| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SCN5A | Deleterious | 78|22 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN5A | Benign | 2|198 | without_ | No | Single base exchange | N/A | |||||||
| SCN5A | Benign | 6|194 | without_ | No | Single base exchange | N/A | |||||||
ENST00000413689(MANE Select) | SCN5A | Benign | 35|65 | simple_ | No | Single base exchange | Normal |
| |||||
| SCN5A | Benign | 35|65 | simple_ | No | Single base exchange | Normal |
| ||||||
| SCN5A | Benign | 38|62 | simple_ | No | Single base exchange | Normal |
| ||||||
ENST00000423572(MANE Select) | SCN5A | Benign | 42|58 | simple_ | No | Single base exchange | Normal |
| |||||
| SCN5A | Benign | 42|58 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | ||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:38579416G>A (GRCh38) | ||||||||||||||||||||||||||
| Gene symbol | SCN5A | ||||||||||||||||||||||||||
| Gene constraints | LOEUF: 0.99, LOF (oe): 0.21, misssense (oe): 0.93, synonymous (oe): 0.90 (gnomAD) | ||||||||||||||||||||||||||
| Ensembl transcript ID | ENST00000327956.7 | ||||||||||||||||||||||||||
| Genbank transcript ID | |||||||||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN5A_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||||||||||||
| Gene region | CDS | ||||||||||||||||||||||||||
| DNA changes | c.3305C>T g.70328C>T | ||||||||||||||||||||||||||
| 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 | 3 | ||||||||||||||||||||||||||
| Strand | -1 | ||||||||||||||||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Original cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Altered cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL KHASFLFRQQ AGSGLSEEDA PEREGLIAYV MSENFSRPLG PPSSSSISST SFPPSYDSVT RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV* | ||||||||||||||||||||||||||
| Mutated AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP VSGGPEAPPD SRTWSQVSAT AFSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL KHASFLFRQQ AGSGLSEEDA PEREGLIAYV MSENFSRPLG PPSSSSISST SFPPSYDSVT RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV* | ||||||||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 6048 / 6048 | ||||||||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2016 / 2016 | ||||||||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 6186 / 6186 | ||||||||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 139 / 139 | ||||||||||||||||||||||||||
| Last intron/exon boundary | 4948 | ||||||||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4759 | ||||||||||||||||||||||||||
| Length of CDS | 6048 | ||||||||||||||||||||||||||
| Coding sequence (CDS) position | 3305 | ||||||||||||||||||||||||||
| cDNA position | 3443 | ||||||||||||||||||||||||||
| gDNA position | 70328 | ||||||||||||||||||||||||||
| Chromosomal position | 38579416 | ||||||||||||||||||||||||||
| Speed | 0.05 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 | Chr3:38579416G>A (GRCh38) | |||||||||||||
| Gene symbol | SCN5A | |||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.27, misssense (oe): 0.74, synonymous (oe): 0.91 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000450102.6 | |||||||||||||
| Genbank transcript ID | NM_001160161 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.3228+1515C>T g.70328C>T | |||||||||||||
| 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 | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQTPED SCSEGSTADM TNTAELLEQI PDLGQDVKDP EDCFTEGCVR RCPCCAVDTT QAPGKVWWRL RKTCYHIVEH SWFETFIIFM ILLSSGALAF EDIYLEERKT IKVLLEYADK MFTYVFVLEM LLKWVAYGFK KYFTNAWCWL DFLIVDVSLV SLVANTLGFA EMGPIKSLRT LRALRPLRAL SRFEGMRVVV NALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFGRCI NQTEGDLPLN YTIVNNKSQC ESLNLTGELY WTKVKVNFDN VGAGYLALLQ VATFKGWMDI MYAAVDSRGY EEQPQWEYNL YMYIYFVIFI IFGSFFTLNL FIGVIIDNFN QQKKKLGGQD IFMTEEQKKY YNAMKKLGSK KPQKPIPRPL NKYQGFIFDI VTKQAFDVTI MFLICLNMVT MMVETDDQSP EKINILAKIN LLFVAIFTGE CIVKLAALRH YYFTNSWNIF DFVVVILSIV GTVLSDIIQK YFFSPTLFRV IRLARIGRIL RLIRGAKGIR TLLFALMMSL PALFNIGLLL FLVMFIYSIF GMANFAYVKW EAGIDDMFNF QTFANSMLCL FQITTSAGWD GLLSPILNTG PPYCDPTLPN SNGSRGDCGS PAVGILFFTT YIIISFLIVV NMYIAIILEN FSVATEESTE PLSEDDFDMF YEIWEKFDPE ATQFIEYSVL SDFADALSEP LRIAKPNQIS LINMDLPMVS GDRIHCMDIL FAFTKRVLGE SGEMDALKIQ MEEKFMAANP SKISYEPITT TLRRKHEEVS AMVIQRAFRR HLLQRSLKHA SFLFRQQAGS GLSEEDAPER EGLIAYVMSE NFSRPLGPPS SSSISSTSFP PSYDSVTRAT SDNLQVRGSD YSHSEDLADF PPSPDRDRES IV* | |||||||||||||
| 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 | 43 / 43 | |||||||||||||
| Last intron/exon boundary | 4693 | |||||||||||||
| Theoretical NMD boundary in CDS | 4600 | |||||||||||||
| Length of CDS | 5889 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 70328 | |||||||||||||
| Chromosomal position | 38579416 | |||||||||||||
| Speed | 0.02 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 | Chr3:38579416G>A (GRCh38) | |||||||||||||
| Gene symbol | SCN5A | |||||||||||||
| Gene constraints | LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.73, synonymous (oe): 0.91 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000449557.6 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.3228+1515C>T g.70328C>T | |||||||||||||
| 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 | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQTPED SCSEGSTADM TNTAELLEQI PDLGQDVKDP EDCFTEGCVR RCPCCAVDTT QAPGKVWWRL RKTCYHIVEH SWFETFIIFM ILLSSGALAF EDIYLEERKT IKVLLEYADK MFTYVFVLEM LLKWVAYGFK KYFTNAWCWL DFLIVDVSLV SLVANTLGFA EMGPIKSLRT LRALRPLRAL SRFEGMRVVV NALVGAIPSI MNVLLVCLIF WLIFSIMGVN LFAGKFGRCI NQTEGDLPLN YTIVNNKSQC ESLNLTGELY WTKVKVNFDN VGAGYLALLQ VATFKGWMDI MYAAVDSRGY EEQPQWEYNL YMYIYFVIFI IFGSFFTLNL FIGVIIDNFN QQKKKLGGQD IFMTEEQKKY YNAMKKLGSK KPQKPIPRPL NKYQGFIFDI VTKQAFDVTI MFLICLNMVT MMVETDDQSP EKINILAKIN LLFVAIFTGE CIVKLAALRH YYFTNSWNIF DFVVVILSIV GTVLSDIIQK YFFSPTLFRV IRLARIGRIL RLIRGAKGIR TLLFALMMSL PALFNIGLLL FLVMFIYSIF GMANFAYVKW EAGIDDMFNF QTFANSMLCL FQITTSAGWD GLLSPILNTG PPYCDPTLPN SNGSRGDCGS PAVGILFFTT YIIISFLIVV NMYIAIILEN FSVATEESTE PLSEDDFDMF YEIWEKFDPE ATQFIEYSVL SDFADALSEP LRIAKPNQIS LINMDLPMVS GDRIHCMDIL FAFTKRVLGE SGEMDALKIQ MEEKFMAANP SKISYEPITT TLRRKHEEVS AMVIQRAFRR HLLQRSLKHA SFLFRQQAGS GLSEEDAPER EGLIAYVMSE NFSRPLGPPS SSSISSTSFP PSYDSVTRAT SDNLQVRGSD YSHSEDLADF PPSPDRDRES IV* | |||||||||||||
| 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 | 10 / 10 | |||||||||||||
| Last intron/exon boundary | 4660 | |||||||||||||
| Theoretical NMD boundary in CDS | 4600 | |||||||||||||
| Length of CDS | 5889 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 70328 | |||||||||||||
| Chromosomal position | 38579416 | |||||||||||||
| Speed | 0.02 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 | Chr3:38579416G>A (GRCh38) | |||||||||||||
| Gene symbol | SCN5A | |||||||||||||
| Gene constraints | LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.75, synonymous (oe): 0.91 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000413689.6 | |||||||||||||
| Genbank transcript ID | NM_001099404 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3308C>T g.70328C>T | |||||||||||||
| 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 | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Original cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS LKHASFLFRQ QAGSGLSEED APEREGLIAY VMSENFSRPL GPPSSSSISS TSFPPSYDSV TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV* | |||||||||||||
| Mutated AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ PVSGGPEAPP DSRTWSQVSA TAFSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS LKHASFLFRQ QAGSGLSEED APEREGLIAY VMSENFSRPL GPPSSSSISS TSFPPSYDSV TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 6051 / 6051 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2017 / 2017 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 6260 / 6260 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 210 / 210 | |||||||||||||
| Last intron/exon boundary | 5022 | |||||||||||||
| Theoretical NMD boundary in CDS | 4762 | |||||||||||||
| Length of CDS | 6051 | |||||||||||||
| Coding sequence (CDS) position | 3308 | |||||||||||||
| cDNA position | 3517 | |||||||||||||
| gDNA position | 70328 | |||||||||||||
| Chromosomal position | 38579416 | |||||||||||||
| Speed | 0.05 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 | Chr3:38579416G>A (GRCh38) | |||||||||||||
| Gene symbol | SCN5A | |||||||||||||
| Gene constraints | LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.75, synonymous (oe): 0.91 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000414099.6 | |||||||||||||
| Genbank transcript ID | NM_001354701 (by similarity), NM_001099405 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3308C>T g.70328C>T | |||||||||||||
| 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 | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Original cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVYEEQP QWEYNLYMYI YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KLGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPLNKYQ GFIFDIVTKQ AFDVTIMFLI CLNMVTMMVE TDDQSPEKIN ILAKINLLFV AIFTGECIVK LAALRHYYFT NSWNIFDFVV VILSIVGTVL SDIIQKYFFS PTLFRVIRLA RIGRILRLIR GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYSIFGMAN FAYVKWEAGI DDMFNFQTFA NSMLCLFQIT TSAGWDGLLS PILNTGPPYC DPTLPNSNGS RGDCGSPAVG ILFFTTYIII SFLIVVNMYI AIILENFSVA TEESTEPLSE DDFDMFYEIW EKFDPEATQF IEYSVLSDFA DALSEPLRIA KPNQISLINM DLPMVSGDRI HCMDILFAFT KRVLGESGEM DALKIQMEEK FMAANPSKIS YEPITTTLRR KHEEVSAMVI QRAFRRHLLQ RSLKHASFLF RQQAGSGLSE EDAPEREGLI AYVMSENFSR PLGPPSSSSI SSTSFPPSYD SVTRATSDNL QVRGSDYSHS EDLADFPPSP DRDRESIV* | |||||||||||||
| Mutated AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ PVSGGPEAPP DSRTWSQVSA TAFSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVYEEQP QWEYNLYMYI YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KLGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPLNKYQ GFIFDIVTKQ AFDVTIMFLI CLNMVTMMVE TDDQSPEKIN ILAKINLLFV AIFTGECIVK LAALRHYYFT NSWNIFDFVV VILSIVGTVL SDIIQKYFFS PTLFRVIRLA RIGRILRLIR GAKGIRTLLF ALMMSLPALF NIGLLLFLVM FIYSIFGMAN FAYVKWEAGI DDMFNFQTFA NSMLCLFQIT TSAGWDGLLS PILNTGPPYC DPTLPNSNGS RGDCGSPAVG ILFFTTYIII SFLIVVNMYI AIILENFSVA TEESTEPLSE DDFDMFYEIW EKFDPEATQF IEYSVLSDFA DALSEPLRIA KPNQISLINM DLPMVSGDRI HCMDILFAFT KRVLGESGEM DALKIQMEEK FMAANPSKIS YEPITTTLRR KHEEVSAMVI QRAFRRHLLQ RSLKHASFLF RQQAGSGLSE EDAPEREGLI AYVMSENFSR PLGPPSSSSI SSTSFPPSYD SVTRATSDNL QVRGSDYSHS EDLADFPPSP DRDRESIV* | |||||||||||||
| 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 | 6039 / 6039 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 43 / 43 | |||||||||||||
| Last intron/exon boundary | 4801 | |||||||||||||
| Theoretical NMD boundary in CDS | 4708 | |||||||||||||
| Length of CDS | 5997 | |||||||||||||
| Coding sequence (CDS) position | 3308 | |||||||||||||
| cDNA position | 3350 | |||||||||||||
| gDNA position | 70328 | |||||||||||||
| Chromosomal position | 38579416 | |||||||||||||
| 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 | Chr3:38579416G>A (GRCh38) | |||||||||||||
| Gene symbol | SCN5A | |||||||||||||
| Gene constraints | LOEUF: 0.36, LOF (oe): 0.28, misssense (oe): 0.74, synonymous (oe): 0.91 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000455624.6 | |||||||||||||
| Genbank transcript ID | NM_001160160 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3305C>T g.70328C>T | |||||||||||||
| 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 | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Original cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Altered cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | |||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA KINLLFVAIF TGTVLSDIIQ KYFFSPTLFR VIRLARIGRI LRLIRGAKGI RTLLFALMMS LPALFNIGLL LFLVMFIYSI FGMANFAYVK WEAGIDDMFN FQTFANSMLC LFQITTSAGW DGLLSPILNT GPPYCDPTLP NSNGSRGDCG SPAVGILFFT TYIIISFLIV VNMYIAIILE NFSVATEEST EPLSEDDFDM FYEIWEKFDP EATQFIEYSV LSDFADALSE PLRIAKPNQI SLINMDLPMV SGDRIHCMDI LFAFTKRVLG ESGEMDALKI QMEEKFMAAN PSKISYEPIT TTLRRKHEEV SAMVIQRAFR RHLLQRSLKH ASFLFRQQAG SGLSEEDAPE REGLIAYVMS ENFSRPLGPP SSSSISSTSF PPSYDSVTRA TSDNLQVRGS DYSHSEDLAD FPPSPDRDRE SIV* | |||||||||||||
| Mutated AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYVSENI KLGNLSALRT FRVLRALKTI SVIPGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP VSGGPEAPPD SRTWSQVSAT AFSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA KINLLFVAIF TGTVLSDIIQ KYFFSPTLFR VIRLARIGRI LRLIRGAKGI RTLLFALMMS LPALFNIGLL LFLVMFIYSI FGMANFAYVK WEAGIDDMFN FQTFANSMLC LFQITTSAGW DGLLSPILNT GPPYCDPTLP NSNGSRGDCG SPAVGILFFT TYIIISFLIV VNMYIAIILE NFSVATEEST EPLSEDDFDM FYEIWEKFDP EATQFIEYSV LSDFADALSE PLRIAKPNQI SLINMDLPMV SGDRIHCMDI LFAFTKRVLG ESGEMDALKI QMEEKFMAAN PSKISYEPIT TTLRRKHEEV SAMVIQRAFR RHLLQRSLKH ASFLFRQQAG SGLSEEDAPE REGLIAYVMS ENFSRPLGPP SSSSISSTSF PPSYDSVTRA TSDNLQVRGS DYSHSEDLAD FPPSPDRDRE SIV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5952 / 5952 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1984 / 1984 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5977 / 5977 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 26 / 26 | |||||||||||||
| Last intron/exon boundary | 4739 | |||||||||||||
| Theoretical NMD boundary in CDS | 4663 | |||||||||||||
| Length of CDS | 5952 | |||||||||||||
| Coding sequence (CDS) position | 3305 | |||||||||||||
| cDNA position | 3330 | |||||||||||||
| gDNA position | 70328 | |||||||||||||
| Chromosomal position | 38579416 | |||||||||||||
| Speed | 0.05 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 | Chr3:38579416G>A (GRCh38) | ||||||||||||||||||||||||||
| Gene symbol | SCN5A | ||||||||||||||||||||||||||
| Gene constraints | LOEUF: 0.37, LOF (oe): 0.29, misssense (oe): 0.74, synonymous (oe): 0.91 (gnomAD) | ||||||||||||||||||||||||||
| Ensembl transcript ID | ENST00000423572.7 | ||||||||||||||||||||||||||
| Genbank transcript ID | NM_000335 (exact from MANE) | ||||||||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN5A_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||||||||||||
| Gene region | CDS | ||||||||||||||||||||||||||
| DNA changes | c.3305C>T g.70328C>T | ||||||||||||||||||||||||||
| 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 | 3 | ||||||||||||||||||||||||||
| Strand | -1 | ||||||||||||||||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Original cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Altered cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP VSGGPEAPPD SRTWSQVSAT ASSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL KHASFLFRQQ AGSGLSEEDA PEREGLIAYV MSENFSRPLG PPSSSSISST SFPPSYDSVT RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV* | ||||||||||||||||||||||||||
| Mutated AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQESQP VSGGPEAPPD SRTWSQVSAT AFSEAEASAS QADWRQQWKA EPQAPGCGET PEDSCSEGST ADMTNTAELL EQIPDLGQDV KDPEDCFTEG CVRRCPCCAV DTTQAPGKVW WRLRKTCYHI VEHSWFETFI IFMILLSSGA LAFEDIYLEE RKTIKVLLEY ADKMFTYVFV LEMLLKWVAY GFKKYFTNAW CWLDFLIVDV SLVSLVANTL GFAEMGPIKS LRTLRALRPL RALSRFEGMR VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKFG RCINQTEGDL PLNYTIVNNK SQCESLNLTG ELYWTKVKVN FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RGYEEQPQWE YNLYMYIYFV IFIIFGSFFT LNLFIGVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMKKL GSKKPQKPIP RPLNKYQGFI FDIVTKQAFD VTIMFLICLN MVTMMVETDD QSPEKINILA KINLLFVAIF TGECIVKLAA LRHYYFTNSW NIFDFVVVIL SIVGTVLSDI IQKYFFSPTL FRVIRLARIG RILRLIRGAK GIRTLLFALM MSLPALFNIG LLLFLVMFIY SIFGMANFAY VKWEAGIDDM FNFQTFANSM LCLFQITTSA GWDGLLSPIL NTGPPYCDPT LPNSNGSRGD CGSPAVGILF FTTYIIISFL IVVNMYIAII LENFSVATEE STEPLSEDDF DMFYEIWEKF DPEATQFIEY SVLSDFADAL SEPLRIAKPN QISLINMDLP MVSGDRIHCM DILFAFTKRV LGESGEMDAL KIQMEEKFMA ANPSKISYEP ITTTLRRKHE EVSAMVIQRA FRRHLLQRSL KHASFLFRQQ AGSGLSEEDA PEREGLIAYV MSENFSRPLG PPSSSSISST SFPPSYDSVT RATSDNLQVR GSDYSHSEDL ADFPPSPDRD RESIV* | ||||||||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 6048 / 6048 | ||||||||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2016 / 2016 | ||||||||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 6257 / 6257 | ||||||||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 210 / 210 | ||||||||||||||||||||||||||
| Last intron/exon boundary | 5019 | ||||||||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4759 | ||||||||||||||||||||||||||
| Length of CDS | 6048 | ||||||||||||||||||||||||||
| Coding sequence (CDS) position | 3305 | ||||||||||||||||||||||||||
| cDNA position | 3514 | ||||||||||||||||||||||||||
| gDNA position | 70328 | ||||||||||||||||||||||||||
| Chromosomal position | 38579416 | ||||||||||||||||||||||||||
| 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 | Chr3:38579416G>A (GRCh38) | ||||||||||||||||||||||||||
| Gene symbol | SCN5A | ||||||||||||||||||||||||||
| Gene constraints | LOEUF: 0.37, LOF (oe): 0.29, misssense (oe): 0.74, synonymous (oe): 0.91 (gnomAD) | ||||||||||||||||||||||||||
| Ensembl transcript ID | ENST00000333535.9 | ||||||||||||||||||||||||||
| Genbank transcript ID | NM_198056 (by similarity) | ||||||||||||||||||||||||||
| UniProt / AlphaMissense peptide | SCN5A_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||||||||||||
| Gene region | CDS | ||||||||||||||||||||||||||
| DNA changes | c.3308C>T g.70328C>T | ||||||||||||||||||||||||||
| 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 | 3 | ||||||||||||||||||||||||||
| Strand | -1 | ||||||||||||||||||||||||||
| Original gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Altered gDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Original cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Altered cDNA sequence snippet | CCAGGTGTCAGCGACTGCCTTCTCTGAGGCCGAGGCCAGTG | ||||||||||||||||||||||||||
| Wildtype AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ PVSGGPEAPP DSRTWSQVSA TASSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS LKHASFLFRQ QAGSGLSEED APEREGLIAY VMSENFSRPL GPPSSSSISS TSFPPSYDSV TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV* | ||||||||||||||||||||||||||
| Mutated AA sequence | MANFLLPRGT SSFRRFTRES LAAIEKRMAE KQARGSTTLQ ESREGLPEEE APRPQLDLQA SKKLPDLYGN PPQELIGEPL EDLDPFYSTQ KTFIVLNKGK TIFRFSATNA LYVLSPFHPI RRAAVKILVH SLFNMLIMCT ILTNCVFMAQ HDPPPWTKYV EYTFTAIYTF ESLVKILARG FCLHAFTFLR DPWNWLDFSV IIMAYTTEFV DLGNVSALRT FRVLRALKTI SVISGLKTIV GALIQSVKKL ADVMVLTVFC LSVFALIGLQ LFMGNLRHKC VRNFTALNGT NGSVEADGLV WESLDLYLSD PENYLLKNGT SDVLLCGNSS DAGTCPEGYR CLKAGENPDH GYTSFDSFAW AFLALFRLMT QDCWERLYQQ TLRSAGKIYM IFFMLVIFLG SFYLVNLILA VVAMAYEEQN QATIAETEEK EKRFQEAMEM LKKEHEALTI RGVDTVSRSS LEMSPLAPVN SHERRSKRRK RMSSGTEECG EDRLPKSDSE DGPRAMNHLS LTRGLSRTSM KPRSSRGSIF TFRRRDLGSE ADFADDENST AGESESHHTS LLVPWPLRRT SAQGQPSPGT SAPGHALHGK KNSTVDCNGV VSLLGAGDPE ATSPGSHLLR PVMLEHPPDT TTPSEEPGGP QMLTSQAPCV DGFEEPGARQ RALSAVSVLT SALEELEESR HKCPPCWNRL AQRYLIWECC PLWMSIKQGV KLVVMDPFTD LTITMCIVLN TLFMALEHYN MTSEFEEMLQ VGNLVFTGIF TAEMTFKIIA LDPYYYFQQG WNIFDSIIVI LSLMELGLSR MSNLSVLRSF RLLRVFKLAK SWPTLNTLIK IIGNSVGALG NLTLVLAIIV FIFAVVGMQL FGKNYSELRD SDSGLLPRWH MMDFFHAFLI IFRILCGEWI ETMWDCMEVS GQSLCLLVFL LVMVIGNLVV LNLFLALLLS SFSADNLTAP DEDREMNNLQ LALARIQRGL RFVKRTTWDF CCGLLRQRPQ KPAALAAQGQ LPSCIATPYS PPPPETEKVP PTRKETRFEE GEQPGQGTPG DPEPVCVPIA VAESDTDDQE EDEENSLGTE EESSKQQESQ PVSGGPEAPP DSRTWSQVSA TAFSEAEASA SQADWRQQWK AEPQAPGCGE TPEDSCSEGS TADMTNTAEL LEQIPDLGQD VKDPEDCFTE GCVRRCPCCA VDTTQAPGKV WWRLRKTCYH IVEHSWFETF IIFMILLSSG ALAFEDIYLE ERKTIKVLLE YADKMFTYVF VLEMLLKWVA YGFKKYFTNA WCWLDFLIVD VSLVSLVANT LGFAEMGPIK SLRTLRALRP LRALSRFEGM RVVVNALVGA IPSIMNVLLV CLIFWLIFSI MGVNLFAGKF GRCINQTEGD LPLNYTIVNN KSQCESLNLT GELYWTKVKV NFDNVGAGYL ALLQVATFKG WMDIMYAAVD SRGYEEQPQW EYNLYMYIYF VIFIIFGSFF TLNLFIGVII DNFNQQKKKL GGQDIFMTEE QKKYYNAMKK LGSKKPQKPI PRPLNKYQGF IFDIVTKQAF DVTIMFLICL NMVTMMVETD DQSPEKINIL AKINLLFVAI FTGECIVKLA ALRHYYFTNS WNIFDFVVVI LSIVGTVLSD IIQKYFFSPT LFRVIRLARI GRILRLIRGA KGIRTLLFAL MMSLPALFNI GLLLFLVMFI YSIFGMANFA YVKWEAGIDD MFNFQTFANS MLCLFQITTS AGWDGLLSPI LNTGPPYCDP TLPNSNGSRG DCGSPAVGIL FFTTYIIISF LIVVNMYIAI ILENFSVATE ESTEPLSEDD FDMFYEIWEK FDPEATQFIE YSVLSDFADA LSEPLRIAKP NQISLINMDL PMVSGDRIHC MDILFAFTKR VLGESGEMDA LKIQMEEKFM AANPSKISYE PITTTLRRKH EEVSAMVIQR AFRRHLLQRS LKHASFLFRQ QAGSGLSEED APEREGLIAY VMSENFSRPL GPPSSSSISS TSFPPSYDSV TRATSDNLQV RGSDYSHSED LADFPPSPDR DRESIV* | ||||||||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 6051 / 6051 | ||||||||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2017 / 2017 | ||||||||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 6260 / 6260 | ||||||||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 210 / 210 | ||||||||||||||||||||||||||
| Last intron/exon boundary | 5022 | ||||||||||||||||||||||||||
| Theoretical NMD boundary in CDS | 4762 | ||||||||||||||||||||||||||
| Length of CDS | 6051 | ||||||||||||||||||||||||||
| Coding sequence (CDS) position | 3308 | ||||||||||||||||||||||||||
| cDNA position | 3517 | ||||||||||||||||||||||||||
| gDNA position | 70328 | ||||||||||||||||||||||||||
| Chromosomal position | 38579416 | ||||||||||||||||||||||||||
| 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