| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000645818(MANE Select) | SPG7 | Deleterious | 74|26 | simple_ | No | Yes | Single base exchange | Normal |
| ||||
| SPG7 | Deleterious | 76|24 | simple_ | No | Yes | Single base exchange | Normal |
| |||||
| SPG7 | Deleterious | 79|21 | simple_ | No | Yes | Single base exchange | Normal |
| |||||
| SPG7 | Deleterious | 79|21 | simple_ | No | Yes | Single base exchange | Normal |
| |||||
| SPG7 | Deleterious | 80|20 | simple_ | No | Yes | Single base exchange | Normal |
| |||||
| SPG7 | Deleterious | 80|20 | simple_ | No | Yes | Single base exchange | Normal |
| |||||
| SPG7 | Deleterious | 80|20 | simple_ | No | Yes | Single base exchange | Normal |
| |||||
| SPG7 | Deleterious | 80|20 | simple_ | No | Yes | Single base exchange | Normal |
| |||||
| SPG7 | Deleterious | 81|19 | simple_ | No | Yes | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr16:89546737C>T (GRCh38) | |||||||||||||||||||||
| Gene symbol | SPG7 | |||||||||||||||||||||
| Gene constraints | LOEUF: 1.55, LOF (oe): 1.30, misssense (oe): 1.12, synonymous (oe): 1.17 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000645818.2 | |||||||||||||||||||||
| Genbank transcript ID | NM_003119 (exact from MANE) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | SPG7_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.1529C>T g.56019C>T | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| Phylogenetic conservation |
| |||||||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||||||||||
| Distance from splice site | 24 | |||||||||||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||||||||||
| poly(A) signal | N/A | |||||||||||||||||||||
| AA sequence altered | Yes | |||||||||||||||||||||
| Chromosome | 16 | |||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||||||||||
| Wildtype AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLA ELTPGFSGAD IANICNEAAL HAAREGHTSV HTLNFEYAVE RVLAGTAKKS KILSKEEQKV VAFHESGHAL VGWMLEHTEA VMKVSITPRT NAALGFAQML PRDQHLFTKE QLFERMCMAL GGRASEALSF NEVTSGAQDD LRKVTRIAYS MVKQFGMAPG IGPISFPEAQ EGLMGIGRRP FSQGLQQMMD HEARLLVAKA YRHTEKVLQD NLDKLQALAN ALLEKEVINY EDIEALIGPP PHGPKKMIAP QRWIDAQREK QDLGEEETEE TQQPPLGGEE PTWPK* | |||||||||||||||||||||
| Mutated AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLV ELTPGFSGAD IANICNEAAL HAAREGHTSV HTLNFEYAVE RVLAGTAKKS KILSKEEQKV VAFHESGHAL VGWMLEHTEA VMKVSITPRT NAALGFAQML PRDQHLFTKE QLFERMCMAL GGRASEALSF NEVTSGAQDD LRKVTRIAYS MVKQFGMAPG IGPISFPEAQ EGLMGIGRRP FSQGLQQMMD HEARLLVAKA YRHTEKVLQD NLDKLQALAN ALLEKEVINY EDIEALIGPP PHGPKKMIAP QRWIDAQREK QDLGEEETEE TQQPPLGGEE PTWPK* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2388 / 2388 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 796 / 796 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2403 / 2403 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 16 / 16 | |||||||||||||||||||||
| Last intron/exon boundary | 2196 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 2130 | |||||||||||||||||||||
| Length of CDS | 2388 | |||||||||||||||||||||
| Coding sequence (CDS) position | 1529 | |||||||||||||||||||||
| cDNA position | 1544 | |||||||||||||||||||||
| gDNA position | 56019 | |||||||||||||||||||||
| Chromosomal position | 89546737 | |||||||||||||||||||||
| Speed | 0.14 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 | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.46, LOF (oe): 1.20, misssense (oe): 1.02, synonymous (oe): 1.07 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000647079.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1121C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MYRERLRTLL VIAVVMSLLN ALSTSGGSIS WNDFVHEMLA KGEVQRVQVV PESDVVEVYL HPGAVVFGRP RLALMYRMQV ANIDKFEEKL RAAEDELNIE AKDRIPVSYK RTGFFGNALY SVGMTAVGLA ILWYVFRLAG MTGREGGFSA FNQLKMARFT IVDGKMGKGV SFKDVAGMHE AKLEVREFVD YLKSPERFLQ LGAKVPKGAL LLGPPGCGKT LLAKAVATEA QVPFLAMAGP EFVEVIGGLG AARVRSLFKE ARARAPCIVY IDEIDAVGKK RSTTMSGFSN TEEEQTLNQL LVEMDGMGTT DHVIVLASTN RADILDGALM RPGRLDRHVF IDLPTLQERR EIFEQHLKSL KLTQSSTFYS QRLAELTPGF SGADIANICN EAALHAAREG HTSVHTLNFE YAVERVLAGT AKKSKILSKE EQKVVAFHES GHALVGWMLE HTEAVMKVSI TPRTNAALGF AQMLPRDQHL FTKEQLFERM CMALGGRASE ALSFNEVTSG AQDDLRKVTR IAYSMVKQFG MAPGIGPISF PEAQEGLMGI GRRPFSQGLQ QMMDHEARLL VAKAYRHTEK VLQDNLDKLQ ALANALLEKE VINYEDIEAL IGPPPHGPKK MIAPQRWIDA QREKQDLGEE ETEETQQPPL GGEEPTWPK* | |||||||||||||
| Mutated AA sequence | MYRERLRTLL VIAVVMSLLN ALSTSGGSIS WNDFVHEMLA KGEVQRVQVV PESDVVEVYL HPGAVVFGRP RLALMYRMQV ANIDKFEEKL RAAEDELNIE AKDRIPVSYK RTGFFGNALY SVGMTAVGLA ILWYVFRLAG MTGREGGFSA FNQLKMARFT IVDGKMGKGV SFKDVAGMHE AKLEVREFVD YLKSPERFLQ LGAKVPKGAL LLGPPGCGKT LLAKAVATEA QVPFLAMAGP EFVEVIGGLG AARVRSLFKE ARARAPCIVY IDEIDAVGKK RSTTMSGFSN TEEEQTLNQL LVEMDGMGTT DHVIVLASTN RADILDGALM RPGRLDRHVF IDLPTLQERR EIFEQHLKSL KLTQSSTFYS QRLVELTPGF SGADIANICN EAALHAAREG HTSVHTLNFE YAVERVLAGT AKKSKILSKE EQKVVAFHES GHALVGWMLE HTEAVMKVSI TPRTNAALGF AQMLPRDQHL FTKEQLFERM CMALGGRASE ALSFNEVTSG AQDDLRKVTR IAYSMVKQFG MAPGIGPISF PEAQEGLMGI GRRPFSQGLQ QMMDHEARLL VAKAYRHTEK VLQDNLDKLQ ALANALLEKE VINYEDIEAL IGPPPHGPKK MIAPQRWIDA QREKQDLGEE ETEETQQPPL GGEEPTWPK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1980 / 1980 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 660 / 660 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2675 / 2675 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 696 / 696 | |||||||||||||
| Last intron/exon boundary | 2468 | |||||||||||||
| Theoretical NMD boundary in CDS | 1722 | |||||||||||||
| Length of CDS | 1980 | |||||||||||||
| Coding sequence (CDS) position | 1121 | |||||||||||||
| cDNA position | 1816 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| 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 | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.62, LOF (oe): 1.34, misssense (oe): 1.17, synonymous (oe): 1.21 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000645897.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1067C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKE RREIFEQHLK SLKLTQSSTF YSQRLAELTP GFSGADIANI CNEAALHAAR EGHTSVHTLN FEYAVERVLA GTAKKSKILS KEEQKVVAFH ESGHALVGWM LEHTEAVMKV SITPRTNAAL GFAQMLPRDQ HLFTKEQLFE RMCMALGGRA SEALSFNEVT SGAQDDLRKV TRIAYSMVKQ FGMAPGIGPI SFPEAQEGLM GIGRRPFSQG LQQMMDHEAR LLVAKAYRHT EKVLQDNLDK LQALANALLE KEVINYEDIE ALIGPPPHGP KKMIAPQRWI DAQREKQDLG EEETEETQQP PLGGEEPTWP K* | |||||||||||||
| Mutated AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKE RREIFEQHLK SLKLTQSSTF YSQRLVELTP GFSGADIANI CNEAALHAAR EGHTSVHTLN FEYAVERVLA GTAKKSKILS KEEQKVVAFH ESGHALVGWM LEHTEAVMKV SITPRTNAAL GFAQMLPRDQ HLFTKEQLFE RMCMALGGRA SEALSFNEVT SGAQDDLRKV TRIAYSMVKQ FGMAPGIGPI SFPEAQEGLM GIGRRPFSQG LQQMMDHEAR LLVAKAYRHT EKVLQDNLDK LQALANALLE KEVINYEDIE ALIGPPPHGP KKMIAPQRWI DAQREKQDLG EEETEETQQP PLGGEEPTWP K* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1926 / 1926 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 642 / 642 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 1947 / 1947 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 22 / 22 | |||||||||||||
| Last intron/exon boundary | 1740 | |||||||||||||
| Theoretical NMD boundary in CDS | 1668 | |||||||||||||
| Length of CDS | 1926 | |||||||||||||
| Coding sequence (CDS) position | 1067 | |||||||||||||
| cDNA position | 1088 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| Speed | 0.13 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 | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.54, LOF (oe): 1.30, misssense (oe): 1.12, synonymous (oe): 1.17 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000268704.7 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1508C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKL GAKVPKGALL LGPPGCGKTL LAKAVATEAQ VPFLAMAGPE FVEVIGGLGA ARVRSLFKEA RARAPCIVYI DEIDAVGKKR STTMSGFSNT EEEQTLNQLL VEMDGMGTTD HVIVLASTNR ADILDGALMR PGRLDRHVFI DLPTLQERRE IFEQHLKSLK LTQSSTFYSQ RLAELTPGFS GADIANICNE AALHAAREGH TSVHTLNFEY AVERVLAGTA KKSKILSKEE QKVVAFHESG HALVGWMLEH TEAVMKVSIT PRTNAALGFA QMLPRDQHLF TKEQLFERMC MALGGRASEA LSFNEVTSGA QDDLRKVTRI AYSMVKQFGM APGIGPISFP EAQEGLMGIG RRPFSQGLQQ MMDHEARLLV AKAYRHTEKV LQDNLDKLQA LANALLEKEV INYEDIEALI GPPPHGPKKM IAPQRWIDAQ REKQDLGEEE TEETQQPPLG GEEPTWPK* | |||||||||||||
| Mutated AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKL GAKVPKGALL LGPPGCGKTL LAKAVATEAQ VPFLAMAGPE FVEVIGGLGA ARVRSLFKEA RARAPCIVYI DEIDAVGKKR STTMSGFSNT EEEQTLNQLL VEMDGMGTTD HVIVLASTNR ADILDGALMR PGRLDRHVFI DLPTLQERRE IFEQHLKSLK LTQSSTFYSQ RLVELTPGFS GADIANICNE AALHAAREGH TSVHTLNFEY AVERVLAGTA KKSKILSKEE QKVVAFHESG HALVGWMLEH TEAVMKVSIT PRTNAALGFA QMLPRDQHLF TKEQLFERMC MALGGRASEA LSFNEVTSGA QDDLRKVTRI AYSMVKQFGM APGIGPISFP EAQEGLMGIG RRPFSQGLQQ MMDHEARLLV AKAYRHTEKV LQDNLDKLQA LANALLEKEV INYEDIEALI GPPPHGPKKM IAPQRWIDAQ REKQDLGEEE TEETQQPPLG GEEPTWPK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2367 / 2367 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 789 / 789 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2375 / 2375 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 9 / 9 | |||||||||||||
| Last intron/exon boundary | 2168 | |||||||||||||
| Theoretical NMD boundary in CDS | 2109 | |||||||||||||
| Length of CDS | 2367 | |||||||||||||
| Coding sequence (CDS) position | 1508 | |||||||||||||
| cDNA position | 1516 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| 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 | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.53, LOF (oe): 1.28, misssense (oe): 1.05, synonymous (oe): 1.09 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000646303.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1397C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MGSRSGRGRT EARSASESLQ LRLLTPTFEG INGLLLKQHL VQNPVRLWQL LGGTFYFNTS RLKQKNKEKD KSKGKAPEED EEERRRRERD DQMYRERLRT LLVIAVVMSL LNALSTSGGS ISWNDFVHEM LAKGEVQRVQ VVPESDVVEV YLHPGAVVFG RPRLALMYRM QVANIDKFEE KLRAAEDELN IEAKDRIPVS YKRTGFFGNA LYSVGMTAVG LAILWYVFRL AGMTGREGGF SAFNQLKMAR FTIVDGKMGK GVSFKDVAGM HEAKLEVREF VDYLKSPERF LQLGAKVPKG ALLLGPPGCG KTLLAKAVAT EAQVPFLAMA GPEFVEVIGG LGAARVRSLF KEARARAPCI VYIDEIDAVG KKRSTTMSGF SNTEEEQTLN QLLVEMDGMG TTDHVIVLAS TNRADILDGA LMRPGRLDRH VFIDLPTLQE RREIFEQHLK SLKLTQSSTF YSQRLAELTP GFSGADIANI CNEAALHAAR EGHTSVHTLN FEYAVERVLA GTAKKSKILS KEEQKVVAFH ESGHALVGWM LEHTEAVMKV SITPRTNAAL GFAQMLPRDQ HLFTKEQLFE RMCMALGGRA SEALSFNEVT SGAQDDLRKV TRIAYSMVKQ FGMAPGIGPI SFPEAQEGLM GIGRRPFSQG LQQMMDHEAR LLVAKAYRHT EKVLQDNLDK LQALANALLE KEVINYEDIE ALIGPPPHGP KKMIAPQRWI DAQREKQDLG EEETEETQQP PLGGEEPTWP K* | |||||||||||||
| Mutated AA sequence | MGSRSGRGRT EARSASESLQ LRLLTPTFEG INGLLLKQHL VQNPVRLWQL LGGTFYFNTS RLKQKNKEKD KSKGKAPEED EEERRRRERD DQMYRERLRT LLVIAVVMSL LNALSTSGGS ISWNDFVHEM LAKGEVQRVQ VVPESDVVEV YLHPGAVVFG RPRLALMYRM QVANIDKFEE KLRAAEDELN IEAKDRIPVS YKRTGFFGNA LYSVGMTAVG LAILWYVFRL AGMTGREGGF SAFNQLKMAR FTIVDGKMGK GVSFKDVAGM HEAKLEVREF VDYLKSPERF LQLGAKVPKG ALLLGPPGCG KTLLAKAVAT EAQVPFLAMA GPEFVEVIGG LGAARVRSLF KEARARAPCI VYIDEIDAVG KKRSTTMSGF SNTEEEQTLN QLLVEMDGMG TTDHVIVLAS TNRADILDGA LMRPGRLDRH VFIDLPTLQE RREIFEQHLK SLKLTQSSTF YSQRLVELTP GFSGADIANI CNEAALHAAR EGHTSVHTLN FEYAVERVLA GTAKKSKILS KEEQKVVAFH ESGHALVGWM LEHTEAVMKV SITPRTNAAL GFAQMLPRDQ HLFTKEQLFE RMCMALGGRA SEALSFNEVT SGAQDDLRKV TRIAYSMVKQ FGMAPGIGPI SFPEAQEGLM GIGRRPFSQG LQQMMDHEAR LLVAKAYRHT EKVLQDNLDK LQALANALLE KEVINYEDIE ALIGPPPHGP KKMIAPQRWI DAQREKQDLG EEETEETQQP PLGGEEPTWP K* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2256 / 2256 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 752 / 752 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2444 / 2444 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 189 / 189 | |||||||||||||
| Last intron/exon boundary | 2237 | |||||||||||||
| Theoretical NMD boundary in CDS | 1998 | |||||||||||||
| Length of CDS | 2256 | |||||||||||||
| Coding sequence (CDS) position | 1397 | |||||||||||||
| cDNA position | 1585 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| Speed | 0.05 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.55, LOF (oe): 1.30, misssense (oe): 1.13, synonymous (oe): 1.18 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000643649.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1529C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLA ELTPGFSGTA KKSKILSKEE QKVVAFHESG HALVGWMLEH TEAVMKVSIT PRTNAALGFA QMLPRDQHLF TKEQLFERMC MALGGRASEA LSFNEVTSGA QDDLRKVTRI AYSMVKQFGM APGIGPISFP EAQEGLMGIG RRPFSQGLQQ MMDHEARLLV AKAYRHTEKV LQDNLDKLQA LANALLEKEV INYEDIEALI GPPPHGPKKM IAPQRWIDAQ REKQDLGEEE TEETQQPPLG GEEPTWPK* | |||||||||||||
| Mutated AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLV ELTPGFSGTA KKSKILSKEE QKVVAFHESG HALVGWMLEH TEAVMKVSIT PRTNAALGFA QMLPRDQHLF TKEQLFERMC MALGGRASEA LSFNEVTSGA QDDLRKVTRI AYSMVKQFGM APGIGPISFP EAQEGLMGIG RRPFSQGLQQ MMDHEARLLV AKAYRHTEKV LQDNLDKLQA LANALLEKEV INYEDIEALI GPPPHGPKKM IAPQRWIDAQ REKQDLGEEE TEETQQPPLG GEEPTWPK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2277 / 2277 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 759 / 759 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2328 / 2328 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 52 / 52 | |||||||||||||
| Last intron/exon boundary | 2121 | |||||||||||||
| Theoretical NMD boundary in CDS | 2019 | |||||||||||||
| Length of CDS | 2277 | |||||||||||||
| Coding sequence (CDS) position | 1529 | |||||||||||||
| cDNA position | 1580 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| 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 | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.78, LOF (oe): 1.43, misssense (oe): 1.25, synonymous (oe): 1.20 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000646716.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.581C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEGMGTT DHVIVLASTN RADILDGALM RPGRLDRHVF IDLPTLQERR EIFEQHLKSL KLTQSSTFYS QRLAELTPGF SGADIANICN EAALHAAREG HTSVHTLNFE YAVERVLAGT AKKSKILSKE EQKVVAFHES GHALVGWMLE HTEAVMKVSI TPRTNAALGF AQMLPRDQHL FTKEQLFERM CMALGGRASE ALSFNEVTSG AQDDLRKVTR IAYSMVKQFG MAPGIGPISF PEAQEGLMGI GRRPFSQGLQ QMMDHEARLL VAKAYRHTEK VLQDNLDKLQ ARALCVTWGS CLGPLDCRPQ PAAAASGQVW AVPSPAEAGL PVDPCSSRLT KQLCRARAHH SGSHNGSKAA AGKRPSGKGS DKL* | |||||||||||||
| Mutated AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEGMGTT DHVIVLASTN RADILDGALM RPGRLDRHVF IDLPTLQERR EIFEQHLKSL KLTQSSTFYS QRLVELTPGF SGADIANICN EAALHAAREG HTSVHTLNFE YAVERVLAGT AKKSKILSKE EQKVVAFHES GHALVGWMLE HTEAVMKVSI TPRTNAALGF AQMLPRDQHL FTKEQLFERM CMALGGRASE ALSFNEVTSG AQDDLRKVTR IAYSMVKQFG MAPGIGPISF PEAQEGLMGI GRRPFSQGLQ QMMDHEARLL VAKAYRHTEK VLQDNLDKLQ ARALCVTWGS CLGPLDCRPQ PAAAASGQVW AVPSPAEAGL PVDPCSSRLT KQLCRARAHH SGSHNGSKAA AGKRPSGKGS DKL* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1482 / 1482 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 494 / 494 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 1490 / 1490 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 9 / 9 | |||||||||||||
| Last intron/exon boundary | 1449 | |||||||||||||
| Theoretical NMD boundary in CDS | 1390 | |||||||||||||
| Length of CDS | 1482 | |||||||||||||
| Coding sequence (CDS) position | 581 | |||||||||||||
| cDNA position | 589 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| Speed | 0.04 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 | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.55, LOF (oe): 1.30, misssense (oe): 1.13, synonymous (oe): 1.17 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000645063.1 | |||||||||||||
| Genbank transcript ID | NM_001363850 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1529C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLA ELTPGFSGAD IANICNEAAL HAAREGHTSV HTLNFEYAVE RVLAGTAKKS KILSKEEQKV VAFHESGHAL VGWMLEHTEA VMKVSITPRT NAALGFAQML PRDQHLFTKE QLFERMCMAL GGRASEALSF NEVTSGAQDD LRKVTRIAYS MVKQFGMAPG IGPISFPEAQ EGLMGIGRRP FSQGLQQMMD HEARLLVAKA YRHTEKVLQD NLDKLQARAL CVTWGSCLGP LDCRPQPAAA ASGQVWAVPS PAEAGLPVDP CSSRLTKQLC RARAHHSGSH NGSKAAAGKR PSGKGSDKL* | |||||||||||||
| Mutated AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLV ELTPGFSGAD IANICNEAAL HAAREGHTSV HTLNFEYAVE RVLAGTAKKS KILSKEEQKV VAFHESGHAL VGWMLEHTEA VMKVSITPRT NAALGFAQML PRDQHLFTKE QLFERMCMAL GGRASEALSF NEVTSGAQDD LRKVTRIAYS MVKQFGMAPG IGPISFPEAQ EGLMGIGRRP FSQGLQQMMD HEARLLVAKA YRHTEKVLQD NLDKLQARAL CVTWGSCLGP LDCRPQPAAA ASGQVWAVPS PAEAGLPVDP CSSRLTKQLC RARAHHSGSH NGSKAAAGKR PSGKGSDKL* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2430 / 2430 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 810 / 810 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2445 / 2445 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 16 / 16 | |||||||||||||
| Last intron/exon boundary | 2404 | |||||||||||||
| Theoretical NMD boundary in CDS | 2338 | |||||||||||||
| Length of CDS | 2430 | |||||||||||||
| Coding sequence (CDS) position | 1529 | |||||||||||||
| cDNA position | 1544 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| Speed | 0.04 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 | Chr16:89546737C>T (GRCh38) | |||||||||||||
| Gene symbol | SPG7 | |||||||||||||
| Gene constraints | LOEUF: 1.58, LOF (oe): 1.34, misssense (oe): 1.13, synonymous (oe): 1.18 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000644781.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1529C>T g.56019C>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) |
| |||||||||||||
| 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 | 24 | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 16 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered gDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Original cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGCAGAGCTGACACCAGGATTCA | |||||||||||||
| Altered cDNA sequence snippet | CTTTTACTCCCAGCGTCTGGTAGAGCTGACACCAGGATTCA | |||||||||||||
| Wildtype AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLA ELTPGFSGAD IANICNEAAL HAAREGHTSV HTLNFEYAVE RVLAGTAKKS KILSKEEQKV VAFHESGHAL VGWMLEHTEA VMKMLPRDQH LFTKEQLFER MCMALGGRAS EALSFNEVTS GAQDDLRKVT RIAYSMVKQF GMAPGIGPIS FPEAQEGLMG IGRRPFSQGL QQMMDHEARL LVAKAYRHTE KVLQDNLDKL QALANALLEK EVINYEDIEA LIGPPPHGPK KMIAPQRWID AQREKQDLGE EETEETQQPP LGGEEPTWPK * | |||||||||||||
| Mutated AA sequence | MAVLLLLLRA LRRGPGPGPR PLWGPGPAWS PGFPARPGRG RPYMASRPPG DLAEAGGRAL QSLQLRLLTP TFEGINGLLL KQHLVQNPVR LWQLLGGTFY FNTSRLKQKN KEKDKSKGKA PEEDEEERRR RERDDQMYRE RLRTLLVIAV VMSLLNALST SGGSISWNDF VHEMLAKGEV QRVQVVPESD VVEVYLHPGA VVFGRPRLAL MYRMQVANID KFEEKLRAAE DELNIEAKDR IPVSYKRTGF FGNALYSVGM TAVGLAILWY VFRLAGMTGR EGGFSAFNQL KMARFTIVDG KMGKGVSFKD VAGMHEAKLE VREFVDYLKS PERFLQLGAK VPKGALLLGP PGCGKTLLAK AVATEAQVPF LAMAGPEFVE VIGGLGAARV RSLFKEARAR APCIVYIDEI DAVGKKRSTT MSGFSNTEEE QTLNQLLVEM DGMGTTDHVI VLASTNRADI LDGALMRPGR LDRHVFIDLP TLQERREIFE QHLKSLKLTQ SSTFYSQRLV ELTPGFSGAD IANICNEAAL HAAREGHTSV HTLNFEYAVE RVLAGTAKKS KILSKEEQKV VAFHESGHAL VGWMLEHTEA VMKMLPRDQH LFTKEQLFER MCMALGGRAS EALSFNEVTS GAQDDLRKVT RIAYSMVKQF GMAPGIGPIS FPEAQEGLMG IGRRPFSQGL QQMMDHEARL LVAKAYRHTE KVLQDNLDKL QALANALLEK EVINYEDIEA LIGPPPHGPK KMIAPQRWID AQREKQDLGE EETEETQQPP LGGEEPTWPK * | |||||||||||||
| Position of stopcodon in wt / mu CDS | 2343 / 2343 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 781 / 781 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2358 / 2358 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 16 / 16 | |||||||||||||
| Last intron/exon boundary | 2151 | |||||||||||||
| Theoretical NMD boundary in CDS | 2085 | |||||||||||||
| Length of CDS | 2343 | |||||||||||||
| Coding sequence (CDS) position | 1529 | |||||||||||||
| cDNA position | 1544 | |||||||||||||
| gDNA position | 56019 | |||||||||||||
| Chromosomal position | 89546737 | |||||||||||||
| Speed | 0.04 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