| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| COL7A1 | Deleterious | 194|6 | without_ | No | Single base exchange | N/A |
| ||||||
ENST00000681320(MANE Select) | COL7A1 | Deleterious | 194|6 | without_ | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:48571280T>A (GRCh38) | |||||||||||||
| Gene symbol | COL7A1 | |||||||||||||
| Gene constraints | LOEUF: 0.69, LOF (oe): 0.63, misssense (oe): 0.83, synonymous (oe): 0.93 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000328333.12 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | CO7A1_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.7069-2A>T g.24050A>T | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | alteration within used splice site, likely to disturb normal splicing MaxEntScan:
| |||||||||||||
| Distance from splice site | 2 | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | GCTGTTTGCTGGGTTTTCTTAGGGTCAGAAAGGGGCTCCAG | |||||||||||||
| Altered gDNA sequence snippet | GCTGTTTGCTGGGTTTTCTTTGGGTCAGAAAGGGGCTCCAG | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MTLRLLVAAL CAGILAEAPR VRAQHRERVT CTRLYAADIV FLLDGSSSIG RSNFREVRSF LEGLVLPFSG AASAQGVRFA TVQYSDDPRT EFGLDALGSG GDVIRAIREL SYKGGNTRTG AAILHVADHV FLPQLARPGV PKVCILITDG KSQDLVDTAA QRLKGQGVKL FAVGIKNADP EELKRVASQP TSDFFFFVND FSILRTLLPL VSRRVCTTAG GVPVTRPPDD STSAPRDLVL SEPSSQSLRV QWTAASGPVT GYKVQYTPLT GLGQPLPSER QEVNVPAGET SVRLRGLRPL TEYQVTVIAL YANSIGEAVS GTARTTALEG PELTIQNTTA HSLLVAWRSV PGATGYRVTW RVLSGGPTQQ QELGPGQGSV LLRDLEPGTD YEVTVSTLFG RSVGPATSLM ARTDASVEQT LRPVILGPTS ILLSWNLVPE ARGYRLEWRR ETGLEPPQKV VLPSDVTRYQ LDGLQPGTEY RLTLYTLLEG HEVATPATVV PTGPELPVSP VTDLQATELP GQRVRVSWSP VPGATQYRII VRSTQGVERT LVLPGSQTAF DLDDVQAGLS YTVRVSARVG PREGSASVLT VRREPETPLA VPGLRVVVSD ATRVRVAWGP VPGASGFRIS WSTGSGPESS QTLPPDSTAT DITGLQPGTT YQVAVSVLRG REEGPAAVIV ARTDPLGPVR TVHVTQASSS SVTITWTRVP GATGYRVSWH SAHGPEKSQL VSGEATVAEL DGLEPDTEYT VHVRAHVAGV DGPPASVVVR TAPEPVGRVS RLQILNASSD VLRITWVGVT GATAYRLAWG RSEGGPMRHQ ILPGNTDSAE IRGLEGGVSY SVRVTALVGD REGTPVSIVV TTPPEAPPAL GTLHVVQRGE HSLRLRWEPV PRAQGFLLHW QPEGGQEQSR VLGPELSSYH LDGLEPATQY RVRLSVLGPA GEGPSAEVTA RTESPRVPSI ELRVVDTSID SVTLAWTPVS RASSYILSWR PLRGPGQEVP GSPQTLPGIS SSQRVTGLEP GVSYIFSLTP VLDGVRGPEA SVTQTPVCPR GLADVVFLPH ATQDNAHRAE ATRRVLERLV LALGPLGPQA VQVGLLSYSH RPSPLFPLNG SHDLGIILQR IRDMPYMDPS GNNLGTAVVT AHRYMLAPDA PGRRQHVPGV MVLLVDEPLR GDIFSPIREA QASGLNVVML GMAGADPEQL RRLAPGMDSV QTFFAVDDGP SLDQAVSGLA TALCQASFTT QPRPEPCPVY CPKGQKGEPG EMGLRGQVGP PGDPGLPGRT GAPGPQGPPG SATAKGERGF PGADGRPGSP GRAGNPGTPG APGLKGSPGL PGPRGDPGER GPRGPKGEPG APGQVIGGEG PGLPGRKGDP GPSGPPGPRG PLGDPGPRGP PGLPGTAMKG DKGDRGERGP PGPGEGGIAP GEPGLPGLPG SPGPQGPVGP PGKKGEKGDS EDGAPGLPGQ PGSPGEQGPR GPPGAIGPKG DRGFPGPLGE AGEKGERGPP GPAGSRGLPG VAGRPGAKGP EGPPGPTGRQ GEKGEPGRPG DPAVVGPAVA GPKGEKGDVG PAGPRGATGV QGERGPPGLV LPGDPGPKGD PGDRGPIGLT GRAGPPGDSG PPGEKGDPGR PGPPGPVGPR GRDGEVGEKG DEGPPGDPGL PGKAGERGLR GAPGVRGPVG EKGDQGDPGE DGRNGSPGSS GPKGDRGEPG PPGPPGRLVD TGPGAREKGE PGDRGQEGPR GPKGDPGLPG APGERGIEGF RGPPGPQGDP GVRGPAGEKG DRGPPGLDGR SGLDGKPGAA GPSGPNGAAG KAGDPGRDGL PGLRGEQGLP GPSGPPGLPG KPGEDGKPGL NGKNGEPGDP GEDGRKGEKG DSGASGREGR DGPKGERGAP GILGPQGPPG LPGPVGPPGQ GFPGVPGGTG PKGDRGETGS KGEQGLPGER GLRGEPGSVP NVDRLLETAG IKASALREIV ETWDESSGSF LPVPERRRGP KGDSGEQGPP GKEGPIGFPG ERGLKGDRGD PGPQGPPGLA LGERGPPGPS GLAGEPGKPG IPGLPGRAGG VGEAGRPGER GERGEKGERG EQGRDGPPGL PGTPGPPGPP GPKVSVDEPG PGLSGEQGPP GLKGAKGEPG SNGDQGPKGD RGVPGIKGDR GEPGPRGQDG NPGLPGERGM AGPEGKPGLQ GPRGPPGPVG GHGDPGPPGA PGLAGPAGPQ GPSGLKGEPG ETGPPGRGLT GPTGAVGLPG PPGPSGLVGP QGSPGLPGQV GETGKPGAPG RDGASGKDGD RGSPGVPGSP GLPGPVGPKG EPGPTGAPGQ AVVGLPGAKG EKGAPGGLAG DLVGEPGAKG DRGLPGPRGE KGEAGRAGEP GDPGEDGQKG APGPKGFKGD PGVGVPGSPG PPGPPGVKGD LGLPGLPGAP GVVGFPGQTG PRGEMGQPGP SGERGLAGPP GREGIPGPLG PPGPPGSVGP PGASGLKGDK GDPGVGLPGP RGERGEPGIR GEDGRPGQEG PRGLTGPPGS RGERGEKGDV GSAGLKGDKG DSAVILGPPG PRGAKGDMGE RGPRGLDGDK GPRGDNGDPG DKGSKGEPGD KGSAGLPGLR GLLGPQGQPG AAGIPGDPGS PGKDGVPGIR GEKGDVGFMG PRGLKGERGV KGACGLDGEK GDKGEAGPPG RPGLAGHKGE MGEPGVPGQS GAPGKEGLIG PKGDRGFDGQ PGPKGDQGEK GERGTPGIGG FPGPSGNDGS AGPPGPPGSV GPRGPEGLQG QKGERGPPGE RVVGAPGVPG APGERGEQGR PGPAGPRGEK GEAALTEDDI RGFVRQEMSQ HCACQGQFIA SGSRPLPSYA ADTAGSQLHA VPVLRVSHAE EEERVPPEDD EYSEYSEYSV EEYQDPEAPW DSDDPCSLPL DEGSCTAYTL RWYHRAVTGS TEACHPFVYG GCGGNANRFG TREACERRCP PRVVQSQGTG TAQD* | |||||||||||||
| 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 | 109 / 109 | |||||||||||||
| Last intron/exon boundary | 8926 | |||||||||||||
| Theoretical NMD boundary in CDS | 8767 | |||||||||||||
| Length of CDS | 8835 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 24050 | |||||||||||||
| Chromosomal position | 48571280 | |||||||||||||
| Speed | 0.02 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:48571280T>A (GRCh38) | |||||||||||||
| Gene symbol | COL7A1 | |||||||||||||
| Gene constraints | LOEUF: 0.69, LOF (oe): 0.63, misssense (oe): 0.83, synonymous (oe): 0.93 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000681320.1 | |||||||||||||
| Genbank transcript ID | NM_000094 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | CO7A1_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.7069-2A>T g.24050A>T | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | alteration within used splice site, likely to disturb normal splicing MaxEntScan:
| |||||||||||||
| Distance from splice site | 2 | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | GCTGTTTGCTGGGTTTTCTTAGGGTCAGAAAGGGGCTCCAG | |||||||||||||
| Altered gDNA sequence snippet | GCTGTTTGCTGGGTTTTCTTTGGGTCAGAAAGGGGCTCCAG | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MTLRLLVAAL CAGILAEAPR VRAQHRERVT CTRLYAADIV FLLDGSSSIG RSNFREVRSF LEGLVLPFSG AASAQGVRFA TVQYSDDPRT EFGLDALGSG GDVIRAIREL SYKGGNTRTG AAILHVADHV FLPQLARPGV PKVCILITDG KSQDLVDTAA QRLKGQGVKL FAVGIKNADP EELKRVASQP TSDFFFFVND FSILRTLLPL VSRRVCTTAG GVPVTRPPDD STSAPRDLVL SEPSSQSLRV QWTAASGPVT GYKVQYTPLT GLGQPLPSER QEVNVPAGET SVRLRGLRPL TEYQVTVIAL YANSIGEAVS GTARTTALEG PELTIQNTTA HSLLVAWRSV PGATGYRVTW RVLSGGPTQQ QELGPGQGSV LLRDLEPGTD YEVTVSTLFG RSVGPATSLM ARTDASVEQT LRPVILGPTS ILLSWNLVPE ARGYRLEWRR ETGLEPPQKV VLPSDVTRYQ LDGLQPGTEY RLTLYTLLEG HEVATPATVV PTGPELPVSP VTDLQATELP GQRVRVSWSP VPGATQYRII VRSTQGVERT LVLPGSQTAF DLDDVQAGLS YTVRVSARVG PREGSASVLT VRREPETPLA VPGLRVVVSD ATRVRVAWGP VPGASGFRIS WSTGSGPESS QTLPPDSTAT DITGLQPGTT YQVAVSVLRG REEGPAAVIV ARTDPLGPVR TVHVTQASSS SVTITWTRVP GATGYRVSWH SAHGPEKSQL VSGEATVAEL DGLEPDTEYT VHVRAHVAGV DGPPASVVVR TAPEPVGRVS RLQILNASSD VLRITWVGVT GATAYRLAWG RSEGGPMRHQ ILPGNTDSAE IRGLEGGVSY SVRVTALVGD REGTPVSIVV TTPPEAPPAL GTLHVVQRGE HSLRLRWEPV PRAQGFLLHW QPEGGQEQSR VLGPELSSYH LDGLEPATQY RVRLSVLGPA GEGPSAEVTA RTESPRVPSI ELRVVDTSID SVTLAWTPVS RASSYILSWR PLRGPGQEVP GSPQTLPGIS SSQRVTGLEP GVSYIFSLTP VLDGVRGPEA SVTQTPVCPR GLADVVFLPH ATQDNAHRAE ATRRVLERLV LALGPLGPQA VQVGLLSYSH RPSPLFPLNG SHDLGIILQR IRDMPYMDPS GNNLGTAVVT AHRYMLAPDA PGRRQHVPGV MVLLVDEPLR GDIFSPIREA QASGLNVVML GMAGADPEQL RRLAPGMDSV QTFFAVDDGP SLDQAVSGLA TALCQASFTT QPRPEPCPVY CPKGQKGEPG EMGLRGQVGP PGDPGLPGRT GAPGPQGPPG SATAKGERGF PGADGRPGSP GRAGNPGTPG APGLKGSPGL PGPRGDPGER GPRGPKGEPG APGQVIGGEG PGLPGRKGDP GPSGPPGPRG PLGDPGPRGP PGLPGTAMKG DKGDRGERGP PGPGEGGIAP GEPGLPGLPG SPGPQGPVGP PGKKGEKGDS EDGAPGLPGQ PGSPGEQGPR GPPGAIGPKG DRGFPGPLGE AGEKGERGPP GPAGSRGLPG VAGRPGAKGP EGPPGPTGRQ GEKGEPGRPG DPAVVGPAVA GPKGEKGDVG PAGPRGATGV QGERGPPGLV LPGDPGPKGD PGDRGPIGLT GRAGPPGDSG PPGEKGDPGR PGPPGPVGPR GRDGEVGEKG DEGPPGDPGL PGKAGERGLR GAPGVRGPVG EKGDQGDPGE DGRNGSPGSS GPKGDRGEPG PPGPPGRLVD TGPGAREKGE PGDRGQEGPR GPKGDPGLPG APGERGIEGF RGPPGPQGDP GVRGPAGEKG DRGPPGLDGR SGLDGKPGAA GPSGPNGAAG KAGDPGRDGL PGLRGEQGLP GPSGPPGLPG KPGEDGKPGL NGKNGEPGDP GEDGRKGEKG DSGASGREGR DGPKGERGAP GILGPQGPPG LPGPVGPPGQ GFPGVPGGTG PKGDRGETGS KGEQGLPGER GLRGEPGSVP NVDRLLETAG IKASALREIV ETWDESSGSF LPVPERRRGP KGDSGEQGPP GKEGPIGFPG ERGLKGDRGD PGPQGPPGLA LGERGPPGPS GLAGEPGKPG IPGLPGRAGG VGEAGRPGER GERGEKGERG EQGRDGPPGL PGTPGPPGPP GPKVSVDEPG PGLSGEQGPP GLKGAKGEPG SNGDQGPKGD RGVPGIKGDR GEPGPRGQDG NPGLPGERGM AGPEGKPGLQ GPRGPPGPVG GHGDPGPPGA PGLAGPAGPQ GPSGLKGEPG ETGPPGRGLT GPTGAVGLPG PPGPSGLVGP QGSPGLPGQV GETGKPGAPG RDGASGKDGD RGSPGVPGSP GLPGPVGPKG EPGPTGAPGQ AVVGLPGAKG EKGAPGGLAG DLVGEPGAKG DRGLPGPRGE KGEAGRAGEP GDPGEDGQKG APGPKGFKGD PGVGVPGSPG PPGPPGVKGD LGLPGLPGAP GVVGFPGQTG PRGEMGQPGP SGERGLAGPP GREGIPGPLG PPGPPGSVGP PGASGLKGDK GDPGVGLPGP RGERGEPGIR GEDGRPGQEG PRGLTGPPGS RGERGEKGDV GSAGLKGDKG DSAVILGPPG PRGAKGDMGE RGPRGLDGDK GPRGDNGDPG DKGSKGEPGD KGSAGLPGLR GLLGPQGQPG AAGIPGDPGS PGKDGVPGIR GEKGDVGFMG PRGLKGERGV KGACGLDGEK GDKGEAGPPG RPGLAGHKGE MGEPGVPGQS GAPGKEGLIG PKGDRGFDGQ PGPKGDQGEK GERGTPGIGG FPGPSGNDGS AGPPGPPGSV GPRGPEGLQG QKGERGPPGE RVVGAPGVPG APGERGEQGR PGPAGPRGEK GEAALTEDDI RGFVRQEMSQ HCACQGQFIA SGSRPLPSYA ADTAGSQLHA VPVLRVSHAE EEERVPPEDD EYSEYSEYSV EEYQDPEAPW DSDDPCSLPL DEGSCTAYTL RWYHRAVTGS TEACHPFVYG GCGGNANRFG TREACERRCP PRVVQSQGTG TAQD* | |||||||||||||
| 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 | 64 / 64 | |||||||||||||
| Last intron/exon boundary | 8881 | |||||||||||||
| Theoretical NMD boundary in CDS | 8767 | |||||||||||||
| Length of CDS | 8835 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 24050 | |||||||||||||
| Chromosomal position | 48571280 | |||||||||||||
| Speed | 0.03 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