| Transcript | Gene symbol | Prediction | Tree vote | Model | Prediction problem | Splice site change | Known ClinVar disease mutation | Potential ClinVar disease mutation | Amino acid changes | Variant type | dbSNP ID | Protein length | Features at a glance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SCN1A | Deleterious | 88|12 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN1A | Deleterious | 90|10 | 3utr | No | Single base exchange | N/A | |||||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| ||||||
ENST00000674923(MANE Select) | SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
| |||||
| SCN1A | Deleterious | 98|2 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||
| Gene symbol | SCN1A | |||||||||||||
| Gene constraints | no data | |||||||||||||
| Ensembl transcript ID | ENST00000713692.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.5531A>G g.191309A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| Wildtype AA sequence | MVSEPLEDLD PYYINKKTFI VLNKGKAIFR FSATSALYIL TPFNPLRKIA IKILVHSLFS MLIMCTILTN CVFMTMSNPP DWTKNVEYTF TGIYTFESLI KIIARGFCLE DFTFLRDPWN WLDFTVITFA YVTEFVDLGN VSALRTFRVL RALKTISVIP GLKTIVGALI QSVKKLSDVM ILTVFCLSVF ALIGLQLFMG NLRNKCIQWP PTNASLEEHS IEKNITVNYN GTLINETVFE FDWKSYIQDS RYHYFLEGFL DALLCGNSSD AGQCPEGYMC VKAGRNPNYG YTSFDTFSWA FLSLFRLMTQ DFWENLYQLT LRAAGKTYMI FFVLVIFLGS FYLINLILAV VAMAYEEQNQ ATLEEAEQKE AEFQQMIEQL KKQQEAAQQA ATATASEHSR EPSAAGRLSD SSSEASKLSS KSAKERRNRR KKRKQKEQSG GEEKDEDEFQ KSESEDSIRR KGFRFSIEGN RLTYEKRYSS PHQSLLSIRG SLFSPRRNSR TSLFSFRGRA KDVGSENDFA DDEHSTFEDN ESRRDSLFVP RRHGERRNSN LSQTSRSSRM LAVFPANGKM HSTVDCNGVV SLVGGPSVPT SPVGQLLPEG TTTETEMRKR RSSSFHVSMD FLEDPSQRQR AMSIASILTN TVEELEESRQ KCPPCWYKFS NIFLIWDCSP YWLKVKHVVN LVVMDPFVDL AITICIVLNT LFMAMEHYPM TDHFNNVLTV GNLVFTGIFT AEMFLKIIAM DPYYYFQEGW NIFDGFIVTL SLVELGLANV EGLSVLRSFR LLRVFKLAKS WPTLNMLIKI IGNSVGALGN LTLVLAIIVF IFAVVGMQLF GKSYKDCVCK IASDCQLPRW HMNDFFHSFL IVFRVLCGEW IETMWDCMEV AGQAMCLTVF MMVMVIGNLV VLNLFLALLL SSFSADNLAA TDDDNEMNNL QIAVDRMHKG VAYVKRKIYE FIQQSFIRKQ KILDEIKPLD DLNNKKDSCM SNHTAEIGKD LDYLKDVNGT TSGIGTGSSV EKYIIDESDY MSFINNPSLT VTVPIAVGES DFENLNTEDF SSESDLEESK EKLNESSSSS EGSTVDIGAP VEEQPVVEPE ETLEPEACFT EGCVQRFKCC QINVEEGRGK QWWNLRRTCF RIVEHNWFET FIVFMILLSS GALAFEDIYI DQRKTIKTML EYADKVFTYI FILEMLLKWV AYGYQTYFTN AWCWLDFLIV DVSLVSLTAN ALGYSELGAI KSLRTLRALR PLRALSRFEG MRVVVNALLG AIPSIMNVLL VCLIFWLIFS IMGVNLFAGK FYHCINTTTG DRFDIEDVNN HTDCLKLIER NETARWKNVK VNFDNVGFGY LSLLQVATFK GWMDIMYAAV DSRNVELQPK YEESLYMYLY FVIFIIFGSF FTLNLFIGVI IDNFNQQKKK FGGQDIFMTE EQKKYYNAMK KLGSKKPQKP IPRPGNKFQG MVFDFVTRQV FDISIMILIC LNMVTMMVET DDQSEYVTTI LSRINLVFIV LFTGECVLKL ISLRHYYFTI GWNIFDFVVV ILSIVGMFLA ELIEKYFVSP TLFRVIRLAR IGRILRLIKG AKGIRTLLFA LMMSLPALFN IGLLLFLVMF IYAIFGMSNF AYVKREVGID DMFNFETFGN SMICLFQITT SAGWDGLLAP ILNSKPPDCD PNKVNPGSSV KGDCGNPSVG IFFFVSYIII SFLVVVNMYI AVILENFSVA TEESAEPLSE DDFEMFYEVW EKFDPDATQF MEFEKLSQFA AALEPPLNLP QPNKLQLIAM DLPMVSGDRI HCLDILFAFT KRVLGESGEM DALRIQMEER FMASNPSKVS YQPITTTLKR KQEEVSAVII QRAYRRHLLK RTVKQASFTY NKNKIKGGAN LLIKEDMIID RINENSITEK TDLTMSTAAC PPSYDRVTKP IVEKHEQEGK DEKAKGK* | |||||||||||||
| Mutated AA sequence | MVSEPLEDLD PYYINKKTFI VLNKGKAIFR FSATSALYIL TPFNPLRKIA IKILVHSLFS MLIMCTILTN CVFMTMSNPP DWTKNVEYTF TGIYTFESLI KIIARGFCLE DFTFLRDPWN WLDFTVITFA YVTEFVDLGN VSALRTFRVL RALKTISVIP GLKTIVGALI QSVKKLSDVM ILTVFCLSVF ALIGLQLFMG NLRNKCIQWP PTNASLEEHS IEKNITVNYN GTLINETVFE FDWKSYIQDS RYHYFLEGFL DALLCGNSSD AGQCPEGYMC VKAGRNPNYG YTSFDTFSWA FLSLFRLMTQ DFWENLYQLT LRAAGKTYMI FFVLVIFLGS FYLINLILAV VAMAYEEQNQ ATLEEAEQKE AEFQQMIEQL KKQQEAAQQA ATATASEHSR EPSAAGRLSD SSSEASKLSS KSAKERRNRR KKRKQKEQSG GEEKDEDEFQ KSESEDSIRR KGFRFSIEGN RLTYEKRYSS PHQSLLSIRG SLFSPRRNSR TSLFSFRGRA KDVGSENDFA DDEHSTFEDN ESRRDSLFVP RRHGERRNSN LSQTSRSSRM LAVFPANGKM HSTVDCNGVV SLVGGPSVPT SPVGQLLPEG TTTETEMRKR RSSSFHVSMD FLEDPSQRQR AMSIASILTN TVEELEESRQ KCPPCWYKFS NIFLIWDCSP YWLKVKHVVN LVVMDPFVDL AITICIVLNT LFMAMEHYPM TDHFNNVLTV GNLVFTGIFT AEMFLKIIAM DPYYYFQEGW NIFDGFIVTL SLVELGLANV EGLSVLRSFR LLRVFKLAKS WPTLNMLIKI IGNSVGALGN LTLVLAIIVF IFAVVGMQLF GKSYKDCVCK IASDCQLPRW HMNDFFHSFL IVFRVLCGEW IETMWDCMEV AGQAMCLTVF MMVMVIGNLV VLNLFLALLL SSFSADNLAA TDDDNEMNNL QIAVDRMHKG VAYVKRKIYE FIQQSFIRKQ KILDEIKPLD DLNNKKDSCM SNHTAEIGKD LDYLKDVNGT TSGIGTGSSV EKYIIDESDY MSFINNPSLT VTVPIAVGES DFENLNTEDF SSESDLEESK EKLNESSSSS EGSTVDIGAP VEEQPVVEPE ETLEPEACFT EGCVQRFKCC QINVEEGRGK QWWNLRRTCF RIVEHNWFET FIVFMILLSS GALAFEDIYI DQRKTIKTML EYADKVFTYI FILEMLLKWV AYGYQTYFTN AWCWLDFLIV DVSLVSLTAN ALGYSELGAI KSLRTLRALR PLRALSRFEG MRVVVNALLG AIPSIMNVLL VCLIFWLIFS IMGVNLFAGK FYHCINTTTG DRFDIEDVNN HTDCLKLIER NETARWKNVK VNFDNVGFGY LSLLQVATFK GWMDIMYAAV DSRNVELQPK YEESLYMYLY FVIFIIFGSF FTLNLFIGVI IDNFNQQKKK FGGQDIFMTE EQKKYYNAMK KLGSKKPQKP IPRPGNKFQG MVFDFVTRQV FDISIMILIC LNMVTMMVET DDQSEYVTTI LSRINLVFIV LFTGECVLKL ISLRHYYFTI GWNIFDFVVV ILSIVGMFLA ELIEKYFVSP TLFRVIRLAR IGRILRLIKG AKGIRTLLFA LMMSLPALFN IGLLLFLVMF IYAIFGMSNF AYVKREVGID DMFNFETFGN SMICLFQITT SAGWDGLLAP ILNSKPPDCD PNKVNPGSSV KGDCGNPSVG IFFFVSYIII SFLVVVNMYI AVILENFSVA TEESAEPLSE DDFEMFYEVW EKFDPDATQF MEFEKLSQFA AALEPPLNLP QPNKLQLIAM DLPMVSGDRI HCLDILFAFT KRVLGESGEM DALRIQMEER FMASNPSKVS YQPITTTLKR KQEEVSAVII QRACRRHLLK RTVKQASFTY NKNKIKGGAN LLIKEDMIID RINENSITEK TDLTMSTAAC PPSYDRVTKP IVEKHEQEGK DEKAKGK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5784 / 5784 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1928 / 1928 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 6301 / 6301 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 518 / 518 | |||||||||||||
| Last intron/exon boundary | 5123 | |||||||||||||
| Theoretical NMD boundary in CDS | 4555 | |||||||||||||
| Length of CDS | 5784 | |||||||||||||
| Coding sequence (CDS) position | 5531 | |||||||||||||
| cDNA position | 6048 | |||||||||||||
| gDNA position | 191309 | |||||||||||||
| Chromosomal position | 165991498 | |||||||||||||
| Speed | 0.09 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||
| Gene symbol | SCN1A | |||||||||||||
| Gene constraints | LOEUF: 0.08, LOF (oe): 0.04, misssense (oe): 0.57, synonymous (oe): 0.89 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000635776.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | 3'UTR | |||||||||||||
| DNA changes | cDNA.7769A>G g.191309A>G | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | polyA signal ok | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGKKY LKFLNSVK* | |||||||||||||
| Mutated AA sequence | ||||||||||||||
| Position of stopcodon in wt / mu CDS | N/A | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | N/A | |||||||||||||
| Position of stopcodon in wt / mu cDNA | N/A | |||||||||||||
| Position of start ATG in wt / mu cDNA | 303 / 303 | |||||||||||||
| Last intron/exon boundary | 4850 | |||||||||||||
| Theoretical NMD boundary in CDS | 4497 | |||||||||||||
| Length of CDS | 4857 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | 7769 | |||||||||||||
| gDNA position | 191309 | |||||||||||||
| Chromosomal position | 165991498 | |||||||||||||
| Speed | 0.11 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||
| Gene symbol | SCN1A | |||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.58, synonymous (oe): 0.90 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000641603.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.5495A>G g.191309A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| 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 EGMRATFKGW MDIMYAAVDS RNVELQPKYE ESLYMYLYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKFG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPGNKFQGMV FDFVTRQVFD ISIMILICLN MVTMMVETDD QSEYVTTILS RINLVFIVLF TGECVLKLIS LRHYYFTIGW NIFDFVVVIL SIVGMFLAEL IEKYFVSPTL FRVIRLARIG RILRLIKGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY AIFGMSNFAY VKREVGIDDM FNFETFGNSM ICLFQITTSA GWDGLLAPIL NSKPPDCDPN KVNPGSSVKG DCGNPSVGIF FFVSYIIISF LVVVNMYIAV ILENFSVATE ESAEPLSEDD FEMFYEVWEK FDPDATQFME FEKLSQFAAA LEPPLNLPQP NKLQLIAMDL PMVSGDRIHC LDILFAFTKR VLGESGEMDA LRIQMEERFM ASNPSKVSYQ PITTTLKRKQ EEVSAVIIQR AYRRHLLKRT VKQASFTYNK NKIKGGANLL IKEDMIIDRI NENSITEKTD LTMSTAACPP SYDRVTKPIV EKHEQEGKDE KAKGK* | |||||||||||||
| 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 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 EGMRATFKGW MDIMYAAVDS RNVELQPKYE ESLYMYLYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKFG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPGNKFQGMV FDFVTRQVFD ISIMILICLN MVTMMVETDD QSEYVTTILS RINLVFIVLF TGECVLKLIS LRHYYFTIGW NIFDFVVVIL SIVGMFLAEL IEKYFVSPTL FRVIRLARIG RILRLIKGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY AIFGMSNFAY VKREVGIDDM FNFETFGNSM ICLFQITTSA GWDGLLAPIL NSKPPDCDPN KVNPGSSVKG DCGNPSVGIF FFVSYIIISF LVVVNMYIAV ILENFSVATE ESAEPLSEDD FEMFYEVWEK FDPDATQFME FEKLSQFAAA LEPPLNLPQP NKLQLIAMDL PMVSGDRIHC LDILFAFTKR VLGESGEMDA LRIQMEERFM ASNPSKVSYQ PITTTLKRKQ EEVSAVIIQR ACRRHLLKRT VKQASFTYNK NKIKGGANLL IKEDMIIDRI NENSITEKTD LTMSTAACPP SYDRVTKPIV EKHEQEGKDE KAKGK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5748 / 5748 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1916 / 1916 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5902 / 5902 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 155 / 155 | |||||||||||||
| Last intron/exon boundary | 4724 | |||||||||||||
| Theoretical NMD boundary in CDS | 4519 | |||||||||||||
| Length of CDS | 5748 | |||||||||||||
| Coding sequence (CDS) position | 5495 | |||||||||||||
| cDNA position | 5649 | |||||||||||||
| gDNA position | 191309 | |||||||||||||
| Chromosomal position | 165991498 | |||||||||||||
| Speed | 0.08 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||
| Gene symbol | SCN1A | |||||||||||||
| Gene constraints | LOEUF: 0.09, LOF (oe): 0.05, misssense (oe): 0.56, synonymous (oe): 0.89 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000641575.1 | |||||||||||||
| Genbank transcript ID | NM_001353955 (by similarity), NM_001353954 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.5741A>G g.191309A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| 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 LKKQQEAAQA ATATASEHSR EPSAAGRLSD SSSEASKLSS KSAKERRNRR KKRKQKEQSG GEEKDEDEFQ KSESEDSIRR KGFRFSIEGN RLTYEKRYSS PHQSLLSIRG SLFSPRRNSR TSLFSFRGRA KDVGSENDFA DDEHSTFEDN ESRRDSLFVP RRHGERRNSN LSQTSRSSRM LAVFPANGKM HSTVDCNGVV SLVGGPSVPT SPVGQLLPEG TTTETEMRKR RSSSFHVSMD FLEDPSQRQR AMSIASILTN TVEELEESRQ KCPPCWYKFS NIFLIWDCSP YWLKVKHVVN LVVMDPFVDL AITICIVLNT LFMAMEHYPM TDHFNNVLTV GNLVFTGIFT AEMFLKIIAM DPYYYFQEGW NIFDGFIVTL SLVELGLANV EGLSVLRSFR LLRVFKLAKS WPTLNMLIKI IGNSVGALGN LTLVLAIIVF IFAVVGMQLF GKSYKDCVCK IASDCQLPRW HMNDFFHSFL IVFRVLCGEW IETMWDCMEV AGQAMCLTVF MMVMVIGNLV VLNLFLALLL SSFSADNLAA TDDDNEMNNL QIAVDRMHKG VAYVKRKIYE FIQQSFIRKQ KILDEIKPLD DLNNKKDSCM SNHTAEIGKD LDYLKDVNGT TSGIGTGSSV EKYIIDESDY MSFINNPSLT VTVPIAVGES DFENLNTEDF SSESDLEESK EKLNESSSSS EGSTVDIGAP VEEQPVVEPE ETLEPEACFT EGCVQRFKCC QINVEEGRGK QWWNLRRTCF RIVEHNWFET FIVFMILLSS GALAFEDIYI DQRKTIKTML EYADKVFTYI FILEMLLKWV AYGYQTYFTN AWCWLDFLIV DVSLVSLTAN ALGYSELGAI KSLRTLRALR PLRALSRFEG MRVVVNALLG AIPSIMNVLL VCLIFWLIFS IMGVNLFAGK FYHCINTTTG DRFDIEDVNN HTDCLKLIER NETARWKNVK VNFDNVGFGY LSLLQVATFK GWMDIMYAAV DSRNVELQPK YEESLYMYLY FVIFIIFGSF FTLNLFIGVI IDNFNQQKKK FGGQDIFMTE EQKKYYNAMK KLGSKKPQKP IPRPGNKFQG MVFDFVTRQV FDISIMILIC LNMVTMMVET DDQSEYVTTI LSRINLVFIV LFTGECVLKL ISLRHYYFTI GWNIFDFVVV ILSIVGMFLA ELIEKYFVSP TLFRVIRLAR IGRILRLIKG AKGIRTLLFA LMMSLPALFN IGLLLFLVMF IYAIFGMSNF AYVKREVGID DMFNFETFGN SMICLFQITT SAGWDGLLAP ILNSKPPDCD PNKVNPGSSV KGDCGNPSVG IFFFVSYIII SFLVVVNMYI AVILENFSVA TEESAEPLSE DDFEMFYEVW EKFDPDATQF MEFEKLSQFA AALEPPLNLP QPNKLQLIAM DLPMVSGDRI HCLDILFAFT KRVLGESGEM DALRIQMEER FMASNPSKVS YQPITTTLKR KQEEVSAVII QRAYRRHLLK RTVKQASFTY NKNKIKGGAN LLIKEDMIID RINENSITEK TDLTMSTAAC PPSYDRVTKP IVEKHEQEGK DEKAKGK* | |||||||||||||
| 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 LKKQQEAAQA ATATASEHSR EPSAAGRLSD SSSEASKLSS KSAKERRNRR KKRKQKEQSG GEEKDEDEFQ KSESEDSIRR KGFRFSIEGN RLTYEKRYSS PHQSLLSIRG SLFSPRRNSR TSLFSFRGRA KDVGSENDFA DDEHSTFEDN ESRRDSLFVP RRHGERRNSN LSQTSRSSRM LAVFPANGKM HSTVDCNGVV SLVGGPSVPT SPVGQLLPEG TTTETEMRKR RSSSFHVSMD FLEDPSQRQR AMSIASILTN TVEELEESRQ KCPPCWYKFS NIFLIWDCSP YWLKVKHVVN LVVMDPFVDL AITICIVLNT LFMAMEHYPM TDHFNNVLTV GNLVFTGIFT AEMFLKIIAM DPYYYFQEGW NIFDGFIVTL SLVELGLANV EGLSVLRSFR LLRVFKLAKS WPTLNMLIKI IGNSVGALGN LTLVLAIIVF IFAVVGMQLF GKSYKDCVCK IASDCQLPRW HMNDFFHSFL IVFRVLCGEW IETMWDCMEV AGQAMCLTVF MMVMVIGNLV VLNLFLALLL SSFSADNLAA TDDDNEMNNL QIAVDRMHKG VAYVKRKIYE FIQQSFIRKQ KILDEIKPLD DLNNKKDSCM SNHTAEIGKD LDYLKDVNGT TSGIGTGSSV EKYIIDESDY MSFINNPSLT VTVPIAVGES DFENLNTEDF SSESDLEESK EKLNESSSSS EGSTVDIGAP VEEQPVVEPE ETLEPEACFT EGCVQRFKCC QINVEEGRGK QWWNLRRTCF RIVEHNWFET FIVFMILLSS GALAFEDIYI DQRKTIKTML EYADKVFTYI FILEMLLKWV AYGYQTYFTN AWCWLDFLIV DVSLVSLTAN ALGYSELGAI KSLRTLRALR PLRALSRFEG MRVVVNALLG AIPSIMNVLL VCLIFWLIFS IMGVNLFAGK FYHCINTTTG DRFDIEDVNN HTDCLKLIER NETARWKNVK VNFDNVGFGY LSLLQVATFK GWMDIMYAAV DSRNVELQPK YEESLYMYLY FVIFIIFGSF FTLNLFIGVI IDNFNQQKKK FGGQDIFMTE EQKKYYNAMK KLGSKKPQKP IPRPGNKFQG MVFDFVTRQV FDISIMILIC LNMVTMMVET DDQSEYVTTI LSRINLVFIV LFTGECVLKL ISLRHYYFTI GWNIFDFVVV ILSIVGMFLA ELIEKYFVSP TLFRVIRLAR IGRILRLIKG AKGIRTLLFA LMMSLPALFN IGLLLFLVMF IYAIFGMSNF AYVKREVGID DMFNFETFGN SMICLFQITT SAGWDGLLAP ILNSKPPDCD PNKVNPGSSV KGDCGNPSVG IFFFVSYIII SFLVVVNMYI AVILENFSVA TEESAEPLSE DDFEMFYEVW EKFDPDATQF MEFEKLSQFA AALEPPLNLP QPNKLQLIAM DLPMVSGDRI HCLDILFAFT KRVLGESGEM DALRIQMEER FMASNPSKVS YQPITTTLKR KQEEVSAVII QRACRRHLLK RTVKQASFTY NKNKIKGGAN LLIKEDMIID RINENSITEK TDLTMSTAAC PPSYDRVTKP IVEKHEQEGK DEKAKGK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5994 / 5994 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1998 / 1998 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 6270 / 6270 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 277 / 277 | |||||||||||||
| Last intron/exon boundary | 5092 | |||||||||||||
| Theoretical NMD boundary in CDS | 4765 | |||||||||||||
| Length of CDS | 5994 | |||||||||||||
| Coding sequence (CDS) position | 5741 | |||||||||||||
| cDNA position | 6017 | |||||||||||||
| gDNA position | 191309 | |||||||||||||
| Chromosomal position | 165991498 | |||||||||||||
| Speed | 0.12 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||
| Gene symbol | SCN1A | |||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.57, synonymous (oe): 0.88 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000640036.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.5744A>G g.191309A>G | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||
| Wildtype AA sequence | MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK PNSDLEAGKN LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF RFSATSALYI LTPFNPLRKI AIKILVHSLF SMLIMCTILT NCVFMTMSNP PDWTKNVEYT FTGIYTFESL IKIIARGFCL EDFTFLRDPW NWLDFTVITF AFVTEFVNLG NFSALRTFRV 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRAYRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||
| Mutated AA sequence | MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK PNSDLEAGKN LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF RFSATSALYI LTPFNPLRKI AIKILVHSLF SMLIMCTILT NCVFMTMSNP PDWTKNVEYT FTGIYTFESL IKIIARGFCL EDFTFLRDPW NWLDFTVITF AFVTEFVNLG NFSALRTFRV 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRACRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5997 / 5997 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1999 / 1999 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 6046 / 6046 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 50 / 50 | |||||||||||||
| Last intron/exon boundary | 4868 | |||||||||||||
| Theoretical NMD boundary in CDS | 4768 | |||||||||||||
| Length of CDS | 5997 | |||||||||||||
| Coding sequence (CDS) position | 5744 | |||||||||||||
| cDNA position | 5793 | |||||||||||||
| gDNA position | 191309 | |||||||||||||
| Chromosomal position | 165991498 | |||||||||||||
| Speed | 0.11 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||||||||||
| Gene symbol | SCN1A | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.56, synonymous (oe): 0.89 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000637988.1 | |||||||||||||||||||||
| Genbank transcript ID | NM_001353952 (by similarity), NM_006920 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN1A_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.5744A>G g.191309A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| Phylogenetic conservation |
| |||||||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||||||||||
| Distance from splice site | N/A | |||||||||||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||||||||||
| poly(A) signal | N/A | |||||||||||||||||||||
| AA sequence altered | Yes | |||||||||||||||||||||
| Chromosome | 2 | |||||||||||||||||||||
| Strand | -1 | |||||||||||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRAYRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||||||||||
| 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRACRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 5997 / 5997 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1999 / 1999 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 6477 / 6477 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 481 / 481 | |||||||||||||||||||||
| Last intron/exon boundary | 5299 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4768 | |||||||||||||||||||||
| Length of CDS | 5997 | |||||||||||||||||||||
| Coding sequence (CDS) position | 5744 | |||||||||||||||||||||
| cDNA position | 6224 | |||||||||||||||||||||
| gDNA position | 191309 | |||||||||||||||||||||
| Chromosomal position | 165991498 | |||||||||||||||||||||
| Speed | 0.08 s | |||||||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||||||||||
| Gene symbol | SCN1A | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.56, synonymous (oe): 0.89 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000375405.7 | |||||||||||||||||||||
| Genbank transcript ID | NM_001353951 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN1A_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.5744A>G g.191309A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| Phylogenetic conservation |
| |||||||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||||||||||
| Distance from splice site | N/A | |||||||||||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||||||||||
| poly(A) signal | N/A | |||||||||||||||||||||
| AA sequence altered | Yes | |||||||||||||||||||||
| Chromosome | 2 | |||||||||||||||||||||
| Strand | -1 | |||||||||||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRAYRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||||||||||
| 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRACRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 5997 / 5997 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1999 / 1999 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 6015 / 6015 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 19 / 19 | |||||||||||||||||||||
| Last intron/exon boundary | 4837 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4768 | |||||||||||||||||||||
| Length of CDS | 5997 | |||||||||||||||||||||
| Coding sequence (CDS) position | 5744 | |||||||||||||||||||||
| cDNA position | 5762 | |||||||||||||||||||||
| gDNA position | 191309 | |||||||||||||||||||||
| Chromosomal position | 165991498 | |||||||||||||||||||||
| Speed | 0.11 s | |||||||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | ||||||||||||||||
| Gene symbol | SCN1A | ||||||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.56, synonymous (oe): 0.89 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000409050.2 | ||||||||||||||||
| Genbank transcript ID | NM_001353958 (by similarity), NM_001353957 (by similarity), NM_001353960 (by similarity), NM_001165964 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | SCN1A_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.5693A>G g.191309A>G | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 2 | ||||||||||||||||
| Strand | -1 | ||||||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | ||||||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | ||||||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | ||||||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | ||||||||||||||||
| 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 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 AVIIQRACRR HLLKRTVKQA SFTYNKNKIK GGANLLIKED MIIDRINENS ITEKTDLTMS TAACPPSYDR VTKPIVEKHE QEGKDEKAKG K* | ||||||||||||||||
| 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 | 6231 / 6231 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 286 / 286 | ||||||||||||||||
| Last intron/exon boundary | 5053 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 4717 | ||||||||||||||||
| Length of CDS | 5946 | ||||||||||||||||
| Coding sequence (CDS) position | 5693 | ||||||||||||||||
| cDNA position | 5978 | ||||||||||||||||
| gDNA position | 191309 | ||||||||||||||||
| Chromosomal position | 165991498 | ||||||||||||||||
| Speed | 0.11 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||||||||||
| Gene symbol | SCN1A | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.56, synonymous (oe): 0.89 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000303395.9 | |||||||||||||||||||||
| Genbank transcript ID | NM_001202435 (by similarity), NM_001353948 (by similarity), NM_001353961 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN1A_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.5777A>G g.191309A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| Phylogenetic conservation |
| |||||||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||||||||||
| Distance from splice site | N/A | |||||||||||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||||||||||
| poly(A) signal | N/A | |||||||||||||||||||||
| AA sequence altered | Yes | |||||||||||||||||||||
| Chromosome | 2 | |||||||||||||||||||||
| Strand | -1 | |||||||||||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| 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 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 IIQRACRRHL LKRTVKQASF TYNKNKIKGG ANLLIKEDMI IDRINENSIT EKTDLTMSTA ACPPSYDRVT KPIVEKHEQE GKDEKAKGK* | |||||||||||||||||||||
| 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 | 6421 / 6421 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 392 / 392 | |||||||||||||||||||||
| Last intron/exon boundary | 5243 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4801 | |||||||||||||||||||||
| Length of CDS | 6030 | |||||||||||||||||||||
| Coding sequence (CDS) position | 5777 | |||||||||||||||||||||
| cDNA position | 6168 | |||||||||||||||||||||
| gDNA position | 191309 | |||||||||||||||||||||
| Chromosomal position | 165991498 | |||||||||||||||||||||
| Speed | 0.11 s | |||||||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||||||||||
| Gene symbol | SCN1A | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.56, synonymous (oe): 0.89 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000674923.1 | |||||||||||||||||||||
| Genbank transcript ID | NM_001165963 (exact from MANE) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN1A_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.5777A>G g.191309A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| Phylogenetic conservation |
| |||||||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||||||||||
| Distance from splice site | N/A | |||||||||||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||||||||||
| poly(A) signal | N/A | |||||||||||||||||||||
| AA sequence altered | Yes | |||||||||||||||||||||
| Chromosome | 2 | |||||||||||||||||||||
| Strand | -1 | |||||||||||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| 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 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 IIQRACRRHL LKRTVKQASF TYNKNKIKGG ANLLIKEDMI IDRINENSIT EKTDLTMSTA ACPPSYDRVT KPIVEKHEQE GKDEKAKGK* | |||||||||||||||||||||
| 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 | 6508 / 6508 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 479 / 479 | |||||||||||||||||||||
| Last intron/exon boundary | 5330 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4801 | |||||||||||||||||||||
| Length of CDS | 6030 | |||||||||||||||||||||
| Coding sequence (CDS) position | 5777 | |||||||||||||||||||||
| cDNA position | 6255 | |||||||||||||||||||||
| gDNA position | 191309 | |||||||||||||||||||||
| Chromosomal position | 165991498 | |||||||||||||||||||||
| Speed | 0.10 s | |||||||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:165991498T>C (GRCh38) | |||||||||||||||||||||
| Gene symbol | SCN1A | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.56, synonymous (oe): 0.89 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000635750.1 | |||||||||||||||||||||
| Genbank transcript ID | NM_001353949 (by similarity), NM_001353950 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN1A_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.5744A>G g.191309A>G | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| Phylogenetic conservation |
| |||||||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||||||||||
| Distance from splice site | N/A | |||||||||||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||||||||||
| poly(A) signal | N/A | |||||||||||||||||||||
| AA sequence altered | Yes | |||||||||||||||||||||
| Chromosome | 2 | |||||||||||||||||||||
| Strand | -1 | |||||||||||||||||||||
| Original gDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered gDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Original cDNA sequence snippet | TGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| Altered cDNA sequence snippet | TGTCATTATTCAGCGTGCTTGCAGACGCCACCTTTTAAAGC | |||||||||||||||||||||
| 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRAYRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||||||||||
| 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 GTTTETEMRK RRSSSFHVSM DFLEDPSQRQ RAMSIASILT NTVEELEESR QKCPPCWYKF SNIFLIWDCS PYWLKVKHVV NLVVMDPFVD LAITICIVLN TLFMAMEHYP MTDHFNNVLT VGNLVFTGIF TAEMFLKIIA MDPYYYFQEG WNIFDGFIVT LSLVELGLAN VEGLSVLRSF RLLRVFKLAK SWPTLNMLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKSYKDCVC KIASDCQLPR WHMNDFFHSF LIVFRVLCGE WIETMWDCME VAGQAMCLTV FMMVMVIGNL VVLNLFLALL LSSFSADNLA ATDDDNEMNN LQIAVDRMHK GVAYVKRKIY EFIQQSFIRK QKILDEIKPL DDLNNKKDSC MSNHTAEIGK DLDYLKDVNG TTSGIGTGSS VEKYIIDESD YMSFINNPSL TVTVPIAVGE SDFENLNTED FSSESDLEES KEKLNESSSS SEGSTVDIGA PVEEQPVVEP EETLEPEACF TEGCVQRFKC CQINVEEGRG KQWWNLRRTC FRIVEHNWFE TFIVFMILLS SGALAFEDIY IDQRKTIKTM LEYADKVFTY IFILEMLLKW VAYGYQTYFT NAWCWLDFLI VDVSLVSLTA NALGYSELGA IKSLRTLRAL RPLRALSRFE GMRVVVNALL GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYHCINTTT GDRFDIEDVN NHTDCLKLIE RNETARWKNV KVNFDNVGFG YLSLLQVATF KGWMDIMYAA VDSRNVELQP KYEESLYMYL YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPGNKFQ GMVFDFVTRQ VFDISIMILI CLNMVTMMVE TDDQSEYVTT ILSRINLVFI VLFTGECVLK LISLRHYYFT IGWNIFDFVV VILSIVGMFL AELIEKYFVS PTLFRVIRLA RIGRILRLIK GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYAIFGMSN FAYVKREVGI DDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPNKVNPGSS VKGDCGNPSV GIFFFVSYII ISFLVVVNMY IAVILENFSV ATEESAEPLS EDDFEMFYEV WEKFDPDATQ FMEFEKLSQF AAALEPPLNL PQPNKLQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDALRIQMEE RFMASNPSKV SYQPITTTLK RKQEEVSAVI IQRACRRHLL KRTVKQASFT YNKNKIKGGA NLLIKEDMII DRINENSITE KTDLTMSTAA CPPSYDRVTK PIVEKHEQEG KDEKAKGK* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 5997 / 5997 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1999 / 1999 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 6214 / 6214 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 218 / 218 | |||||||||||||||||||||
| Last intron/exon boundary | 5036 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4768 | |||||||||||||||||||||
| Length of CDS | 5997 | |||||||||||||||||||||
| Coding sequence (CDS) position | 5744 | |||||||||||||||||||||
| cDNA position | 5961 | |||||||||||||||||||||
| gDNA position | 191309 | |||||||||||||||||||||
| Chromosomal position | 165991498 | |||||||||||||||||||||
| Speed | 0.08 s | |||||||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project