| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TSC2 | Deleterious | 57|43 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 59|41 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 59|41 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 59|41 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 59|41 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 60|40 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 60|40 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 60|40 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 61|39 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 61|39 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 61|39 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 61|39 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 61|39 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 62|38 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 62|38 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 68|32 | simple_ | No | Single base exchange | Normal |
| ||||||
| TSC2 | Deleterious | 78|22 | simple_ | No | Single base exchange | Normal |
| ||||||
ENST00000219476(MANE Select) | TSC2 | Benign | 43|57 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.22, LOF (oe): 0.16, misssense (oe): 0.99, synonymous (oe): 1.31 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000642365.2 | |||||||||||||
| Genbank transcript ID | NM_001406663 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4103G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRRI QTSLTSASLG SADENSVAQA DDSLKNLHLE LTETCLDMMA RYVFSNFTAV PKRSPVGEFL LAGGRTKTWL VGNKLVTVTT SVGTGTRSLL GLDSGELQSG PESSSSPGVH VRQTKEAPAK LESQAGQQVS RGARDRVRSM SGGHGLRVGA LDVPASQFLG SATSPGPRTA PAAKPEKASA GTRVPVQEKT NLAAYVPLLT QGWAEILVRR PTGNTSWLMS LENPLSPFSS DINNMPLQEL SNALMAAERF KEHRDTALYK SLSVPAASTA KPPPLPRSNT VASFSSLYQS SCQGQLHRSV SWADSAVVME EGSPGEVPVL VEPPGLEDVE AALGMDRRTD AYSRSSSVSS QEEKSLHAEE LVGRGIPIER VVSSEGGRPS VDLSFQPSQP LSKSSSSPEL QTLQDILGDP GDKADVGRLS PEVKARSQSG TLDGESAAWS ASGEDSRGQP EGPLPSSSPR SPSGLRPRGY TISDSAPSRR GKRVERDALK SRATASNAEK VPGINPSFVF LQLYHSPFFG DESNKPILLP NESQSFERSV QLLDQIPSYD THKIAVLYVG EGQSNSELAI LSNEHGSYRY TEFLTGLGRL IELKDCQPDK VYLGGLDVCG EDGQFTYCWH DDIMQAVFHI ATLMPTKDVD KHRCDKKRHL GNDFVSIVYN DSGEDFKLGT IKGQFNFVHV IVTPLDYECN LVSLQCRKDM EGLVDTSVAK IVSDRNLPFV ARQMALHANM ASQVHHSRSN PTDIYPSKWI ARLRHIKRLR QRICEEAAYS NPSLPLVHPP SHSKAPAQTP AEPTPGYEVG QRKRLISSVE DFTEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRRI QTSLTSASLG SADENSVAQA DDSLKNLHLE LTETCLDMMA RYVFSNFTAV PKRSPVGEFL LAGGRTKTWL VGNKLVTVTT SVGTGTRSLL GLDSGELQSG PESSSSPGVH VRQTKEAPAK LESQAGQQVS RGARDRVRSM SGGHGLRVGA LDVPASQFLG SATSPGPRTA PAAKPEKASA GTRVPVQEKT NLAAYVPLLT QGWAEILVRR PTGNTSWLMS LENPLSPFSS DINNMPLQEL SNALMAAERF KEHRDTALYK SLSVPAASTA KPPPLPRSNT VASFSSLYQS SCQGQLHRSV SWADSAVVME EGSPGEVPVL VEPPGLEDVE AALGMDRRTD AYSRSSSVSS QEEKSLHAEE LVGRGIPIER VVSSEGGQPS VDLSFQPSQP LSKSSSSPEL QTLQDILGDP GDKADVGRLS PEVKARSQSG TLDGESAAWS ASGEDSRGQP EGPLPSSSPR SPSGLRPRGY TISDSAPSRR GKRVERDALK SRATASNAEK VPGINPSFVF LQLYHSPFFG DESNKPILLP NESQSFERSV QLLDQIPSYD THKIAVLYVG EGQSNSELAI LSNEHGSYRY TEFLTGLGRL IELKDCQPDK VYLGGLDVCG EDGQFTYCWH DDIMQAVFHI ATLMPTKDVD KHRCDKKRHL GNDFVSIVYN DSGEDFKLGT IKGQFNFVHV IVTPLDYECN LVSLQCRKDM EGLVDTSVAK IVSDRNLPFV ARQMALHANM ASQVHHSRSN PTDIYPSKWI ARLRHIKRLR QRICEEAAYS NPSLPLVHPP SHSKAPAQTP AEPTPGYEVG QRKRLISSVE DFTEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5421 / 5421 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1807 / 1807 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5492 / 5492 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 72 / 72 | |||||||||||||
| Last intron/exon boundary | 5327 | |||||||||||||
| Theoretical NMD boundary in CDS | 5205 | |||||||||||||
| Length of CDS | 5421 | |||||||||||||
| Coding sequence (CDS) position | 4103 | |||||||||||||
| cDNA position | 4174 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.18, LOF (oe): 0.13, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000643088.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3905G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTDSA VVMEEGSPGE VPVLVEPPGL EDVEAALGMD RRTDAYSRSS SVSSQEEKSL HAEELVGRGI PIERVVSSEG GRPSVDLSFQ PSQPLSKSSS SPELQTLQDI LGDPGDKADV GRLSPEVKAR SQSGTLDGES AAWSASGEDS RGQPEGPLPS SSPRSPSGLR PRGYTISDSA PSRRGKRVER DALKSRATAS NAEKVPGINP SFVFLQLYHS PFFGDESNKP ILLPNESFER SVQLLDQIPS YDTHKIAVLY VGEGQSNSEL AILSNEHGSY RYTEFLTGLG RLIELKDCQP DKVYLGGLDV CGEDGQFTYC WHDDIMQAVF HIATLMPTKD VDKHRCDKKR HLGNDFVSIV YNDSGEDFKL GTIKGQFNFV HVIVTPLDYE CNLVSLQCRK DMEGLVDTSV AKIVSDRNLP FVARQMALHA NMASQVHHSR SNPTDIYPSK WIARLRHIKR LRQRICEEAA YSNPSLPLVH PPSHSKAPAQ TPAEPTPGYE VGQRKRLISS VEDFTEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTDSA VVMEEGSPGE VPVLVEPPGL EDVEAALGMD RRTDAYSRSS SVSSQEEKSL HAEELVGRGI PIERVVSSEG GQPSVDLSFQ PSQPLSKSSS SPELQTLQDI LGDPGDKADV GRLSPEVKAR SQSGTLDGES AAWSASGEDS RGQPEGPLPS SSPRSPSGLR PRGYTISDSA PSRRGKRVER DALKSRATAS NAEKVPGINP SFVFLQLYHS PFFGDESNKP ILLPNESFER SVQLLDQIPS YDTHKIAVLY VGEGQSNSEL AILSNEHGSY RYTEFLTGLG RLIELKDCQP DKVYLGGLDV CGEDGQFTYC WHDDIMQAVF HIATLMPTKD VDKHRCDKKR HLGNDFVSIV YNDSGEDFKL GTIKGQFNFV HVIVTPLDYE CNLVSLQCRK DMEGLVDTSV AKIVSDRNLP FVARQMALHA NMASQVHHSR SNPTDIYPSK WIARLRHIKR LRQRICEEAA YSNPSLPLVH PPSHSKAPAQ TPAEPTPGYE VGQRKRLISS VEDFTEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5217 / 5217 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1739 / 1739 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5335 / 5335 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 119 / 119 | |||||||||||||
| Last intron/exon boundary | 5170 | |||||||||||||
| Theoretical NMD boundary in CDS | 5001 | |||||||||||||
| Length of CDS | 5217 | |||||||||||||
| Coding sequence (CDS) position | 3905 | |||||||||||||
| cDNA position | 4023 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.21, LOF (oe): 0.15, misssense (oe): 0.99, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000644329.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3905G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTDSA VVMEEGSPGE VPVLVEPPGL EDVEAALGMD RRTDAYSRSS SVSSQEEKSL HAEELVGRGI PIERVVSSEG GRPSVDLSFQ PSQPLSKSSS SPELQTLQDI LGDPGDKADV GRLSPEVKAR SQSGTLDGES AAWSASGEDS RGQPEGPLPS SSPRSPSGLR PRGYTISDSA PSRRGKRVER DALKSRATAS NAEKVPGINP SFVFLQLYHS PFFGDESNKP ILLPNESQSF ERSVQLLDQI PSYDTHKIAV LYVGEGQSNS ELAILSNEHG SYRYTEFLTG LGRLIELKDC QPDKVYLGGL DVCGEDGQFT YCWHDDIMQA VFHIATLMPT KDVDKHRCDK KRHLGNDFVS IVYNDSGEDF KLGTIKGQFN FVHVIVTPLD YECNLVSLQC RKDMEGLVDT SVAKIVSDRN LPFVARQMAL HANVSGGGSR RELVGQAQVP PDSELTPCLR PQMASQVHHS RSNPTDIYPS KWIARLRHIK RLRQRICEEA AYSNPSLPLV HPPSHSKAPA QTPAEPTPGY EVGQRKRLIS SVEDFTEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTDSA VVMEEGSPGE VPVLVEPPGL EDVEAALGMD RRTDAYSRSS SVSSQEEKSL HAEELVGRGI PIERVVSSEG GQPSVDLSFQ PSQPLSKSSS SPELQTLQDI LGDPGDKADV GRLSPEVKAR SQSGTLDGES AAWSASGEDS RGQPEGPLPS SSPRSPSGLR PRGYTISDSA PSRRGKRVER DALKSRATAS NAEKVPGINP SFVFLQLYHS PFFGDESNKP ILLPNESQSF ERSVQLLDQI PSYDTHKIAV LYVGEGQSNS ELAILSNEHG SYRYTEFLTG LGRLIELKDC QPDKVYLGGL DVCGEDGQFT YCWHDDIMQA VFHIATLMPT KDVDKHRCDK KRHLGNDFVS IVYNDSGEDF KLGTIKGQFN FVHVIVTPLD YECNLVSLQC RKDMEGLVDT SVAKIVSDRN LPFVARQMAL HANVSGGGSR RELVGQAQVP PDSELTPCLR PQMASQVHHS RSNPTDIYPS KWIARLRHIK RLRQRICEEA AYSNPSLPLV HPPSHSKAPA QTPAEPTPGY EVGQRKRLIS SVEDFTEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5310 / 5310 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1770 / 1770 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5372 / 5372 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 63 / 63 | |||||||||||||
| Last intron/exon boundary | 5207 | |||||||||||||
| Theoretical NMD boundary in CDS | 5094 | |||||||||||||
| Length of CDS | 5310 | |||||||||||||
| Coding sequence (CDS) position | 3905 | |||||||||||||
| cDNA position | 3967 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| Speed | 0.07 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.20, LOF (oe): 0.15, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000644043.1 | |||||||||||||
| Genbank transcript ID | NM_001406690 (by similarity), NM_021055 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | TSC2_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3977G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTVA SFSSLYQSSC QGQLHRSVSW ADSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGRPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANMAS QVHHSRSNPT DIYPSKWIAR LRHIKRLRQR ICEEAAYSNP SLPLVHPPSH SKAPAQTPAE PTPGYEVGQR KRLISSVEDF TEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTVA SFSSLYQSSC QGQLHRSVSW ADSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGQPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANMAS QVHHSRSNPT DIYPSKWIAR LRHIKRLRQR ICEEAAYSNP SLPLVHPPSH SKAPAQTPAE PTPGYEVGQR KRLISSVEDF TEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5295 / 5295 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1765 / 1765 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5349 / 5349 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 55 / 55 | |||||||||||||
| Last intron/exon boundary | 5184 | |||||||||||||
| Theoretical NMD boundary in CDS | 5079 | |||||||||||||
| Length of CDS | 5295 | |||||||||||||
| Coding sequence (CDS) position | 3977 | |||||||||||||
| cDNA position | 4031 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.21, LOF (oe): 0.15, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000642936.1 | |||||||||||||
| Genbank transcript ID | NM_001406691 (by similarity), NM_001406665 (by similarity), NM_001370404 (by similarity), NM_001318831 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | TSC2_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3974G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTVAS FSSLYQSSCQ GQLHRSVSWA DSAVVMEEGS PGEVPVLVEP PGLEDVEAAL GMDRRTDAYS RSSSVSSQEE KSLHAEELVG RGIPIERVVS SEGGRPSVDL SFQPSQPLSK SSSSPELQTL QDILGDPGDK ADVGRLSPEV KARSQSGTLD GESAAWSASG EDSRGQPEGP LPSSSPRSPS GLRPRGYTIS DSAPSRRGKR VERDALKSRA TASNAEKVPG INPSFVFLQL YHSPFFGDES NKPILLPNES QSFERSVQLL DQIPSYDTHK IAVLYVGEGQ SNSELAILSN EHGSYRYTEF LTGLGRLIEL KDCQPDKVYL GGLDVCGEDG QFTYCWHDDI MQAVFHIATL MPTKDVDKHR CDKKRHLGND FVSIVYNDSG EDFKLGTIKG QFNFVHVIVT PLDYECNLVS LQCRKDMEGL VDTSVAKIVS DRNLPFVARQ MALHANMASQ VHHSRSNPTD IYPSKWIARL RHIKRLRQRI CEEAAYSNPS LPLVHPPSHS KAPAQTPAEP TPGYEVGQRK RLISSVEDFT EFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTVAS FSSLYQSSCQ GQLHRSVSWA DSAVVMEEGS PGEVPVLVEP PGLEDVEAAL GMDRRTDAYS RSSSVSSQEE KSLHAEELVG RGIPIERVVS SEGGQPSVDL SFQPSQPLSK SSSSPELQTL QDILGDPGDK ADVGRLSPEV KARSQSGTLD GESAAWSASG EDSRGQPEGP LPSSSPRSPS GLRPRGYTIS DSAPSRRGKR VERDALKSRA TASNAEKVPG INPSFVFLQL YHSPFFGDES NKPILLPNES QSFERSVQLL DQIPSYDTHK IAVLYVGEGQ SNSELAILSN EHGSYRYTEF LTGLGRLIEL KDCQPDKVYL GGLDVCGEDG QFTYCWHDDI MQAVFHIATL MPTKDVDKHR CDKKRHLGND FVSIVYNDSG EDFKLGTIKG QFNFVHVIVT PLDYECNLVS LQCRKDMEGL VDTSVAKIVS DRNLPFVARQ MALHANMASQ VHHSRSNPTD IYPSKWIARL RHIKRLRQRI CEEAAYSNPS LPLVHPPSHS KAPAQTPAEP TPGYEVGQRK RLISSVEDFT EFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5292 / 5292 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1764 / 1764 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5401 / 5401 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 110 / 110 | |||||||||||||
| Last intron/exon boundary | 5236 | |||||||||||||
| Theoretical NMD boundary in CDS | 5076 | |||||||||||||
| Length of CDS | 5292 | |||||||||||||
| Coding sequence (CDS) position | 3974 | |||||||||||||
| cDNA position | 4083 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.17, LOF (oe): 0.12, misssense (oe): 0.98, synonymous (oe): 1.29 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000382538.10 | |||||||||||||
| Genbank transcript ID | NM_001406687 (by similarity), NM_001406692 (by similarity), NM_001406697 (by similarity), NM_001406698 (by similarity), NM_001406694 (by similarity), NM_001406695 (by similarity), NM_001406696 (by similarity), NM_001406681 (by similarity), NM_001406677 (by similarity), NM_001406675 (by similarity), NM_001406676 (by similarity), NM_001318829 (by similarity), NM_001406679 (by similarity), NM_001406686 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | TSC2_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3761G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MECGLNNRIR MIGQICEVAK TKKFEEHAVE ALWKAVADLL QPERPLEARH AVLALLKAIV QGQGERLGVL RALFFKVIKD YPSNEDLHER LEVFKALTDN GRHITYLEEE LADFVLQWMD VGLSSEFLLV LVNLVKFNSC YLDEYIARMV QMICLLCVRT ASSVDIEVSL QVLDAVVCYN CLPAESLPLF IVTLCRTINV KELCEPCWKL MRNLLGTHLG HSAIYNMCHL MEDRAYMEDA PLLRGAVFFV GMALWGAHRL YSLRNSPTSV LPSFYQAMAC PNEVVSYEIV LSITRLIKKY RKELQVVAWD ILLNIIERLL QQLQTLDSPE LRTIVHDLLT TVEELCDQNE FHGSQERYFE LVERCADQRP ESSLLNLISY RAQSIHPAKD GWIQNLQALM ERFFRSESRG AVRIKVLDVL SFVLLINRQF YEEELINSVV ISQLSHIPED KDHQVRKLAT QLLVDLAEGC HTHHFNSLLD IIEKVMARSL SPPPELEERD VAAYSASLED VKTAVLGLLV ILQTKLYTLP ASHATRVYEM LVSHIQLHYK HSYTLPIASS IRLQAFDFLL LLRADSLHRL GLPNKDGVVR FSPYCVCDYM EPERGSEKKT SGPLSPPTGP PGPAPAGPAV RLGSVPYSLL FRVLLQCLKQ ESDWKVLKLV LGRLPESLRY KVLIFTSPCS VDQLCSALCS MLSGPKTLER LRGAPEGFSR TDLHLAVVPV LTALISYHNY LDKTKQREMV YCLEQGLIHR CASQCVVALS ICSVEMPDII IKALPVLVVK LTHISATASM AVPLLEFLST LARLPHLYRN FAAEQYASVF AISLPYTNPS KFNQYIVCLA HHVIAMWFIR CRLPFRKDFV PFITKGLRSN VLLSFDDTPE KDSFRARSTS LNERPKSRIQ TSLTSASLGS ADENSVAQAD DSLKNLHLEL TETCLDMMAR YVFSNFTAVP KRSPVGEFLL AGGRTKTWLV GNKLVTVTTS VGTGTRSLLG LDSGELQSGP ESSSSPGVHV RQTKEAPAKL ESQAGQQVSR GARDRVRSMS GGHGLRVGAL DVPASQFLGS ATSPGPRTAP AAKPEKASAG TRVPVQEKTN LAAYVPLLTQ GWAEILVRRP TGNTSWLMSL ENPLSPFSSD INNMPLQELS NALMAAERFK EHRDTALYKS LSVPAASTAK PPPLPRSNTD SAVVMEEGSP GEVPVLVEPP GLEDVEAALG MDRRTDAYSR SSSVSSQEEK SLHAEELVGR GIPIERVVSS EGGRPSVDLS FQPSQPLSKS SSSPELQTLQ DILGDPGDKA DVGRLSPEVK ARSQSGTLDG ESAAWSASGE DSRGQPEGPL PSSSPRSPSG LRPRGYTISD SAPSRRGKRV ERDALKSRAT ASNAEKVPGI NPSFVFLQLY HSPFFGDESN KPILLPNESQ SFERSVQLLD QIPSYDTHKI AVLYVGEGQS NSELAILSNE HGSYRYTEFL TGLGRLIELK DCQPDKVYLG GLDVCGEDGQ FTYCWHDDIM QAVFHIATLM PTKDVDKHRC DKKRHLGNDF VSIVYNDSGE DFKLGTIKGQ FNFVHVIVTP LDYECNLVSL QCRKDMEGLV DTSVAKIVSD RNLPFVARQM ALHANMASQV HHSRSNPTDI YPSKWIARLR HIKRLRQRIC EEAAYSNPSL PLVHPPSHSK APAQTPAEPT PGYEVGQRKR LISSVEDFTE FV* | |||||||||||||
| Mutated AA sequence | MECGLNNRIR MIGQICEVAK TKKFEEHAVE ALWKAVADLL QPERPLEARH AVLALLKAIV QGQGERLGVL RALFFKVIKD YPSNEDLHER LEVFKALTDN GRHITYLEEE LADFVLQWMD VGLSSEFLLV LVNLVKFNSC YLDEYIARMV QMICLLCVRT ASSVDIEVSL QVLDAVVCYN CLPAESLPLF IVTLCRTINV KELCEPCWKL MRNLLGTHLG HSAIYNMCHL MEDRAYMEDA PLLRGAVFFV GMALWGAHRL YSLRNSPTSV LPSFYQAMAC PNEVVSYEIV LSITRLIKKY RKELQVVAWD ILLNIIERLL QQLQTLDSPE LRTIVHDLLT TVEELCDQNE FHGSQERYFE LVERCADQRP ESSLLNLISY RAQSIHPAKD GWIQNLQALM ERFFRSESRG AVRIKVLDVL SFVLLINRQF YEEELINSVV ISQLSHIPED KDHQVRKLAT QLLVDLAEGC HTHHFNSLLD IIEKVMARSL SPPPELEERD VAAYSASLED VKTAVLGLLV ILQTKLYTLP ASHATRVYEM LVSHIQLHYK HSYTLPIASS IRLQAFDFLL LLRADSLHRL GLPNKDGVVR FSPYCVCDYM EPERGSEKKT SGPLSPPTGP PGPAPAGPAV RLGSVPYSLL FRVLLQCLKQ ESDWKVLKLV LGRLPESLRY KVLIFTSPCS VDQLCSALCS MLSGPKTLER LRGAPEGFSR TDLHLAVVPV LTALISYHNY LDKTKQREMV YCLEQGLIHR CASQCVVALS ICSVEMPDII IKALPVLVVK LTHISATASM AVPLLEFLST LARLPHLYRN FAAEQYASVF AISLPYTNPS KFNQYIVCLA HHVIAMWFIR CRLPFRKDFV PFITKGLRSN VLLSFDDTPE KDSFRARSTS LNERPKSRIQ TSLTSASLGS ADENSVAQAD DSLKNLHLEL TETCLDMMAR YVFSNFTAVP KRSPVGEFLL AGGRTKTWLV GNKLVTVTTS VGTGTRSLLG LDSGELQSGP ESSSSPGVHV RQTKEAPAKL ESQAGQQVSR GARDRVRSMS GGHGLRVGAL DVPASQFLGS ATSPGPRTAP AAKPEKASAG TRVPVQEKTN LAAYVPLLTQ GWAEILVRRP TGNTSWLMSL ENPLSPFSSD INNMPLQELS NALMAAERFK EHRDTALYKS LSVPAASTAK PPPLPRSNTD SAVVMEEGSP GEVPVLVEPP GLEDVEAALG MDRRTDAYSR SSSVSSQEEK SLHAEELVGR GIPIERVVSS EGGQPSVDLS FQPSQPLSKS SSSPELQTLQ DILGDPGDKA DVGRLSPEVK ARSQSGTLDG ESAAWSASGE DSRGQPEGPL PSSSPRSPSG LRPRGYTISD SAPSRRGKRV ERDALKSRAT ASNAEKVPGI NPSFVFLQLY HSPFFGDESN KPILLPNESQ SFERSVQLLD QIPSYDTHKI AVLYVGEGQS NSELAILSNE HGSYRYTEFL TGLGRLIELK DCQPDKVYLG GLDVCGEDGQ FTYCWHDDIM QAVFHIATLM PTKDVDKHRC DKKRHLGNDF VSIVYNDSGE DFKLGTIKGQ FNFVHVIVTP LDYECNLVSL QCRKDMEGLV DTSVAKIVSD RNLPFVARQM ALHANMASQV HHSRSNPTDI YPSKWIARLR HIKRLRQRIC EEAAYSNPSL PLVHPPSHSK APAQTPAEPT PGYEVGQRKR LISSVEDFTE FV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5079 / 5079 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1693 / 1693 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5174 / 5174 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 96 / 96 | |||||||||||||
| Last intron/exon boundary | 5009 | |||||||||||||
| Theoretical NMD boundary in CDS | 4863 | |||||||||||||
| Length of CDS | 5079 | |||||||||||||
| Coding sequence (CDS) position | 3761 | |||||||||||||
| cDNA position | 3856 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.21, LOF (oe): 0.15, misssense (oe): 0.99, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000646388.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4106G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TVASFSSLYQ SSCQGQLHRS VSWADSAVVM EEGSPGEVPV LVEPPGLEDV EAALGMDRRT DAYSRSSSVS SQEEKSLHAE ELVGRGIPIE RVVSSEGGRP SVDLSFQPSQ PLSKSSSSPE LQTLQDILGD PGDKADVGRL SPEVKARSQS GTLDGESAAW SASGEDSRGQ PEGPLPSSSP RSPSGLRPRG YTISDSAPSR RGKRVERDAL KSRATASNAE KVPGINPSFV FLQLYHSPFF GDESNKPILL PNESFERSVQ LLDQIPSYDT HKIAVLYVGE GQSNSELAIL SNEHGSYRYT EFLTGLGRLI ELKDCQPDKV YLGGLDVCGE DGQFTYCWHD DIMQAVFHIA TLMPTKDVDK HRCDKKRHLG NDFVSIVYND SGEDFKLGTI KGQFNFVHVI VTPLDYECNL VSLQCRKDME GLVDTSVAKI VSDRNLPFVA RQMALHANMA SQVHHSRSNP TDIYPSKWIA RLRHIKRLRQ RICEEAAYSN PSLPLVHPPS HSKAPAQTPA EPTPGYEVGQ RKRLISSVED FTEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TVASFSSLYQ SSCQGQLHRS VSWADSAVVM EEGSPGEVPV LVEPPGLEDV EAALGMDRRT DAYSRSSSVS SQEEKSLHAE ELVGRGIPIE RVVSSEGGQP SVDLSFQPSQ PLSKSSSSPE LQTLQDILGD PGDKADVGRL SPEVKARSQS GTLDGESAAW SASGEDSRGQ PEGPLPSSSP RSPSGLRPRG YTISDSAPSR RGKRVERDAL KSRATASNAE KVPGINPSFV FLQLYHSPFF GDESNKPILL PNESFERSVQ LLDQIPSYDT HKIAVLYVGE GQSNSELAIL SNEHGSYRYT EFLTGLGRLI ELKDCQPDKV YLGGLDVCGE DGQFTYCWHD DIMQAVFHIA TLMPTKDVDK HRCDKKRHLG NDFVSIVYND SGEDFKLGTI KGQFNFVHVI VTPLDYECNL VSLQCRKDME GLVDTSVAKI VSDRNLPFVA RQMALHANMA SQVHHSRSNP TDIYPSKWIA RLRHIKRLRQ RICEEAAYSN PSLPLVHPPS HSKAPAQTPA EPTPGYEVGQ RKRLISSVED FTEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5418 / 5418 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1806 / 1806 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5504 / 5504 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 87 / 87 | |||||||||||||
| Last intron/exon boundary | 5339 | |||||||||||||
| Theoretical NMD boundary in CDS | 5202 | |||||||||||||
| Length of CDS | 5418 | |||||||||||||
| Coding sequence (CDS) position | 4106 | |||||||||||||
| cDNA position | 4192 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.21, LOF (oe): 0.15, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000642561.1 | |||||||||||||
| Genbank transcript ID | NM_001370405 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3977G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTVA SFSSLYQSSC QGQLHRSVSW ADSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGRPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANVHH SRSNPTDIYP SKWIARLRHI KRLRQRICEE AAYSNPSLPL VHPPSHSKAP AQTPAEPTPG YEVGQRKRLI SSVEDFTEFV * | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTVA SFSSLYQSSC QGQLHRSVSW ADSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGQPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANVHH SRSNPTDIYP SKWIARLRHI KRLRQRICEE AAYSNPSLPL VHPPSHSKAP AQTPAEPTPG YEVGQRKRLI SSVEDFTEFV * | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5283 / 5283 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1761 / 1761 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5335 / 5335 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 53 / 53 | |||||||||||||
| Last intron/exon boundary | 5170 | |||||||||||||
| Theoretical NMD boundary in CDS | 5067 | |||||||||||||
| Length of CDS | 5283 | |||||||||||||
| Coding sequence (CDS) position | 3977 | |||||||||||||
| cDNA position | 4029 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.18, LOF (oe): 0.13, misssense (oe): 0.99, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000643946.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4037G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TDSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGRPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SFERSVQLLD QIPSYDTHKI AVLYVGEGQS NSELAILSNE HGSYRYTEFL TGLGRLIELK DCQPDKVYLG GLDVCGEDGQ FTYCWHDDIM QAVFHIATLM PTKDVDKHRC DKKRHLGNDF VSIVYNDSGE DFKLGTIKGQ FNFVHVIVTP LDYECNLVSL QCRKDMEGLV DTSVAKIVSD RNLPFVARQM ALHANMASQV HHSRSNPTDI YPSKWIARLR HIKRLRQRIC EEAAYSNPSL PLVHPPSHSK APAQTPAEPT PGYEVGQRKR LISSVEDFTE FV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TDSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGQPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SFERSVQLLD QIPSYDTHKI AVLYVGEGQS NSELAILSNE HGSYRYTEFL TGLGRLIELK DCQPDKVYLG GLDVCGEDGQ FTYCWHDDIM QAVFHIATLM PTKDVDKHRC DKKRHLGNDF VSIVYNDSGE DFKLGTIKGQ FNFVHVIVTP LDYECNLVSL QCRKDMEGLV DTSVAKIVSD RNLPFVARQM ALHANMASQV HHSRSNPTDI YPSKWIARLR HIKRLRQRIC EEAAYSNPSL PLVHPPSHSK APAQTPAEPT PGYEVGQRKR LISSVEDFTE FV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5349 / 5349 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1783 / 1783 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5467 / 5467 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 119 / 119 | |||||||||||||
| Last intron/exon boundary | 5302 | |||||||||||||
| Theoretical NMD boundary in CDS | 5133 | |||||||||||||
| Length of CDS | 5349 | |||||||||||||
| Coding sequence (CDS) position | 4037 | |||||||||||||
| cDNA position | 4155 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| Speed | 0.07 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.18, LOF (oe): 0.12, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000644335.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3908G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTDS AVVMEEGSPG EVPVLVEPPG LEDVEAALGM DRRTDAYSRS SSVSSQEEKS LHAEELVGRG IPIERVVSSE GGRPSVDLSF QPSQPLSKSS SSPELQTLQD ILGDPGDKAD VGRLSPEVKA RSQSGTLDGE SAAWSASGED SRGQPEGPLP SSSPRSPSGL RPRGYTISDS APSRRGKRVE RDALKSRATA SNAEKVPGIN PSFVFLQLYH SPFFGDESNK PILLPNESFE RSVQLLDQIP SYDTHKIAVL YVGEGQSNSE LAILSNEHGS YRYTEFLTGL GRLIELKDCQ PDKVYLGGLD VCGEDGQFTY CWHDDIMQAV FHIATLMPTK DVDKHRCDKK RHLGNDFVSI VYNDSGEDFK LGTIKGQFNF VHVIVTPLDY ECNLVSLQCR KDMEGLVDTS VAKIVSDRNL PFVARQMALH ANMASQVHHS RSNPTDIYPS KWIARLRHIK RLRQRICEEA AYSNPSLPLV HPPSHSKAPA QTPAEPTPGY EVGQRKRLIS SVEDFTEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTDS AVVMEEGSPG EVPVLVEPPG LEDVEAALGM DRRTDAYSRS SSVSSQEEKS LHAEELVGRG IPIERVVSSE GGQPSVDLSF QPSQPLSKSS SSPELQTLQD ILGDPGDKAD VGRLSPEVKA RSQSGTLDGE SAAWSASGED SRGQPEGPLP SSSPRSPSGL RPRGYTISDS APSRRGKRVE RDALKSRATA SNAEKVPGIN PSFVFLQLYH SPFFGDESNK PILLPNESFE RSVQLLDQIP SYDTHKIAVL YVGEGQSNSE LAILSNEHGS YRYTEFLTGL GRLIELKDCQ PDKVYLGGLD VCGEDGQFTY CWHDDIMQAV FHIATLMPTK DVDKHRCDKK RHLGNDFVSI VYNDSGEDFK LGTIKGQFNF VHVIVTPLDY ECNLVSLQCR KDMEGLVDTS VAKIVSDRNL PFVARQMALH ANMASQVHHS RSNPTDIYPS KWIARLRHIK RLRQRICEEA AYSNPSLPLV HPPSHSKAPA QTPAEPTPGY EVGQRKRLIS SVEDFTEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5220 / 5220 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1740 / 1740 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5320 / 5320 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 101 / 101 | |||||||||||||
| Last intron/exon boundary | 5155 | |||||||||||||
| Theoretical NMD boundary in CDS | 5004 | |||||||||||||
| Length of CDS | 5220 | |||||||||||||
| Coding sequence (CDS) position | 3908 | |||||||||||||
| cDNA position | 4008 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| Speed | 0.07 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.18, LOF (oe): 0.12, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000401874.7 | |||||||||||||
| Genbank transcript ID | NM_001077183 (by similarity), NM_001406673 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | TSC2_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3905G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTDSA VVMEEGSPGE VPVLVEPPGL EDVEAALGMD RRTDAYSRSS SVSSQEEKSL HAEELVGRGI PIERVVSSEG GRPSVDLSFQ PSQPLSKSSS SPELQTLQDI LGDPGDKADV GRLSPEVKAR SQSGTLDGES AAWSASGEDS RGQPEGPLPS SSPRSPSGLR PRGYTISDSA PSRRGKRVER DALKSRATAS NAEKVPGINP SFVFLQLYHS PFFGDESNKP ILLPNESQSF ERSVQLLDQI PSYDTHKIAV LYVGEGQSNS ELAILSNEHG SYRYTEFLTG LGRLIELKDC QPDKVYLGGL DVCGEDGQFT YCWHDDIMQA VFHIATLMPT KDVDKHRCDK KRHLGNDFVS IVYNDSGEDF KLGTIKGQFN FVHVIVTPLD YECNLVSLQC RKDMEGLVDT SVAKIVSDRN LPFVARQMAL HANMASQVHH SRSNPTDIYP SKWIARLRHI KRLRQRICEE AAYSNPSLPL VHPPSHSKAP AQTPAEPTPG YEVGQRKRLI SSVEDFTEFV * | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKRIQTS LTSASLGSAD ENSVAQADDS LKNLHLELTE TCLDMMARYV FSNFTAVPKR SPVGEFLLAG GRTKTWLVGN KLVTVTTSVG TGTRSLLGLD SGELQSGPES SSSPGVHVRQ TKEAPAKLES QAGQQVSRGA RDRVRSMSGG HGLRVGALDV PASQFLGSAT SPGPRTAPAA KPEKASAGTR VPVQEKTNLA AYVPLLTQGW AEILVRRPTG NTSWLMSLEN PLSPFSSDIN NMPLQELSNA LMAAERFKEH RDTALYKSLS VPAASTAKPP PLPRSNTDSA VVMEEGSPGE VPVLVEPPGL EDVEAALGMD RRTDAYSRSS SVSSQEEKSL HAEELVGRGI PIERVVSSEG GQPSVDLSFQ PSQPLSKSSS SPELQTLQDI LGDPGDKADV GRLSPEVKAR SQSGTLDGES AAWSASGEDS RGQPEGPLPS SSPRSPSGLR PRGYTISDSA PSRRGKRVER DALKSRATAS NAEKVPGINP SFVFLQLYHS PFFGDESNKP ILLPNESQSF ERSVQLLDQI PSYDTHKIAV LYVGEGQSNS ELAILSNEHG SYRYTEFLTG LGRLIELKDC QPDKVYLGGL DVCGEDGQFT YCWHDDIMQA VFHIATLMPT KDVDKHRCDK KRHLGNDFVS IVYNDSGEDF KLGTIKGQFN FVHVIVTPLD YECNLVSLQC RKDMEGLVDT SVAKIVSDRN LPFVARQMAL HANMASQVHH SRSNPTDIYP SKWIARLRHI KRLRQRICEE AAYSNPSLPL VHPPSHSKAP AQTPAEPTPG YEVGQRKRLI SSVEDFTEFV * | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5223 / 5223 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1741 / 1741 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5329 / 5329 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 107 / 107 | |||||||||||||
| Last intron/exon boundary | 5164 | |||||||||||||
| Theoretical NMD boundary in CDS | 5007 | |||||||||||||
| Length of CDS | 5223 | |||||||||||||
| Coding sequence (CDS) position | 3905 | |||||||||||||
| cDNA position | 4011 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.17, LOF (oe): 0.12, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000642797.1 | |||||||||||||
| Genbank transcript ID | NM_001363528 (by similarity), NM_001406671 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3908G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTDS AVVMEEGSPG EVPVLVEPPG LEDVEAALGM DRRTDAYSRS SSVSSQEEKS LHAEELVGRG IPIERVVSSE GGRPSVDLSF QPSQPLSKSS SSPELQTLQD ILGDPGDKAD VGRLSPEVKA RSQSGTLDGE SAAWSASGED SRGQPEGPLP SSSPRSPSGL RPRGYTISDS APSRRGKRVE RDALKSRATA SNAEKVPGIN PSFVFLQLYH SPFFGDESNK PILLPNESQS FERSVQLLDQ IPSYDTHKIA VLYVGEGQSN SELAILSNEH GSYRYTEFLT GLGRLIELKD CQPDKVYLGG LDVCGEDGQF TYCWHDDIMQ AVFHIATLMP TKDVDKHRCD KKRHLGNDFV SIVYNDSGED FKLGTIKGQF NFVHVIVTPL DYECNLVSLQ CRKDMEGLVD TSVAKIVSDR NLPFVARQMA LHANMASQVH HSRSNPTDIY PSKWIARLRH IKRLRQRICE EAAYSNPSLP LVHPPSHSKA PAQTPAEPTP GYEVGQRKRL ISSVEDFTEF V* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTDS AVVMEEGSPG EVPVLVEPPG LEDVEAALGM DRRTDAYSRS SSVSSQEEKS LHAEELVGRG IPIERVVSSE GGQPSVDLSF QPSQPLSKSS SSPELQTLQD ILGDPGDKAD VGRLSPEVKA RSQSGTLDGE SAAWSASGED SRGQPEGPLP SSSPRSPSGL RPRGYTISDS APSRRGKRVE RDALKSRATA SNAEKVPGIN PSFVFLQLYH SPFFGDESNK PILLPNESQS FERSVQLLDQ IPSYDTHKIA VLYVGEGQSN SELAILSNEH GSYRYTEFLT GLGRLIELKD CQPDKVYLGG LDVCGEDGQF TYCWHDDIMQ AVFHIATLMP TKDVDKHRCD KKRHLGNDFV SIVYNDSGED FKLGTIKGQF NFVHVIVTPL DYECNLVSLQ CRKDMEGLVD TSVAKIVSDR NLPFVARQMA LHANMASQVH HSRSNPTDIY PSKWIARLRH IKRLRQRICE EAAYSNPSLP LVHPPSHSKA PAQTPAEPTP GYEVGQRKRL ISSVEDFTEF V* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5226 / 5226 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1742 / 1742 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5280 / 5280 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 55 / 55 | |||||||||||||
| Last intron/exon boundary | 5115 | |||||||||||||
| Theoretical NMD boundary in CDS | 5010 | |||||||||||||
| Length of CDS | 5226 | |||||||||||||
| Coding sequence (CDS) position | 3908 | |||||||||||||
| cDNA position | 3962 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.18, LOF (oe): 0.13, misssense (oe): 0.98, synonymous (oe): 1.28 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000568454.6 | |||||||||||||
| Genbank transcript ID | NM_001318832 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3938G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MEGFSGASWS TMAKPTSKDS GLKEKFKILL GLGTPRPNPR SAEGKQTEFI ITAEILRELS MECGLNNRIR MIGQICEVAK TKKFEEHAVE ALWKAVADLL QPERPLEARH AVLALLKAIV QGQGERLGVL RALFFKVIKD YPSNEDLHER LEVFKALTDN GRHITYLEEE LADFVLQWMD VGLSSEFLLV LVNLVKFNSC YLDEYIARMV QMICLLCVRT ASSVDIEVSL QVLDAVVCYN CLPAESLPLF IVTLCRTINV KELCEPCWKL MRNLLGTHLG HSAIYNMCHL MEDRAYMEDA PLLRGAVFFV GMALWGAHRL YSLRNSPTSV LPSFYQAMAC PNEVVSYEIV LSITRLIKKY RKELQVVAWD ILLNIIERLL QQLQTLDSPE LRTIVHDLLT TVEELCDQNE FHGSQERYFE LVERCADQRP ESSLLNLISY RAQSIHPAKD GWIQNLQALM ERFFRSESRG AVRIKVLDVL SFVLLINRQF YEEELINSVV ISQLSHIPED KDHQVRKLAT QLLVDLAEGC HTHHFNSLLD IIEKVMARSL SPPPELEERD VAAYSASLED VKTAVLGLLV ILQTKLYTLP ASHATRVYEM LVSHIQLHYK HSYTLPIASS IRLQAFDFLL LLRADSLHRL GLPNKDGVVR FSPYCVCDYM EPERGSEKKT SGPLSPPTGP PGPAPAGPAV RLGSVPYSLL FRVLLQCLKQ ESDWKVLKLV LGRLPESLRY KVLIFTSPCS VDQLCSALCS MLSGPKTLER LRGAPEGFSR TDLHLAVVPV LTALISYHNY LDKTKQREMV YCLEQGLIHR CASQCVVALS ICSVEMPDII IKALPVLVVK LTHISATASM AVPLLEFLST LARLPHLYRN FAAEQYASVF AISLPYTNPS KFNQYIVCLA HHVIAMWFIR CRLPFRKDFV PFITKGLRSN VLLSFDDTPE KDSFRARSTS LNERPKRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTDS AVVMEEGSPG EVPVLVEPPG LEDVEAALGM DRRTDAYSRS SSVSSQEEKS LHAEELVGRG IPIERVVSSE GGRPSVDLSF QPSQPLSKSS SSPELQTLQD ILGDPGDKAD VGRLSPEVKA RSQSGTLDGE SAAWSASGED SRGQPEGPLP SSSPRSPSGL RPRGYTISDS APSRRGKRVE RDALKSRATA SNAEKVPGIN PSFVFLQLYH SPFFGDESNK PILLPNESQS FERSVQLLDQ IPSYDTHKIA VLYVGEGQSN SELAILSNEH GSYRYTEFLT GLGRLIELKD CQPDKVYLGG LDVCGEDGQF TYCWHDDIMQ AVFHIATLMP TKDVDKHRCD KKRHLGNDFV SIVYNDSGED FKLGTIKGQF NFVHVIVTPL DYECNLVSLQ CRKDMEGLVD TSVAKIVSDR NLPFVARQMA LHANMASQVH HSRSNPTDIY PSKWIARLRH IKRLRQRICE EAAYSNPSLP LVHPPSHSKA PAQTPAEPTP GYEVGQRKRL ISSVEDFTEF V* | |||||||||||||
| Mutated AA sequence | MEGFSGASWS TMAKPTSKDS GLKEKFKILL GLGTPRPNPR SAEGKQTEFI ITAEILRELS MECGLNNRIR MIGQICEVAK TKKFEEHAVE ALWKAVADLL QPERPLEARH AVLALLKAIV QGQGERLGVL RALFFKVIKD YPSNEDLHER LEVFKALTDN GRHITYLEEE LADFVLQWMD VGLSSEFLLV LVNLVKFNSC YLDEYIARMV QMICLLCVRT ASSVDIEVSL QVLDAVVCYN CLPAESLPLF IVTLCRTINV KELCEPCWKL MRNLLGTHLG HSAIYNMCHL MEDRAYMEDA PLLRGAVFFV GMALWGAHRL YSLRNSPTSV LPSFYQAMAC PNEVVSYEIV LSITRLIKKY RKELQVVAWD ILLNIIERLL QQLQTLDSPE LRTIVHDLLT TVEELCDQNE FHGSQERYFE LVERCADQRP ESSLLNLISY RAQSIHPAKD GWIQNLQALM ERFFRSESRG AVRIKVLDVL SFVLLINRQF YEEELINSVV ISQLSHIPED KDHQVRKLAT QLLVDLAEGC HTHHFNSLLD IIEKVMARSL SPPPELEERD VAAYSASLED VKTAVLGLLV ILQTKLYTLP ASHATRVYEM LVSHIQLHYK HSYTLPIASS IRLQAFDFLL LLRADSLHRL GLPNKDGVVR FSPYCVCDYM EPERGSEKKT SGPLSPPTGP PGPAPAGPAV RLGSVPYSLL FRVLLQCLKQ ESDWKVLKLV LGRLPESLRY KVLIFTSPCS VDQLCSALCS MLSGPKTLER LRGAPEGFSR TDLHLAVVPV LTALISYHNY LDKTKQREMV YCLEQGLIHR CASQCVVALS ICSVEMPDII IKALPVLVVK LTHISATASM AVPLLEFLST LARLPHLYRN FAAEQYASVF AISLPYTNPS KFNQYIVCLA HHVIAMWFIR CRLPFRKDFV PFITKGLRSN VLLSFDDTPE KDSFRARSTS LNERPKRIQT SLTSASLGSA DENSVAQADD SLKNLHLELT ETCLDMMARY VFSNFTAVPK RSPVGEFLLA GGRTKTWLVG NKLVTVTTSV GTGTRSLLGL DSGELQSGPE SSSSPGVHVR QTKEAPAKLE SQAGQQVSRG ARDRVRSMSG GHGLRVGALD VPASQFLGSA TSPGPRTAPA AKPEKASAGT RVPVQEKTNL AAYVPLLTQG WAEILVRRPT GNTSWLMSLE NPLSPFSSDI NNMPLQELSN ALMAAERFKE HRDTALYKSL SVPAASTAKP PPLPRSNTDS AVVMEEGSPG EVPVLVEPPG LEDVEAALGM DRRTDAYSRS SSVSSQEEKS LHAEELVGRG IPIERVVSSE GGQPSVDLSF QPSQPLSKSS SSPELQTLQD ILGDPGDKAD VGRLSPEVKA RSQSGTLDGE SAAWSASGED SRGQPEGPLP SSSPRSPSGL RPRGYTISDS APSRRGKRVE RDALKSRATA SNAEKVPGIN PSFVFLQLYH SPFFGDESNK PILLPNESQS FERSVQLLDQ IPSYDTHKIA VLYVGEGQSN SELAILSNEH GSYRYTEFLT GLGRLIELKD CQPDKVYLGG LDVCGEDGQF TYCWHDDIMQ AVFHIATLMP TKDVDKHRCD KKRHLGNDFV SIVYNDSGED FKLGTIKGQF NFVHVIVTPL DYECNLVSLQ CRKDMEGLVD TSVAKIVSDR NLPFVARQMA LHANMASQVH HSRSNPTDIY PSKWIARLRH IKRLRQRICE EAAYSNPSLP LVHPPSHSKA PAQTPAEPTP GYEVGQRKRL ISSVEDFTEF V* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5256 / 5256 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1752 / 1752 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5324 / 5324 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 69 / 69 | |||||||||||||
| Last intron/exon boundary | 5159 | |||||||||||||
| Theoretical NMD boundary in CDS | 5040 | |||||||||||||
| Length of CDS | 5256 | |||||||||||||
| Coding sequence (CDS) position | 3938 | |||||||||||||
| cDNA position | 4006 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.17, LOF (oe): 0.12, misssense (oe): 0.98, synonymous (oe): 1.27 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000439673.6 | |||||||||||||
| Genbank transcript ID | NM_001406693 (by similarity), NM_001318827 (by similarity), NM_001406678 (by similarity), NM_001406685 (by similarity), NM_001406688 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | TSC2_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3797G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEGERLG VLRALFFKVI KDYPSNEDLH ERLEVFKALT DNGRHITYLE EELADFVLQW MDVGLSSEFL LVLVNLVKFN SCYLDEYIAR MVQMICLLCV RTASSVDIEV SLQVLDAVVC YNCLPAESLP LFIVTLCRTI NVKELCEPCW KLMRNLLGTH LGHSAIYNMC HLMEDRAYME DAPLLRGAVF FVGMALWGAH RLYSLRNSPT SVLPSFYQAM ACPNEVVSYE IVLSITRLIK KYRKELQVVA WDILLNIIER LLQQLQTLDS PELRTIVHDL LTTVEELCDQ NEFHGSQERY FELVERCADQ RPESSLLNLI SYRAQSIHPA KDGWIQNLQA LMERFFRSES RGAVRIKVLD VLSFVLLINR QFYEEELINS VVISQLSHIP EDKDHQVRKL ATQLLVDLAE GCHTHHFNSL LDIIEKVMAR SLSPPPELEE RDVAAYSASL EDVKTAVLGL LVILQTKLYT LPASHATRVY EMLVSHIQLH YKHSYTLPIA SSIRLQAFDF LLLLRADSLH RLGLPNKDGV VRFSPYCVCD YMEPERGSEK KTSGPLSPPT GPPGPAPAGP AVRLGSVPYS LLFRVLLQCL KQESDWKVLK LVLGRLPESL RYKVLIFTSP CSVDQLCSAL CSMLSGPKTL ERLRGAPEGF SRTDLHLAVV PVLTALISYH NYLDKTKQRE MVYCLEQGLI HRCASQCVVA LSICSVEMPD IIIKALPVLV VKLTHISATA SMAVPLLEFL STLARLPHLY RNFAAEQYAS VFAISLPYTN PSKFNQYIVC LAHHVIAMWF IRCRLPFRKD FVPFITKGLR SNVLLSFDDT PEKDSFRARS TSLNERPKSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TDSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGRPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANMAS QVHHSRSNPT DIYPSKWIAR LRHIKRLRQR ICEEAAYSNP SLPLVHPPSH SKAPAQTPAE PTPGYEVGQR KRLISSVEDF TEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEGERLG VLRALFFKVI KDYPSNEDLH ERLEVFKALT DNGRHITYLE EELADFVLQW MDVGLSSEFL LVLVNLVKFN SCYLDEYIAR MVQMICLLCV RTASSVDIEV SLQVLDAVVC YNCLPAESLP LFIVTLCRTI NVKELCEPCW KLMRNLLGTH LGHSAIYNMC HLMEDRAYME DAPLLRGAVF FVGMALWGAH RLYSLRNSPT SVLPSFYQAM ACPNEVVSYE IVLSITRLIK KYRKELQVVA WDILLNIIER LLQQLQTLDS PELRTIVHDL LTTVEELCDQ NEFHGSQERY FELVERCADQ RPESSLLNLI SYRAQSIHPA KDGWIQNLQA LMERFFRSES RGAVRIKVLD VLSFVLLINR QFYEEELINS VVISQLSHIP EDKDHQVRKL ATQLLVDLAE GCHTHHFNSL LDIIEKVMAR SLSPPPELEE RDVAAYSASL EDVKTAVLGL LVILQTKLYT LPASHATRVY EMLVSHIQLH YKHSYTLPIA SSIRLQAFDF LLLLRADSLH RLGLPNKDGV VRFSPYCVCD YMEPERGSEK KTSGPLSPPT GPPGPAPAGP AVRLGSVPYS LLFRVLLQCL KQESDWKVLK LVLGRLPESL RYKVLIFTSP CSVDQLCSAL CSMLSGPKTL ERLRGAPEGF SRTDLHLAVV PVLTALISYH NYLDKTKQRE MVYCLEQGLI HRCASQCVVA LSICSVEMPD IIIKALPVLV VKLTHISATA SMAVPLLEFL STLARLPHLY RNFAAEQYAS VFAISLPYTN PSKFNQYIVC LAHHVIAMWF IRCRLPFRKD FVPFITKGLR SNVLLSFDDT PEKDSFRARS TSLNERPKSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TDSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGQPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANMAS QVHHSRSNPT DIYPSKWIAR LRHIKRLRQR ICEEAAYSNP SLPLVHPPSH SKAPAQTPAE PTPGYEVGQR KRLISSVEDF TEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5115 / 5115 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1705 / 1705 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5196 / 5196 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 82 / 82 | |||||||||||||
| Last intron/exon boundary | 5031 | |||||||||||||
| Theoretical NMD boundary in CDS | 4899 | |||||||||||||
| Length of CDS | 5115 | |||||||||||||
| Coding sequence (CDS) position | 3797 | |||||||||||||
| cDNA position | 3878 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| Speed | 0.07 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||||||||||
| Gene symbol | TSC2 | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.17, LOF (oe): 0.12, misssense (oe): 0.99, synonymous (oe): 1.28 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000350773.9 | |||||||||||||||||||||
| Genbank transcript ID | NM_001406683 (by similarity), NM_001406689 (by similarity), NM_001114382 (by similarity), NM_001406664 (by similarity), NM_001406670 (by similarity), NM_001406682 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | TSC2_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.4037G>A g.36362G>A | |||||||||||||||||||||
| 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 | 16 | |||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TDSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGRPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANMAS QVHHSRSNPT DIYPSKWIAR LRHIKRLRQR ICEEAAYSNP SLPLVHPPSH SKAPAQTPAE PTPGYEVGQR KRLISSVEDF TEFV* | |||||||||||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TDSAVVMEEG SPGEVPVLVE PPGLEDVEAA LGMDRRTDAY SRSSSVSSQE EKSLHAEELV GRGIPIERVV SSEGGQPSVD LSFQPSQPLS KSSSSPELQT LQDILGDPGD KADVGRLSPE VKARSQSGTL DGESAAWSAS GEDSRGQPEG PLPSSSPRSP SGLRPRGYTI SDSAPSRRGK RVERDALKSR ATASNAEKVP GINPSFVFLQ LYHSPFFGDE SNKPILLPNE SQSFERSVQL LDQIPSYDTH KIAVLYVGEG QSNSELAILS NEHGSYRYTE FLTGLGRLIE LKDCQPDKVY LGGLDVCGED GQFTYCWHDD IMQAVFHIAT LMPTKDVDKH RCDKKRHLGN DFVSIVYNDS GEDFKLGTIK GQFNFVHVIV TPLDYECNLV SLQCRKDMEG LVDTSVAKIV SDRNLPFVAR QMALHANMAS QVHHSRSNPT DIYPSKWIAR LRHIKRLRQR ICEEAAYSNP SLPLVHPPSH SKAPAQTPAE PTPGYEVGQR KRLISSVEDF TEFV* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 5355 / 5355 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1785 / 1785 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 5430 / 5430 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 76 / 76 | |||||||||||||||||||||
| Last intron/exon boundary | 5265 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 5139 | |||||||||||||||||||||
| Length of CDS | 5355 | |||||||||||||||||||||
| Coding sequence (CDS) position | 4037 | |||||||||||||||||||||
| cDNA position | 4112 | |||||||||||||||||||||
| gDNA position | 36362 | |||||||||||||||||||||
| Chromosomal position | 2084328 | |||||||||||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 0.61, LOF (oe): 0.27, misssense (oe): 1.10, synonymous (oe): 1.24 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000645186.2 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4196G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TVASFSSLYQ SSCQGQLHRS VSWAGIASQR EAVGCRAPLC LIGAVLVASS AHPHDSAVVM EEGSPGEVPV LVEPPGLEDV EAALGMDRRT DAYSRSSSVS SQEEKSLHAE ELVGRGIPIE RVVSSEGGRP SVDLSFQPSQ PLSKSSSSPE LQTLQDILGD PGDKADVGRL SPEVKARSQS GTLDGESAAW SASGEDSRGQ PEGPLPSSSP RSPSGLRPRG YTISDSAPSR RGKRVERDAL KSRATASNAE KVPGINPSFV FLQLYHSPFF GDESNKPILL PNESQSFERS VQLLDQIPSY DTHKIAVLYV GEGQSNSELA ILSNEHGSYR YTEFLTGLGR LIELKDCQPD KVYLGGLDVC GEDGQFTYCW HDDIMQAVFH IATLMPTKDV DKHRCDKKRH LGNDFVSIVY NDSGEDFKLG TIKGQFNFVH VIVTPLDYEC NLVSLQCRKD MEGLVDTSVA KIVSDRNLPF VARQMALHAN MASQVHHSRS NPTDIYPSKW IARLRHIKRL RQRICEEAAY SNPSLPLVHP PSHSKAPAQT PAEPTPGYEV GQRKRLISSV EDFTEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TVASFSSLYQ SSCQGQLHRS VSWAGIASQR EAVGCRAPLC LIGAVLVASS AHPHDSAVVM EEGSPGEVPV LVEPPGLEDV EAALGMDRRT DAYSRSSSVS SQEEKSLHAE ELVGRGIPIE RVVSSEGGQP SVDLSFQPSQ PLSKSSSSPE LQTLQDILGD PGDKADVGRL SPEVKARSQS GTLDGESAAW SASGEDSRGQ PEGPLPSSSP RSPSGLRPRG YTISDSAPSR RGKRVERDAL KSRATASNAE KVPGINPSFV FLQLYHSPFF GDESNKPILL PNESQSFERS VQLLDQIPSY DTHKIAVLYV GEGQSNSELA ILSNEHGSYR YTEFLTGLGR LIELKDCQPD KVYLGGLDVC GEDGQFTYCW HDDIMQAVFH IATLMPTKDV DKHRCDKKRH LGNDFVSIVY NDSGEDFKLG TIKGQFNFVH VIVTPLDYEC NLVSLQCRKD MEGLVDTSVA KIVSDRNLPF VARQMALHAN MASQVHHSRS NPTDIYPSKW IARLRHIKRL RQRICEEAAY SNPSLPLVHP PSHSKAPAQT PAEPTPGYEV GQRKRLISSV EDFTEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5514 / 5514 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1838 / 1838 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5624 / 5624 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 111 / 111 | |||||||||||||
| Last intron/exon boundary | 5459 | |||||||||||||
| Theoretical NMD boundary in CDS | 5298 | |||||||||||||
| Length of CDS | 5514 | |||||||||||||
| Coding sequence (CDS) position | 4196 | |||||||||||||
| cDNA position | 4306 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | |||||||||||||
| Gene symbol | TSC2 | |||||||||||||
| Gene constraints | LOEUF: 1.24, LOF (oe): 0.59, misssense (oe): 1.05, synonymous (oe): 0.99 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000642206.2 | |||||||||||||
| Genbank transcript ID | NM_001406667 (by similarity), NM_001406668 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.3953G>A g.36362G>A | |||||||||||||
| 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 | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | |||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEPERPL EARHAVLALL KAIVQGQVRP RATLGWVTSG CPLTVLSLLG RVWTPASGER LGVLRALFFK VIKDYPSNED LHERLEVFKA LTDNGRHITY LEEELADFVL QWMDVGLSSE FLLVLVNLVK FNSCYLDEYI ARMVQMICLL CVRTASSVDI EVSLQVLDAV VCYNCLPAES LPLFIVTLCR TINVKELCEP CWKLMRNLLG THLGHSAIYN MCHLMEDRAY MEDAPLLRGA VFFVGMALWG AHRLYSLRNS PTSVLPSFYQ AMACPNEVVS YEIVLSITRL IKKYRKELQV VAWDILLNII ERLLQQLQTL DSPELRTIVH DLLTTVEELC DQNEFHGSQE RYFELVERCA DQRPESSLLN LISYRAQSIH PAKDGWIQNL QALMERFFRS ESRGAVRIKV LDVLSFVLLI NRQFYEEELI NSVVISQLSH IPEDKDHQVR KLATQLLVDL AEGCHTHHFN SLLDIIEKVM ARSLSPPPEL EERDVAAYSA SLEDVKTAVL GLLVILQTKL YTLPASHATR VYEMLVSHIQ LHYKHSYTLP IASSIRLQAF DFLLLLRADS LHRLGLPNKD GVVRFSPYCV CDYMEPERGS EKKTSGPLSP PTGPPGPAPA GPAVRLGSVP YSLLFRVLLQ CLKQESDWKV LKLVLGRLPE SLRYKVLIFT SPCSVDQLCS ALCSMLSGPK TLERLRGAPE GFSRTDLHLA VVPVLTALIS YHNYLDKTKQ REMVYCLEQG LIHRCASQCV VALSICSVEM PDIIIKALPV LVVKLTHISA TASMAVPLLE FLSTLARLPH LYRNFAAEQY ASVFAISLPY TNPSKFNQYI VCLAHHVIAM WFIRCRLPFR KDFVPFITKG LRSNVLLSFD DTPEKDSFRA RSTSLNERPK SRIQTSLTSA SLGSADENSV AQADDSLKNL HLELTETCLD MMARYVFSNF TAVPKRSPVG EFLLAGGRTK TWLVGNKLVT VTTSVGTGTR SLLGLDSGEL QSGPESSSSP GVHVRQTKEA PAKLESQAGQ QVSRGARDRV RSMSGGHGLR VGALDVPASQ FLGSATSPGP RTAPAAKPEK ASAGTRVPVQ EKTNLAAYVP LLTQGWAEIL VRRPTGNTSW LMSLENPLSP FSSDINNMPL QELSNALMAA ERFKEHRDTA LYKSLSVPAA STAKPPPLPR SNTDSAVVME EGSPGEVPVL VEPPGLEDVE AALGMDRRTD AYSRSSSVSS QEEKSLHAEE LVGRGIPIER VVSSEGGRPS VDLSFQPSQP LSKSSSSPEL QTLQDILGDP GDKADVGRLS PEVKARSQSG TLDGESAAWS ASGEDSRGQP EGPLPSSSPR SPSGLRPRGY TISDSAPSRR GKRVERDALK SRATASNAEK VPGINPSFVF LQLYHSPFFG DESNKPILLP NESQSFERSV QLLDQIPSYD THKIAVLYVG EGQSNSELAI LSNEHGSYRY TEFLTGLGRL IELKDCQPDK VYLGGLDVCG EDGQFTYCWH DDIMQAVFHI ATLMPTKDVD KHRCDKKRHL GNDFVSIVYN DSGEDFKLGT IKGQFNFVHV IVTPLDYECN LVSLQCRKDM EGLVDTSVAK IVSDRNLPFV ARQMALHANM ASQVHHSRSN PTDIYPSKWI ARLRHIKRLR QRICEEAAYS NPSLPLVHPP SHSKAPAQTP AEPTPGYEVG QRKRLISSVE DFTEFV* | |||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEPERPL EARHAVLALL KAIVQGQVRP RATLGWVTSG CPLTVLSLLG RVWTPASGER LGVLRALFFK VIKDYPSNED LHERLEVFKA LTDNGRHITY LEEELADFVL QWMDVGLSSE FLLVLVNLVK FNSCYLDEYI ARMVQMICLL CVRTASSVDI EVSLQVLDAV VCYNCLPAES LPLFIVTLCR TINVKELCEP CWKLMRNLLG THLGHSAIYN MCHLMEDRAY MEDAPLLRGA VFFVGMALWG AHRLYSLRNS PTSVLPSFYQ AMACPNEVVS YEIVLSITRL IKKYRKELQV VAWDILLNII ERLLQQLQTL DSPELRTIVH DLLTTVEELC DQNEFHGSQE RYFELVERCA DQRPESSLLN LISYRAQSIH PAKDGWIQNL QALMERFFRS ESRGAVRIKV LDVLSFVLLI NRQFYEEELI NSVVISQLSH IPEDKDHQVR KLATQLLVDL AEGCHTHHFN SLLDIIEKVM ARSLSPPPEL EERDVAAYSA SLEDVKTAVL GLLVILQTKL YTLPASHATR VYEMLVSHIQ LHYKHSYTLP IASSIRLQAF DFLLLLRADS LHRLGLPNKD GVVRFSPYCV CDYMEPERGS EKKTSGPLSP PTGPPGPAPA GPAVRLGSVP YSLLFRVLLQ CLKQESDWKV LKLVLGRLPE SLRYKVLIFT SPCSVDQLCS ALCSMLSGPK TLERLRGAPE GFSRTDLHLA VVPVLTALIS YHNYLDKTKQ REMVYCLEQG LIHRCASQCV VALSICSVEM PDIIIKALPV LVVKLTHISA TASMAVPLLE FLSTLARLPH LYRNFAAEQY ASVFAISLPY TNPSKFNQYI VCLAHHVIAM WFIRCRLPFR KDFVPFITKG LRSNVLLSFD DTPEKDSFRA RSTSLNERPK SRIQTSLTSA SLGSADENSV AQADDSLKNL HLELTETCLD MMARYVFSNF TAVPKRSPVG EFLLAGGRTK TWLVGNKLVT VTTSVGTGTR SLLGLDSGEL QSGPESSSSP GVHVRQTKEA PAKLESQAGQ QVSRGARDRV RSMSGGHGLR VGALDVPASQ FLGSATSPGP RTAPAAKPEK ASAGTRVPVQ EKTNLAAYVP LLTQGWAEIL VRRPTGNTSW LMSLENPLSP FSSDINNMPL QELSNALMAA ERFKEHRDTA LYKSLSVPAA STAKPPPLPR SNTDSAVVME EGSPGEVPVL VEPPGLEDVE AALGMDRRTD AYSRSSSVSS QEEKSLHAEE LVGRGIPIER VVSSEGGQPS VDLSFQPSQP LSKSSSSPEL QTLQDILGDP GDKADVGRLS PEVKARSQSG TLDGESAAWS ASGEDSRGQP EGPLPSSSPR SPSGLRPRGY TISDSAPSRR GKRVERDALK SRATASNAEK VPGINPSFVF LQLYHSPFFG DESNKPILLP NESQSFERSV QLLDQIPSYD THKIAVLYVG EGQSNSELAI LSNEHGSYRY TEFLTGLGRL IELKDCQPDK VYLGGLDVCG EDGQFTYCWH DDIMQAVFHI ATLMPTKDVD KHRCDKKRHL GNDFVSIVYN DSGEDFKLGT IKGQFNFVHV IVTPLDYECN LVSLQCRKDM EGLVDTSVAK IVSDRNLPFV ARQMALHANM ASQVHHSRSN PTDIYPSKWI ARLRHIKRLR QRICEEAAYS NPSLPLVHPP SHSKAPAQTP AEPTPGYEVG QRKRLISSVE DFTEFV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 5271 / 5271 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1757 / 1757 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 5387 / 5387 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 117 / 117 | |||||||||||||
| Last intron/exon boundary | 5222 | |||||||||||||
| Theoretical NMD boundary in CDS | 5055 | |||||||||||||
| Length of CDS | 5271 | |||||||||||||
| Coding sequence (CDS) position | 3953 | |||||||||||||
| cDNA position | 4069 | |||||||||||||
| gDNA position | 36362 | |||||||||||||
| Chromosomal position | 2084328 | |||||||||||||
| 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 | Chr16:2084328G>A (GRCh38) | ||||||||||||||||
| Gene symbol | TSC2 | ||||||||||||||||
| Gene constraints | LOEUF: 0.20, LOF (oe): 0.15, misssense (oe): 0.99, synonymous (oe): 1.28 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000219476.9 | ||||||||||||||||
| Genbank transcript ID | NM_000548 (exact from MANE), NM_001406680 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | TSC2_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.4106G>A g.36362G>A | ||||||||||||||||
| 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 | 16 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | ||||||||||||||||
| Altered gDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | ||||||||||||||||
| Original cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCT | ||||||||||||||||
| Altered cDNA sequence snippet | CGTCTCCTCGGAGGGTGGCCAGCCCTCTGTGGACCTCTCCT | ||||||||||||||||
| Wildtype AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TVASFSSLYQ SSCQGQLHRS VSWADSAVVM EEGSPGEVPV LVEPPGLEDV EAALGMDRRT DAYSRSSSVS SQEEKSLHAE ELVGRGIPIE RVVSSEGGRP SVDLSFQPSQ PLSKSSSSPE LQTLQDILGD PGDKADVGRL SPEVKARSQS GTLDGESAAW SASGEDSRGQ PEGPLPSSSP RSPSGLRPRG YTISDSAPSR RGKRVERDAL KSRATASNAE KVPGINPSFV FLQLYHSPFF GDESNKPILL PNESQSFERS VQLLDQIPSY DTHKIAVLYV GEGQSNSELA ILSNEHGSYR YTEFLTGLGR LIELKDCQPD KVYLGGLDVC GEDGQFTYCW HDDIMQAVFH IATLMPTKDV DKHRCDKKRH LGNDFVSIVY NDSGEDFKLG TIKGQFNFVH VIVTPLDYEC NLVSLQCRKD MEGLVDTSVA KIVSDRNLPF VARQMALHAN MASQVHHSRS NPTDIYPSKW IARLRHIKRL RQRICEEAAY SNPSLPLVHP PSHSKAPAQT PAEPTPGYEV GQRKRLISSV EDFTEFV* | ||||||||||||||||
| Mutated AA sequence | MAKPTSKDSG LKEKFKILLG LGTPRPNPRS AEGKQTEFII TAEILRELSM ECGLNNRIRM IGQICEVAKT KKFEEHAVEA LWKAVADLLQ PERPLEARHA VLALLKAIVQ GQGERLGVLR ALFFKVIKDY PSNEDLHERL EVFKALTDNG RHITYLEEEL ADFVLQWMDV GLSSEFLLVL VNLVKFNSCY LDEYIARMVQ MICLLCVRTA SSVDIEVSLQ VLDAVVCYNC LPAESLPLFI VTLCRTINVK ELCEPCWKLM RNLLGTHLGH SAIYNMCHLM EDRAYMEDAP LLRGAVFFVG MALWGAHRLY SLRNSPTSVL PSFYQAMACP NEVVSYEIVL SITRLIKKYR KELQVVAWDI LLNIIERLLQ QLQTLDSPEL RTIVHDLLTT VEELCDQNEF HGSQERYFEL VERCADQRPE SSLLNLISYR AQSIHPAKDG WIQNLQALME RFFRSESRGA VRIKVLDVLS FVLLINRQFY EEELINSVVI SQLSHIPEDK DHQVRKLATQ LLVDLAEGCH THHFNSLLDI IEKVMARSLS PPPELEERDV AAYSASLEDV KTAVLGLLVI LQTKLYTLPA SHATRVYEML VSHIQLHYKH SYTLPIASSI RLQAFDFLLL LRADSLHRLG LPNKDGVVRF SPYCVCDYME PERGSEKKTS GPLSPPTGPP GPAPAGPAVR LGSVPYSLLF RVLLQCLKQE SDWKVLKLVL GRLPESLRYK VLIFTSPCSV DQLCSALCSM LSGPKTLERL RGAPEGFSRT DLHLAVVPVL TALISYHNYL DKTKQREMVY CLEQGLIHRC ASQCVVALSI CSVEMPDIII KALPVLVVKL THISATASMA VPLLEFLSTL ARLPHLYRNF AAEQYASVFA ISLPYTNPSK FNQYIVCLAH HVIAMWFIRC RLPFRKDFVP FITKGLRSNV LLSFDDTPEK DSFRARSTSL NERPKSLRIA RPPKQGLNNS PPVKEFKESS AAEAFRCRSI SVSEHVVRSR IQTSLTSASL GSADENSVAQ ADDSLKNLHL ELTETCLDMM ARYVFSNFTA VPKRSPVGEF LLAGGRTKTW LVGNKLVTVT TSVGTGTRSL LGLDSGELQS GPESSSSPGV HVRQTKEAPA KLESQAGQQV SRGARDRVRS MSGGHGLRVG ALDVPASQFL GSATSPGPRT APAAKPEKAS AGTRVPVQEK TNLAAYVPLL TQGWAEILVR RPTGNTSWLM SLENPLSPFS SDINNMPLQE LSNALMAAER FKEHRDTALY KSLSVPAAST AKPPPLPRSN TVASFSSLYQ SSCQGQLHRS VSWADSAVVM EEGSPGEVPV LVEPPGLEDV EAALGMDRRT DAYSRSSSVS SQEEKSLHAE ELVGRGIPIE RVVSSEGGQP SVDLSFQPSQ PLSKSSSSPE LQTLQDILGD PGDKADVGRL SPEVKARSQS GTLDGESAAW SASGEDSRGQ PEGPLPSSSP RSPSGLRPRG YTISDSAPSR RGKRVERDAL KSRATASNAE KVPGINPSFV FLQLYHSPFF GDESNKPILL PNESQSFERS VQLLDQIPSY DTHKIAVLYV GEGQSNSELA ILSNEHGSYR YTEFLTGLGR LIELKDCQPD KVYLGGLDVC GEDGQFTYCW HDDIMQAVFH IATLMPTKDV DKHRCDKKRH LGNDFVSIVY NDSGEDFKLG TIKGQFNFVH VIVTPLDYEC NLVSLQCRKD MEGLVDTSVA KIVSDRNLPF VARQMALHAN MASQVHHSRS NPTDIYPSKW IARLRHIKRL RQRICEEAAY SNPSLPLVHP PSHSKAPAQT PAEPTPGYEV GQRKRLISSV EDFTEFV* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 5424 / 5424 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1808 / 1808 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 5534 / 5534 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 111 / 111 | ||||||||||||||||
| Last intron/exon boundary | 5369 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 5208 | ||||||||||||||||
| Length of CDS | 5424 | ||||||||||||||||
| Coding sequence (CDS) position | 4106 | ||||||||||||||||
| cDNA position | 4216 | ||||||||||||||||
| gDNA position | 36362 | ||||||||||||||||
| Chromosomal position | 2084328 | ||||||||||||||||
| 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