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 ENST00000409050
Genbank transcript ID NM_001165964
UniProt peptide P35498
alteration type single base exchange
alteration region CDS
DNA changes c.3115G>A
cDNA.3115G>A
g.37362G>A
AA changes A1039T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1039
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      1039NKKDSCMSNHTAEIGKDLDYLKDV
mutated  not conserved    1039NKKDSCMSNHTTEIGKDLDYLKD
Ptroglodytes  not conserved  ENSPTRG00000012595  1067NKKDSCMSNHTTEIGKDLDYLKD
Mmulatta  not conserved  ENSMMUG00000008407  969DSCMSNHTTEIGKDLDYLKD
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000064329  1067NRKDNCISNHTTEIGKDLDCLKD
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000010095  1052NGKGNCISNHTSVEITKDPSG
Drerio  all identical  ENSDARG00000062744  1041SDGKENCLSNH-APVAVDLTKDYLKE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
10641064CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
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 5946 / 5946
position (AA) of stopcodon in wt / mu AA sequence 1982 / 1982
position of stopcodon in wt / mu cDNA 5946 / 5946
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 1 / 1
chromosome 2
strand -1
last intron/exon boundary 4769
theoretical NMD boundary in CDS 4718
length of CDS 5946
coding sequence (CDS) position 3115
cDNA position
(for ins/del: last normal base / first normal base)		 3115
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 VSLGTTTETE
MRKRRSSSFH VSMDFLEDPS QRQRAMSIAS ILTNTVEELE ESRQKCPPCW YKFSNIFLIW
DCSPYWLKVK HVVNLVVMDP FVDLAITICI VLNTLFMAME HYPMTDHFNN VLTVGNLVFT
GIFTAEMFLK IIAMDPYYYF QEGWNIFDGF IVTLSLVELG LANVEGLSVL RSFRLLRVFK
LAKSWPTLNM LIKIIGNSVG ALGNLTLVLA IIVFIFAVVG MQLFGKSYKD CVCKIASDCQ
LPRWHMNDFF HSFLIVFRVL CGEWIETMWD CMEVAGQAMC LTVFMMVMVI GNLVVLNLFL
ALLLSSFSAD NLAATDDDNE MNNLQIAVDR MHKGVAYVKR KIYEFIQQSF IRKQKILDEI
KPLDDLNNKK DSCMSNHTAE IGKDLDYLKD VNGTTSGIGT GSSVEKYIID ESDYMSFINN
PSLTVTVPIA VGESDFENLN TEDFSSESDL EESKEKLNES SSSSEGSTVD IGAPVEEQPV
VEPEETLEPE ACFTEGCVQR FKCCQINVEE GRGKQWWNLR RTCFRIVEHN WFETFIVFMI
LLSSGALAFE DIYIDQRKTI KTMLEYADKV FTYIFILEML LKWVAYGYQT YFTNAWCWLD
FLIVDVSLVS LTANALGYSE LGAIKSLRTL RALRPLRALS RFEGMRVVVN ALLGAIPSIM
NVLLVCLIFW LIFSIMGVNL FAGKFYHCIN TTTGDRFDIE DVNNHTDCLK LIERNETARW
KNVKVNFDNV GFGYLSLLQV ATFKGWMDIM YAAVDSRNVE LQPKYEESLY MYLYFVIFII
FGSFFTLNLF IGVIIDNFNQ QKKKFGGQDI FMTEEQKKYY NAMKKLGSKK PQKPIPRPGN
KFQGMVFDFV TRQVFDISIM ILICLNMVTM MVETDDQSEY VTTILSRINL VFIVLFTGEC
VLKLISLRHY YFTIGWNIFD FVVVILSIVG MFLAELIEKY FVSPTLFRVI RLARIGRILR
LIKGAKGIRT LLFALMMSLP ALFNIGLLLF LVMFIYAIFG MSNFAYVKRE VGIDDMFNFE
TFGNSMICLF QITTSAGWDG LLAPILNSKP PDCDPNKVNP GSSVKGDCGN PSVGIFFFVS
YIIISFLVVV NMYIAVILEN FSVATEESAE PLSEDDFEMF YEVWEKFDPD ATQFMEFEKL
SQFAAALEPP LNLPQPNKLQ LIAMDLPMVS GDRIHCLDIL FAFTKRVLGE SGEMDALRIQ
MEERFMASNP SKVSYQPITT TLKRKQEEVS AVIIQRAYRR HLLKRTVKQA SFTYNKNKIK
GGANLLIKED MIIDRINENS ITEKTDLTMS TAACPPSYDR VTKPIVEKHE QEGKDEKAKG
K*
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 VSLGTTTETE
MRKRRSSSFH VSMDFLEDPS QRQRAMSIAS ILTNTVEELE ESRQKCPPCW YKFSNIFLIW
DCSPYWLKVK HVVNLVVMDP FVDLAITICI VLNTLFMAME HYPMTDHFNN VLTVGNLVFT
GIFTAEMFLK IIAMDPYYYF QEGWNIFDGF IVTLSLVELG LANVEGLSVL RSFRLLRVFK
LAKSWPTLNM LIKIIGNSVG ALGNLTLVLA IIVFIFAVVG MQLFGKSYKD CVCKIASDCQ
LPRWHMNDFF HSFLIVFRVL CGEWIETMWD CMEVAGQAMC LTVFMMVMVI GNLVVLNLFL
ALLLSSFSAD NLAATDDDNE MNNLQIAVDR MHKGVAYVKR KIYEFIQQSF IRKQKILDEI
KPLDDLNNKK DSCMSNHTTE IGKDLDYLKD VNGTTSGIGT GSSVEKYIID ESDYMSFINN
PSLTVTVPIA VGESDFENLN TEDFSSESDL EESKEKLNES SSSSEGSTVD IGAPVEEQPV
VEPEETLEPE ACFTEGCVQR FKCCQINVEE GRGKQWWNLR RTCFRIVEHN WFETFIVFMI
LLSSGALAFE DIYIDQRKTI KTMLEYADKV FTYIFILEML LKWVAYGYQT YFTNAWCWLD
FLIVDVSLVS LTANALGYSE LGAIKSLRTL RALRPLRALS RFEGMRVVVN ALLGAIPSIM
NVLLVCLIFW LIFSIMGVNL FAGKFYHCIN TTTGDRFDIE DVNNHTDCLK LIERNETARW
KNVKVNFDNV GFGYLSLLQV ATFKGWMDIM YAAVDSRNVE LQPKYEESLY MYLYFVIFII
FGSFFTLNLF IGVIIDNFNQ QKKKFGGQDI FMTEEQKKYY NAMKKLGSKK PQKPIPRPGN
KFQGMVFDFV TRQVFDISIM ILICLNMVTM MVETDDQSEY VTTILSRINL VFIVLFTGEC
VLKLISLRHY YFTIGWNIFD FVVVILSIVG MFLAELIEKY FVSPTLFRVI RLARIGRILR
LIKGAKGIRT LLFALMMSLP ALFNIGLLLF LVMFIYAIFG MSNFAYVKRE VGIDDMFNFE
TFGNSMICLF QITTSAGWDG LLAPILNSKP PDCDPNKVNP GSSVKGDCGN PSVGIFFFVS
YIIISFLVVV NMYIAVILEN FSVATEESAE PLSEDDFEMF YEVWEKFDPD ATQFMEFEKL
SQFAAALEPP LNLPQPNKLQ LIAMDLPMVS GDRIHCLDIL FAFTKRVLGE SGEMDALRIQ
MEERFMASNP SKVSYQPITT TLKRKQEEVS AVIIQRAYRR HLLKRTVKQA SFTYNKNKIK
GGANLLIKED MIIDRINENS ITEKTDLTMS TAACPPSYDR VTKPIVEKHE QEGKDEKAKG
K*
speed 0.77 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