| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000234420(MANE Select) | MSH6 | Deleterious | 64|36 | simple_ | No | Single base exchange | Normal |
| |||||
| MSH6 | Deleterious | 82|18 | simple_ | No | Single base exchange | Normal |
| ||||||
| MSH6 | Deleterious | 82|18 | simple_ | No | Single base exchange | Normal |
| ||||||
| MSH6 | Deleterious | 83|17 | simple_ | No | Single base exchange | Normal |
| ||||||
| MSH6 | Deleterious | 92|8 | simple_ | No | Single base exchange | Normal |
| ||||||
| MSH6 | Deleterious | 92|8 | simple_ | No | Single base exchange | Normal |
| ||||||
| MSH6 | Deleterious | 94|6 | simple_ | No | Single base exchange | Normal |
| ||||||
| MSH6 | Deleterious | 95|5 | simple_ | No | Single base exchange | Normal |
| ||||||
| MSH6 | Deleterious | 96|4 | simple_ | No | Single base exchange | Normal |
| ||||||
| FBXO11 | Deleterious | 177|23 | without_ | No | Single base exchange | N/A | |||||||
| MSH6 | Benign | 85|115 | without_ | No | Single base exchange | N/A |
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | ||||||||||||||||
| Gene symbol | MSH6 | ||||||||||||||||
| Gene constraints | LOEUF: 0.84, LOF (oe): 0.70, misssense (oe): 1.25, synonymous (oe): 1.35 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000234420.11 | ||||||||||||||||
| Genbank transcript ID | NM_000179 (exact from MANE), NM_001406809 (by similarity), NM_001406796 (by similarity), NM_001406795 (by similarity), NM_001406802 (by similarity), NM_001406813 (by similarity), NM_001406808 (by similarity), NM_001406800 (by similarity), NM_001406798 (by similarity), NM_001406803 (by similarity), NM_001407362 (by similarity), NM_001406804 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | MSH6_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.1637A>C g.104091A>C | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 2 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Wildtype AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS EPEEEEEMEV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYSKYLL SLKEKEEDSS GHTRAYGVCF VDTSLGKFFI GQFSDDRHCS RFRTLVAHYP PVQVLFEKGN LSKETKTILK SSLSCSLQEG LIPGSQFWDA SKTLRTLLEE EYFREKLSDG IGVMLPQVLK GMTSESDSIG LTPGEKSELA LSALGGCVFY LKKCLIDQEL LSMANFEEYI PLDSDTVSTT RSGAIFTKAY QRMVLDAVTL NNLEIFLNGT NGSTEGTLLE RVDTCHTPFG KRLLKQWLCA PLCNHYAIND RLDAIEDLMV VPDKISEVVE LLKKLPDLER LLSKIHNVGS PLKSQNHPDS RAIMYEETTY SKKKIIDFLS ALEGFKVMCK IIGIMEEVAD GFKSKILKQV ISLQTKNPEG RFPDLTVELN RWDTAFDHEK ARKTGLITPK AGFDSDYDQA LADIRENEQS LLEYLEKQRN RIGCRTIVYW GIGRNRYQLE IPENFTTRNL PEEYELKSTK KGCKRYWTKT IEKKLANLIN AEERRDVSLK DCMRRLFYNF DKNYKDWQSA VECIAVLDVL LCLANYSRGG DGPMCRPVIL LPEDTPPFLE LKGSRHPCIT KTFFGDDFIP NDILIGCEEE EQENGKAYCV LVTGPNMGGK STLMRQAGLL AVMAQMGCYV PAEVCRLTPI DRVFTRLGAS DRIMSGESTF FVELSETASI LMHATAHSLV LVDELGRGTA TFDGTAIANA VVKELAETIK CRTLFSTHYH SLVEDYSQNV AVRLGHMACM VENECEDPSQ ETITFLYKFI KGACPKSYGF NAARLANLPE EVIQKGHRKA REFEKMNQSL RLFREVCLAS ERSTVDAEAV HKLLTLIKEL * | ||||||||||||||||
| Mutated AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS EPEEEEEMEV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYSKYLL SLKEKAEDSS GHTRAYGVCF VDTSLGKFFI GQFSDDRHCS RFRTLVAHYP PVQVLFEKGN LSKETKTILK SSLSCSLQEG LIPGSQFWDA SKTLRTLLEE EYFREKLSDG IGVMLPQVLK GMTSESDSIG LTPGEKSELA LSALGGCVFY LKKCLIDQEL LSMANFEEYI PLDSDTVSTT RSGAIFTKAY QRMVLDAVTL NNLEIFLNGT NGSTEGTLLE RVDTCHTPFG KRLLKQWLCA PLCNHYAIND RLDAIEDLMV VPDKISEVVE LLKKLPDLER LLSKIHNVGS PLKSQNHPDS RAIMYEETTY SKKKIIDFLS ALEGFKVMCK IIGIMEEVAD GFKSKILKQV ISLQTKNPEG RFPDLTVELN RWDTAFDHEK ARKTGLITPK AGFDSDYDQA LADIRENEQS LLEYLEKQRN RIGCRTIVYW GIGRNRYQLE IPENFTTRNL PEEYELKSTK KGCKRYWTKT IEKKLANLIN AEERRDVSLK DCMRRLFYNF DKNYKDWQSA VECIAVLDVL LCLANYSRGG DGPMCRPVIL LPEDTPPFLE LKGSRHPCIT KTFFGDDFIP NDILIGCEEE EQENGKAYCV LVTGPNMGGK STLMRQAGLL AVMAQMGCYV PAEVCRLTPI DRVFTRLGAS DRIMSGESTF FVELSETASI LMHATAHSLV LVDELGRGTA TFDGTAIANA VVKELAETIK CRTLFSTHYH SLVEDYSQNV AVRLGHMACM VENECEDPSQ ETITFLYKFI KGACPKSYGF NAARLANLPE EVIQKGHRKA REFEKMNQSL RLFREVCLAS ERSTVDAEAV HKLLTLIKEL * | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 4083 / 4083 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1361 / 1361 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 4172 / 4172 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 90 / 90 | ||||||||||||||||
| Last intron/exon boundary | 4090 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 3950 | ||||||||||||||||
| Length of CDS | 4083 | ||||||||||||||||
| Coding sequence (CDS) position | 1637 | ||||||||||||||||
| cDNA position | 1726 | ||||||||||||||||
| gDNA position | 104091 | ||||||||||||||||
| Chromosomal position | 47799620 | ||||||||||||||||
| Speed | 0.09 s | ||||||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | LOEUF: 0.83, LOF (oe): 0.68, misssense (oe): 1.23, synonymous (oe): 1.36 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000652107.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1340A>C g.104091A>C | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Wildtype AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKEEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Mutated AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKAEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 3786 / 3786 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1262 / 1262 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 4466 / 4466 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 681 / 681 | |||||||||||||
| Last intron/exon boundary | 4384 | |||||||||||||
| Theoretical NMD boundary in CDS | 3653 | |||||||||||||
| Length of CDS | 3786 | |||||||||||||
| Coding sequence (CDS) position | 1340 | |||||||||||||
| cDNA position | 2020 | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.12 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | LOEUF: 0.83, LOF (oe): 0.68, misssense (oe): 1.23, synonymous (oe): 1.36 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000673637.1 | |||||||||||||
| Genbank transcript ID | NM_001406805 (by similarity), NM_001406807 (by similarity), NM_001406799 (by similarity), NM_001406797 (by similarity), NM_001406801 (by similarity), NM_001406806 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1340A>C g.104091A>C | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Wildtype AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKEEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Mutated AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKAEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 3786 / 3786 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1262 / 1262 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 3904 / 3904 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 119 / 119 | |||||||||||||
| Last intron/exon boundary | 3822 | |||||||||||||
| Theoretical NMD boundary in CDS | 3653 | |||||||||||||
| Length of CDS | 3786 | |||||||||||||
| Coding sequence (CDS) position | 1340 | |||||||||||||
| cDNA position | 1458 | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.12 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | ||||||||||||||||
| Gene symbol | MSH6 | ||||||||||||||||
| Gene constraints | LOEUF: 0.83, LOF (oe): 0.68, misssense (oe): 1.27, synonymous (oe): 1.36 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000540021.6 | ||||||||||||||||
| Genbank transcript ID | NM_001406811 (by similarity), NM_001406814 (by similarity), NM_001281493 (by similarity), NM_001406812 (by similarity), NM_001406816 (by similarity), NM_001281492 (by similarity), NM_001406815 (by similarity), NM_001406829 (by similarity), NM_001406823 (by similarity), NM_001281494 (by similarity), NM_001406832 (by similarity), NM_001406831 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | MSH6_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.1247A>C g.104091A>C | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 2 | ||||||||||||||||
| Strand | 1 | ||||||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | ||||||||||||||||
| Wildtype AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYSKYLL SLKEKEEDSS GHTRAYGVCF VDTSLGKFFI GQFSDDRHCS RFRTLVAHYP PVQVLFEKGN LSKETKTILK SSLSCSLQEG LIPGSQFWDA SKTLRTLLEE EYFREKLSDG IGVMLPQVLK GMTSESDSIG LTPGEKSELA LSALGGCVFY LKKCLIDQEL LSMANFEEYI PLDSDTVSTT RSGAIFTKAY QRMVLDAVTL NNLEIFLNGT NGSTEGTLLE RVDTCHTPFG KRLLKQWLCA PLCNHYAIND RLDAIEDLMV VPDKISEVVE LLKKLPDLER LLSKIHNVGS PLKSQNHPDS RAIMYEETTY SKKKIIDFLS ALEGFKVMCK IIGIMEEVAD GFKSKILKQV ISLQTKNPEG RFPDLTVELN RWDTAFDHEK ARKTGLITPK AGFDSDYDQA LADIRENEQS LLEYLEKQRN RIGCRTIVYW GIGRNRYQLE IPENFTTRNL PEEYELKSTK KGCKRYWTKT IEKKLANLIN AEERRDVSLK DCMRRLFYNF DKNYKDWQSA VECIAVLDVL LCLANYSRGG DGPMCRPVIL LPEDTPPFLE LKGSRHPCIT KTFFGDDFIP NDILIGCEEE EQENGKAYCV LVTGPNMGGK STLMRQAGLL AVMAQMGCYV PAEVCRLTPI DRVFTRLGAS DRIMSGESTF FVELSETASI LMHATAHSLV LVDELGRGTA TFDGTAIANA VVKELAETIK CRTLFSTHYH SLVEDYSQNV AVRLGHMACM VENECEDPSQ ETITFLYKFI KGACPKSYGF NAARLANLPE EVIQKGHRKA REFEKMNQSL RLFREVCLAS ERSTVDAEAV HKLLTLIKEL * | ||||||||||||||||
| Mutated AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYSKYLL SLKEKAEDSS GHTRAYGVCF VDTSLGKFFI GQFSDDRHCS RFRTLVAHYP PVQVLFEKGN LSKETKTILK SSLSCSLQEG LIPGSQFWDA SKTLRTLLEE EYFREKLSDG IGVMLPQVLK GMTSESDSIG LTPGEKSELA LSALGGCVFY LKKCLIDQEL LSMANFEEYI PLDSDTVSTT RSGAIFTKAY QRMVLDAVTL NNLEIFLNGT NGSTEGTLLE RVDTCHTPFG KRLLKQWLCA PLCNHYAIND RLDAIEDLMV VPDKISEVVE LLKKLPDLER LLSKIHNVGS PLKSQNHPDS RAIMYEETTY SKKKIIDFLS ALEGFKVMCK IIGIMEEVAD GFKSKILKQV ISLQTKNPEG RFPDLTVELN RWDTAFDHEK ARKTGLITPK AGFDSDYDQA LADIRENEQS LLEYLEKQRN RIGCRTIVYW GIGRNRYQLE IPENFTTRNL PEEYELKSTK KGCKRYWTKT IEKKLANLIN AEERRDVSLK DCMRRLFYNF DKNYKDWQSA VECIAVLDVL LCLANYSRGG DGPMCRPVIL LPEDTPPFLE LKGSRHPCIT KTFFGDDFIP NDILIGCEEE EQENGKAYCV LVTGPNMGGK STLMRQAGLL AVMAQMGCYV PAEVCRLTPI DRVFTRLGAS DRIMSGESTF FVELSETASI LMHATAHSLV LVDELGRGTA TFDGTAIANA VVKELAETIK CRTLFSTHYH SLVEDYSQNV AVRLGHMACM VENECEDPSQ ETITFLYKFI KGACPKSYGF NAARLANLPE EVIQKGHRKA REFEKMNQSL RLFREVCLAS ERSTVDAEAV HKLLTLIKEL * | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 3693 / 3693 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1231 / 1231 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3744 / 3744 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 52 / 52 | ||||||||||||||||
| Last intron/exon boundary | 3662 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 3560 | ||||||||||||||||
| Length of CDS | 3693 | ||||||||||||||||
| Coding sequence (CDS) position | 1247 | ||||||||||||||||
| cDNA position | 1298 | ||||||||||||||||
| gDNA position | 104091 | ||||||||||||||||
| Chromosomal position | 47799620 | ||||||||||||||||
| 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 | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | no data | |||||||||||||
| Ensembl transcript ID | ENST00000700004.2 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1637A>C g.104091A>C | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Wildtype AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS EPEEEEEMEV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYSKYLL SLKEKEEDSS GHTRAYGVCF VDTSLGKFFI GQFSDDRHCS RFRTLVAHYP PVQVLFEKGN LSKETKTILK SSLSCSLQEG LIPGSQFWDA SKTLRTLLEE EYFREKLSDG IGVMLPQVLK GMTSESDSIG LTPGEKSELA LSALGGCVFY LKKCLIDQEL LSMANFEEYI PLDSDTVSTT RSGAIFTKAY QRMVLDAVTL NNLEIFLNGT NGSTEGTLLE RVDTCHTPFG KRLLKQWLCA PLCNHYAIND RLDAIEDLMV VPDKISEVVE LLKKLPDLER LLSKIHNVGS PLKSQNHPDS RAIMYEETTY SKKKIIDFLS ALEGFKVMCK IIGIMEEVAD GFKSKILKQV ISLQTKNPEG RFPDLTVELN RWDTAFDHEK ARKTGLITPK AGFDSDYDQA LADIRENEQS LLEYLEKQRN RIGCRTIVYW GIGRNRYQLE IPENFTTRNL PEEYELKSTK KGCKRYWTKT IEKKLANLIN AEERRDVSLK DCMRRLFYNF DKNYKDWQSA VECIAVLGES TFFVELSETA SILMHATAHS LVLVDELGRG TATFDGTAIA NAVVKELAET IKCRTLFSTH YHSLVEDYSQ NVAVRLGHMA CMVENECEDP SQETITFLYK FIKGACPKSY GFNAARLANL PEEVIQKGHR KAREFEKMNQ SLRLFREVCL ASERSTVDAE AVHKLLTLIK EL* | |||||||||||||
| Mutated AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS EPEEEEEMEV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYSKYLL SLKEKAEDSS GHTRAYGVCF VDTSLGKFFI GQFSDDRHCS RFRTLVAHYP PVQVLFEKGN LSKETKTILK SSLSCSLQEG LIPGSQFWDA SKTLRTLLEE EYFREKLSDG IGVMLPQVLK GMTSESDSIG LTPGEKSELA LSALGGCVFY LKKCLIDQEL LSMANFEEYI PLDSDTVSTT RSGAIFTKAY QRMVLDAVTL NNLEIFLNGT NGSTEGTLLE RVDTCHTPFG KRLLKQWLCA PLCNHYAIND RLDAIEDLMV VPDKISEVVE LLKKLPDLER LLSKIHNVGS PLKSQNHPDS RAIMYEETTY SKKKIIDFLS ALEGFKVMCK IIGIMEEVAD GFKSKILKQV ISLQTKNPEG RFPDLTVELN RWDTAFDHEK ARKTGLITPK AGFDSDYDQA LADIRENEQS LLEYLEKQRN RIGCRTIVYW GIGRNRYQLE IPENFTTRNL PEEYELKSTK KGCKRYWTKT IEKKLANLIN AEERRDVSLK DCMRRLFYNF DKNYKDWQSA VECIAVLGES TFFVELSETA SILMHATAHS LVLVDELGRG TATFDGTAIA NAVVKELAET IKCRTLFSTH YHSLVEDYSQ NVAVRLGHMA CMVENECEDP SQETITFLYK FIKGACPKSY GFNAARLANL PEEVIQKGHR KAREFEKMNQ SLRLFREVCL ASERSTVDAE AVHKLLTLIK EL* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 3699 / 3699 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1233 / 1233 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 3783 / 3783 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 85 / 85 | |||||||||||||
| Last intron/exon boundary | 3701 | |||||||||||||
| Theoretical NMD boundary in CDS | 3566 | |||||||||||||
| Length of CDS | 3699 | |||||||||||||
| Coding sequence (CDS) position | 1637 | |||||||||||||
| cDNA position | 1721 | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.08 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | no data | |||||||||||||
| Ensembl transcript ID | ENST00000700002.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1643A>C g.104091A>C | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Wildtype AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS EPEEEEEMEV GHGTTYVTDK SEEDNEIESE EEVQPKTQGS RRSSRQIKKR RVISDSESDI GGSDVEFKPD TKEEGSSDEI SSGVGDSESE GLNSPVKVAR KRKRMVTGNG SLKRKSSRKE TPSATKQATS ISSETKNTLR AFSAPQNSES QAHVSGGGDD SSRPTVWYHE TLEWLKEEKR RDEHRRRPDH PDFDASTLYV PEDFLNSCTP GMRKWWQIKS QNFDLVICYK VGKFYELYHM DALIGVSELG LVFMKGNWAH SGFPEIAFGR YSDSLVQKGY KVARVEQTET PEMMEARCRK MAHISKYDRV VRREICRIIT KGTQTYSVLE GDPSENYSKY LLSLKEKEED SSGHTRAYGV CFVDTSLGKF FIGQFSDDRH CSRFRTLVAH YPPVQVLFEK GNLSKETKTI LKSSLSCSLQ EGLIPGSQFW DASKTLRTLL EEEYFREKLS DGIGVMLPQV LKGMTSESDS IGLTPGEKSE LALSALGGCV FYLKKCLIDQ ELLSMANFEE YIPLDSDTVS TTRSGAIFTK AYQRMVLDAV TLNNLEIFLN GTNGSTEGTL LERVDTCHTP FGKRLLKQWL CAPLCNHYAI NDRLDAIEDL MVVPDKISEV VELLKKLPDL ERLLSKIHNV GSPLKSQNHP DSRAIMYEET TYSKKKIIDF LSALEGFKVM CKIIGIMEEV ADGFKSKILK QVISLQTKNP EGRFPDLTVE LNRWDTAFDH EKARKTGLIT PKAGFDSDYD QALADIRENE QSLLEYLEKQ RNRIGCRTIV YWGIGRNRYQ LEIPENFTTR NLPEEYELKS TKKGCKRYWT KTIEKKLANL INAEERRDVS LKDCMRRLFY NFDKNYKDWQ SAVECIAVLD VLLCLANYSR GGDGPMCRPV ILLPEDTPPF LELKGSRHPC ITKTFFGDDF IPNDILIGCE EEEQENGKAY CVLVTGPNMG GKSTLMRQAG LLAVMAQMGC YVPAEVCRLT PIDRVFTRLG ASDRIMSGES TFFVELSETA SILMHATAHS LVLVDELGRG TATFDGTAIA NAVVKELAET IKCRTLFSTH YHSLVEDYSQ NVAVRLGHMA CMVENECEDP SQETITFLYK FIKGACPKSY GFNAARLANL PEEVIQKGHR KAREFEKMNQ SLRLFREVCL ASERSTVDAE AVHKLLTLIK EL* | |||||||||||||
| Mutated AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS EPEEEEEMEV GHGTTYVTDK SEEDNEIESE EEVQPKTQGS RRSSRQIKKR RVISDSESDI GGSDVEFKPD TKEEGSSDEI SSGVGDSESE GLNSPVKVAR KRKRMVTGNG SLKRKSSRKE TPSATKQATS ISSETKNTLR AFSAPQNSES QAHVSGGGDD SSRPTVWYHE TLEWLKEEKR RDEHRRRPDH PDFDASTLYV PEDFLNSCTP GMRKWWQIKS QNFDLVICYK VGKFYELYHM DALIGVSELG LVFMKGNWAH SGFPEIAFGR YSDSLVQKGY KVARVEQTET PEMMEARCRK MAHISKYDRV VRREICRIIT KGTQTYSVLE GDPSENYSKY LLSLKEKAED SSGHTRAYGV CFVDTSLGKF FIGQFSDDRH CSRFRTLVAH YPPVQVLFEK GNLSKETKTI LKSSLSCSLQ EGLIPGSQFW DASKTLRTLL EEEYFREKLS DGIGVMLPQV LKGMTSESDS IGLTPGEKSE LALSALGGCV FYLKKCLIDQ ELLSMANFEE YIPLDSDTVS TTRSGAIFTK AYQRMVLDAV TLNNLEIFLN GTNGSTEGTL LERVDTCHTP FGKRLLKQWL CAPLCNHYAI NDRLDAIEDL MVVPDKISEV VELLKKLPDL ERLLSKIHNV GSPLKSQNHP DSRAIMYEET TYSKKKIIDF LSALEGFKVM CKIIGIMEEV ADGFKSKILK QVISLQTKNP EGRFPDLTVE LNRWDTAFDH EKARKTGLIT PKAGFDSDYD QALADIRENE QSLLEYLEKQ RNRIGCRTIV YWGIGRNRYQ LEIPENFTTR NLPEEYELKS TKKGCKRYWT KTIEKKLANL INAEERRDVS LKDCMRRLFY NFDKNYKDWQ SAVECIAVLD VLLCLANYSR GGDGPMCRPV ILLPEDTPPF LELKGSRHPC ITKTFFGDDF IPNDILIGCE EEEQENGKAY CVLVTGPNMG GKSTLMRQAG LLAVMAQMGC YVPAEVCRLT PIDRVFTRLG ASDRIMSGES TFFVELSETA SILMHATAHS LVLVDELGRG TATFDGTAIA NAVVKELAET IKCRTLFSTH YHSLVEDYSQ NVAVRLGHMA CMVENECEDP SQETITFLYK FIKGACPKSY GFNAARLANL PEEVIQKGHR KAREFEKMNQ SLRLFREVCL ASERSTVDAE AVHKLLTLIK EL* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 4089 / 4089 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1363 / 1363 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 4161 / 4161 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 73 / 73 | |||||||||||||
| Last intron/exon boundary | 4079 | |||||||||||||
| Theoretical NMD boundary in CDS | 3956 | |||||||||||||
| Length of CDS | 4089 | |||||||||||||
| Coding sequence (CDS) position | 1643 | |||||||||||||
| cDNA position | 1715 | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.08 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | LOEUF: 1.10, LOF (oe): 0.72, misssense (oe): 1.07, synonymous (oe): 1.14 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000411819.2 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1340A>C g.104091A>C | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Wildtype AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKEEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Mutated AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKAEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 3786 / 3786 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1262 / 1262 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 3881 / 3881 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 96 / 96 | |||||||||||||
| Last intron/exon boundary | 3799 | |||||||||||||
| Theoretical NMD boundary in CDS | 3653 | |||||||||||||
| Length of CDS | 3786 | |||||||||||||
| Coding sequence (CDS) position | 1340 | |||||||||||||
| cDNA position | 1435 | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.12 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | LOEUF: 1.34, LOF (oe): 0.77, misssense (oe): 0.99, synonymous (oe): 1.20 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000420813.6 | |||||||||||||
| Genbank transcript ID | NM_001406821 (by similarity), NM_001406828 (by similarity), NM_001406826 (by similarity), NM_001406825 (by similarity), NM_001406819 (by similarity), NM_001406822 (by similarity), NM_001406827 (by similarity), NM_001406824 (by similarity), NM_001406820 (by similarity), NM_001406830 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1340A>C g.104091A>C | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Wildtype AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKEEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Mutated AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKAEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 3786 / 3786 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1262 / 1262 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 4013 / 4013 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 228 / 228 | |||||||||||||
| Last intron/exon boundary | 3931 | |||||||||||||
| Theoretical NMD boundary in CDS | 3653 | |||||||||||||
| Length of CDS | 3786 | |||||||||||||
| Coding sequence (CDS) position | 1340 | |||||||||||||
| cDNA position | 1567 | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.11 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | LOEUF: 1.21, LOF (oe): 0.75, misssense (oe): 1.02, synonymous (oe): 1.21 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000455383.6 | |||||||||||||
| Genbank transcript ID | NM_001406818 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1340A>C g.104091A>C | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered cDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Wildtype AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKEEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Mutated AA sequence | MEGYPWWPCL VYNHPFDGTF IREKGKSVRV HVQFFDDSPT RGWVSKRLLK PYTGSKSKEA QKGGHFYSAK PEILRAMQRA DEALNKDKIK RLELAVCDEP SEPEEEEEME VGTTYVTDKS EEDNEIESEE EVQPKTQGSR RSSRQIKKRR VISDSESDIG GSDVEFKPDT KEEGSSDEIS SGVGDSESEG LNSPVKVARK RKRMVTGNGS LKRKSSRKET PSATKQATSI SSETKNTLRA FSAPQNSESQ AHVSGGGDDS SRPTVWYHET LEWLKEEKRR DEHRRRPDHP DFDASTLYVP EDFLNSCTPG MRKWWQIKSQ NFDLVICYKV GKFYELYHMD ALIGVSELGL VFMKGNWAHS GFPEIAFGRY SDSLVQKGYK VARVEQTETP EMMEARCRKM AHISKYDRVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKAEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLVAHY PPVQVLFEKG NLSKETKTIL KSSLSCSLQE GLIPGSQFWD ASKTLRTLLE EEYFREKLSD GIGVMLPQVL KGMTSESDSI GLTPGEKSEL ALSALGGCVF YLKKCLIDQE LLSMANFEEY IPLDSDTVST TRSGAIFTKA YQRMVLDAVT LNNLEIFLNG TNGSTEGTLL ERVDTCHTPF GKRLLKQWLC APLCNHYAIN DRLDAIEDLM VVPDKISEVV ELLKKLPDLE RLLSKIHNVG SPLKSQNHPD SRAIMYEETT YSKKKIIDFL SALEGFKVMC KIIGIMEEVA DGFKSKILKQ VISLQTKNPE GRFPDLTVEL NRWDTAFDHE KARKTGLITP KAGFDSDYDQ ALADIRENEQ SLLEYLEKQR NRIGCRTIVY WGIGRNRYQL EIPENFTTRN LPEEYELKST KKGCKRYWTK TIEKKLANLI NAEERRDVSL KDCMRRLFYN FDKNYKDWQS AVECIAVLDV LLCLANYSRG GDGPMCRPVI LLPEDTPPFL ELKGSRHPCI TKTFFGDDFI PNDILIGCEE EEQENGKAYC VLVTGPNMGG KSTLMRQAGL LAVMAQMGCY VPAEVCRLTP IDRVFTRLGA SDRIMSGEST FFVELSETAS ILMHATAHSL VLVDELGRGT ATFDGTAIAN AVVKELAETI KCRTLFSTHY HSLVEDYSQN VAVRLGHMAC MVENECEDPS QETITFLYKF IKGACPKSYG FNAARLANLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 3786 / 3786 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1262 / 1262 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 4017 / 4017 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 232 / 232 | |||||||||||||
| Last intron/exon boundary | 3935 | |||||||||||||
| Theoretical NMD boundary in CDS | 3653 | |||||||||||||
| Length of CDS | 3786 | |||||||||||||
| Coding sequence (CDS) position | 1340 | |||||||||||||
| cDNA position | 1571 | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.12 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | FBXO11 | |||||||||||||
| Gene constraints | LOEUF: 0.41, LOF (oe): 0.00, misssense (oe): 0.47, synonymous (oe): 1.25 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000405808.5 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.169+8575T>G g.106879T>G | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | TATGGCCAGAAGAATCTTCCTCTTTTTCTTTGAGGCTAAGA | |||||||||||||
| Altered gDNA sequence snippet | TATGGCCAGAAGAATCTTCCGCTTTTTCTTTGAGGCTAAGA | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MHDFYRCHTC NTTDRNAICV NCIKKCHQGH DVEFIRHDRF FCDCGAGTLS NPCTLAG* | |||||||||||||
| Mutated AA sequence | ||||||||||||||
| Position of stopcodon in wt / mu CDS | N/A | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | N/A | |||||||||||||
| Position of stopcodon in wt / mu cDNA | N/A | |||||||||||||
| Position of start ATG in wt / mu cDNA | 12 / 12 | |||||||||||||
| Last intron/exon boundary | 180 | |||||||||||||
| Theoretical NMD boundary in CDS | 118 | |||||||||||||
| Length of CDS | 174 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 106879 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.08 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr2:47799620A>C (GRCh38) | |||||||||||||
| Gene symbol | MSH6 | |||||||||||||
| Gene constraints | no data | |||||||||||||
| Ensembl transcript ID | ENST00000700000.1 | |||||||||||||
| Genbank transcript ID | NM_001406817 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.1606+31A>C g.104091A>C | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 2 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGAGGAAGATTCTTCTGGCCATA | |||||||||||||
| Altered gDNA sequence snippet | TCTTAGCCTCAAAGAAAAAGCGGAAGATTCTTCTGGCCATA | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS EPEEEEEMEV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYNVLLC LANYSRGGDG PMCRPVILLP EDTPPFLELK GSRHPCITKT FFGDDFIPND ILIGCEEEEQ ENGKAYCVLV TGPNMGGKST LMRQAGLLAV MAQMGCYVPA EVCRLTPIDR VFTRLGASDR IMSGESTFFV ELSETASILM HATAHSLVLV DELGRGTATF DGTAIANAVV KELAETIKCR TLFSTHYHSL VEDYSQNVAV RLGHMACMVE NECEDPSQET ITFLYKFIKG ACPKSYGFNA ARLANLPEEV IQKGHRKARE FEKMNQSLRL FREVCLASER STVDAEAVHK LLTLIKEL* | |||||||||||||
| Mutated AA sequence | ||||||||||||||
| Position of stopcodon in wt / mu CDS | N/A | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | N/A | |||||||||||||
| Position of stopcodon in wt / mu cDNA | N/A | |||||||||||||
| Position of start ATG in wt / mu cDNA | 84 / 84 | |||||||||||||
| Last intron/exon boundary | 2518 | |||||||||||||
| Theoretical NMD boundary in CDS | 2384 | |||||||||||||
| Length of CDS | 2517 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 104091 | |||||||||||||
| Chromosomal position | 47799620 | |||||||||||||
| Speed | 0.02 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project