQEEVSAV
IIQRAYRRHL LKRTVKQASF TYNKNKIKGG ANLLIKEDMI IDRINENSIT EKTDLTMSTA
ACPPSYDRVT KPIVEKHEQE GKDEKAKGK*
mutated AA sequence MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK PNSDLEAGKN
LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF RFSATSALYI LTPFNPLRKI
AIKILVHSLF SMLIMCTILT NCVFMTMSNP PDWTKNVEYT FTGIYTFESL IKIIARGFCL
EDFTFLRDPW NWLDFTVITF AYVTEFVDLG NVSALRTFRV LRALKTISVI PGLKTIVGAL
IQSVKKLSDV MILTVFCLSV FALIGLQLFM GNLRNKCIQW PPTNASLEEH SIEKNITVNY
NGTLINETVF EFDWKSYIQD SRYHYFLEGF LDALLCGNSS DAGQCPEGYM CVKAGRNPNY
GYTSFDTFSW AFLSLFRLMT QDFWENLYQL TLRAAGKTYM IFFVLVIFLG SFYLINLILA
VVAMAYEEQN QATLEEAEQK EAEFQQMIEQ LKKQQEAAQQ AATATASEHS REPSAAGRLS
DSSSEASKLS SKSAKERRNR RKKRKQKEQS GGEEKDEDEF QKSESEDSIR RKGFRFSIEG
NRLTYEKRYS SPHQSLLSIR GSLFSPRRNS RTSLFSFRGR AKDVGSENDF ADDEHSTFED
NESRRDSLFV PRRHGERRNS NLSQTSRSSR MLAVFPANGK MHSTVDCNGV VSLVGGPSVP
TSPVGQLLPE VIIDKPATDD NGTTTETEMR KRRSSSFHVS MDFLEDPSQR QRAMSIASIL
TNTVEELEES RQKCPPCWYK FSNIFLIWDC SPYWLKVKHV VNLVVMDPFV DLAITICIVL
NTLFMAMEHY PMTDHFNNVL TVGNLVFTGI FTAEMFLKII AMDPYYYFQE GWNIFDGFIV
TLSLVELGLA NVEGLSVLRS FRLLRVFKLA KSWPTLNMLI KIIGNSVGAL GNLTLVLAII
VFIFAVVGMQ LFGKSYKDCV CKIASDCQLP RWHMNDFFHS FLIVFRVLCG EWIETMWDCM
EVAGQAMCLT VFMMVMVIGN LVVLNLFLAL LLSSFSADNL AATDDDNEMN NLQIAVDRMH
KGVAYVKRKI YEFIQQSFIR KQKILDEIKP LDDLNNKKDS CMSNHTTEIG KDLDYLKDVN
GTTSGIGTGS SVEKYIIDES DYMSFINNPS LTVTVPIAVG ESDFENLNTE DFSSESDLEE
SKEKLNESSS SSEGSTVDIG APVEEQPVVE PEETLEPEAC FTEGCVQRFK CCQINVEEGR
GKQWWNLRRT CFRIVEHNWF ETFIVFMILL SSGALAFEDI YIDQRKTIKT MLEYADKVFT
YIFILEMLLK WVAYGYQTYF TNAWCWLDFL IVDVSLVSLT ANALGYSELG AIKSLRTLRA
LRPLRALSRF EGMRVVVNAL LGAIPSIMNV LLVCLIFWLI FSIMGVNLFA GKFYHCINTT
TGDRFDIEDV NNHTDCLKLI ERNETARWKN VKVNFDNVGF GYLSLLQVAT FKGWMDIMYA
AVDSRNVELQ PKYEESLYMY LYFVIFIIFG SFFTLNLFIG VIIDNFNQQK KKFGGQDIFM
TEEQKKYYNA MKKLGSKKPQ KPIPRPGNKF QGMVFDFVTR QVFDISIMIL ICLNMVTMMV
ETDDQSEYVT TILSRINLVF IVLFTGECVL KLISLRHYYF TIGWNIFDFV VVILSIVGMF
LAELIEKYFV SPTLFRVIRL ARIGRILRLI KGAKGIRTLL FALMMSLPAL FNIGLLLFLV
MFIYAIFGMS NFAYVKREVG IDDMFNFETF GNSMICLFQI TTSAGWDGLL APILNSKPPD
CDPNKVNPGS SVKGDCGNPS VGIFFFVSYI IISFLVVVNM YIAVILENFS VATEESAEPL
SEDDFEMFYE VWEKFDPDAT QFMEFEKLSQ FAAALEPPLN LPQPNKLQLI AMDLPMVSGD
RIHCLDILFA FTKRVLGESG EMDALRIQME ERFMASNPSK VSYQPITTTL KRKQEEVSAV
IIQRAYRRHL LKRTVKQASF TYNKNKIKGG ANLLIKEDMI IDRINENSIT EKTDLTMSTA
ACPPSYDRVT KPIVEKHEQE GKDEKAKGK*
speed 1.08 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project