| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000371817(MANE Select) | COL5A1 | Benign | 0|200 | without_ | No | Single base exchange | N/A |
| |||||
| COL5A1 | Benign | 0|200 | without_ | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr9:134801908C>T (GRCh38) | |||||||||||||
| Gene symbol | COL5A1 | |||||||||||||
| Gene constraints | LOEUF: 0.09, LOF (oe): 0.06, misssense (oe): 0.77, synonymous (oe): 0.98 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000371817.8 | |||||||||||||
| Genbank transcript ID | NM_000093 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.2953-46C>T g.160106C>T | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 9 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | AACAGTGCAGGGCAGGGTGGCGCAGGCCACTGCAGCACCGT | |||||||||||||
| Altered gDNA sequence snippet | AACAGTGCAGGGCAGGGTGGTGCAGGCCACTGCAGCACCGT | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MDVHTRWKAR SALRPGAPLL PPLLLLLLWA PPPSRAAQPA DLLKVLDFHN LPDGITKTTG FCATRRSSKG PDVAYRVTKD AQLSAPTKQL YPASAFPEDF SILTTVKAKK GSQAFLVSIY NEQGIQQIGL ELGRSPVFLY EDHTGKPGPE DYPLFRGINL SDGKWHRIAL SVHKKNVTLI LDCKKKTTKF LDRSDHPMID INGIIVFGTR ILDEEVFEGD IQQLLFVSDH RAAYDYCEHY SPDCDTAVPD TPQSQDPNPD EYYTEGDGEG ETYYYEYPYY EDPEDLGKEP TPSKKPVEAA KETTEVPEEL TPTPTEAAPM PETSEGAGKE EDVGIGDYDY VPSEDYYTPS PYDDLTYGEG EENPDQPTDP GAGAEIPTST ADTSNSSNPA PPPGEGADDL EGEFTEETIR NLDENYYDPY YDPTSSPSEI GPGMPANQDT IYEGIGGPRG EKGQKGEPAI IEPGMLIEGP PGPEGPAGLP GPPGTMGPTG QVGDPGERGP PGRPGLPGAD GLPGPPGTML MLPFRFGGGG DAGSKGPMVS AQESQAQAIL QQARLALRGP AGPMGLTGRP GPVGPPGSGG LKGEPGDVGP QGPRGVQGPP GPAGKPGRRG RAGSDGARGM PGQTGPKGDR GFDGLAGLPG EKGHRGDPGP SGPPGPPGDD GERGDDGEVG PRGLPGEPGP RGLLGPKGPP GPPGPPGVTG MDGQPGPKGN VGPQGEPGPP GQQGNPGAQG LPGPQGAIGP PGEKGPLGKP GLPGMPGADG PPGHPGKEGP PGEKGGQGPP GPQGPIGYPG PRGVKGADGI RGLKGTKGEK GEDGFPGFKG DMGIKGDRGE IGPPGPRGED GPEGPKGRGG PNGDPGPLGP PGEKGKLGVP GLPGYPGRQG PKGSIGFPGF PGANGEKGGR GTPGKPGPRG QRGPTGPRGE RGPRGITGKP GPKGNSGGDG PAGPPGERGP NGPQGPTGFP GPKGPPGPPG KDGLPGHPGQ RGETGFQGKT GPPGPPGVVG PQGPTGETGP MGERGHPGPP GPPGEQGLPG LAGKEGTKGD PGPAGLPGKD GPPGLRGFPG DRGLPGPVGA LGLKGNEGPP GPPGPAGSPG ERGPAGAAGP IGIPGRPGPQ GPPGPAGEKG APGEKGPQGP AGRDGLQGPV GLPGPAGPVG PPGEDGDKGE IGEPGQKGSK GDKGEQGPPG PTGPQGPIGQ PGPSGADGEP GPRGQQGLFG QKGDEGPRGF PGPPGPVGLQ GLPGPPGEKG ETGDVGQMGP PGPPGPRGPS GAPGADGPQG PPGGIGNPGA VGEKGEPGEA GEPGLPGEGG PPGPKGERGE KGESGPSGAA GPPGPKGPPG DDGPKGSPGP VGFPGDPGPP GEPGPAGQDG PPGDKGDDGE PGQTGSPGPT GEPGPSGPPG KRGPPGPAGP EGRQGEKGAK GEAGLEGPPG KTGPIGPQGA PGKPGPDGLR GIPGPVGEQG LPGSPGPDGP PGPMGPPGLP GLKGDSGPKG EKGHPGLIGL IGPPGEQGEK GDRGLPGPQG SSGPKGEQGI TGPSGPIGPP GPPGLPGPPG PKGAKGSSGP TGPKGEAGHP GPPGPPGPPG EVIQPLPIQA SRTRRNIDAS QLLDDGNGEN YVDYADGMEE IFGSLNSLKL EIEQMKRPLG TQQNPARTCK DLQLCHPDFP DGEYWVDPNQ GCSRDSFKVY CNFTAGGSTC VFPDKKSEGA RITSWPKENP GSWFSEFKRG KLLSYVDAEG NPVGVVQMTF LRLLSASAHQ NVTYHCYQSV AWQDAATGSY DKALRFLGSN DEEMSYDNNP YIRALVDGCA TKKGYQKTVL EIDTPKVEQV PIVDIMFNDF GEASQKFGFE VGPACFMG* | |||||||||||||
| 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 | 386 / 386 | |||||||||||||
| Last intron/exon boundary | 5755 | |||||||||||||
| Theoretical NMD boundary in CDS | 5319 | |||||||||||||
| Length of CDS | 5517 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 160106 | |||||||||||||
| Chromosomal position | 134801908 | |||||||||||||
| 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 | Chr9:134801908C>T (GRCh38) | |||||||||||||
| Gene symbol | COL5A1 | |||||||||||||
| Gene constraints | LOEUF: 0.68, LOF (oe): 0.38, misssense (oe): 0.85, synonymous (oe): 0.90 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000371820.4 | |||||||||||||
| Genbank transcript ID | NM_001278074 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.2953-46C>T g.160106C>T | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 9 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | AACAGTGCAGGGCAGGGTGGCGCAGGCCACTGCAGCACCGT | |||||||||||||
| Altered gDNA sequence snippet | AACAGTGCAGGGCAGGGTGGTGCAGGCCACTGCAGCACCGT | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MDVHTRWKAR SALRPGAPLL PPLLLLLLWA PPPSRAAQPA DLLKVLDFHN LPDGITKTTG FCATRRSSKG PDVAYRVTKD AQLSAPTKQL YPASAFPEDF SILTTVKAKK GSQAFLVSIY NEQGIQQIGL ELGRSPVFLY EDHTGKPGPE DYPLFRGINL SDGKWHRIAL SVHKKNVTLI LDCKKKTTKF LDRSDHPMID INGIIVFGTR ILDEEVFEGD IQQLLFVSDH RAAYDYCEHY SPDCDTAVPD TPQSQDPNPD EYYTEGDGEG ETYYYEYPYY EDPEDLGKEP TPSKKPVEAA KETTEVPEEL TPTPTEAAPM PETSEGAGKE EDVGIGDYDY VPSEDYYTPS PYDDLTYGEG EENPDQPTDP GAGAEIPTST ADTSNSSNPA PPPGEGADDL EGEFTEETIR NLDENYYDPY YDPTSSPSEI GPGMPANQDT IYEGIGGPRG EKGQKGEPAI IEPGMLIEGP PGPEGPAGLP GPPGTMGPTG QVGDPGERGP PGRPGLPGAD GLPGPPGTML MLPFRFGGGG DAGSKGPMVS AQESQAQAIL QQARLALRGP AGPMGLTGRP GPVGPPGSGG LKGEPGDVGP QGPRGVQGPP GPAGKPGRRG RAGSDGARGM PGQTGPKGDR GFDGLAGLPG EKGHRGDPGP SGPPGPPGDD GERGDDGEVG PRGLPGEPGP RGLLGPKGPP GPPGPPGVTG MDGQPGPKGN VGPQGEPGPP GQQGNPGAQG LPGPQGAIGP PGEKGPLGKP GLPGMPGADG PPGHPGKEGP PGEKGGQGPP GPQGPIGYPG PRGVKGADGI RGLKGTKGEK GEDGFPGFKG DMGIKGDRGE IGPPGPRGED GPEGPKGRGG PNGDPGPLGP PGEKGKLGVP GLPGYPGRQG PKGSIGFPGF PGANGEKGGR GTPGKPGPRG QRGPTGPRGE RGPRGITGKP GPKGNSGGDG PAGPPGERGP NGPQGPTGFP GPKGPPGPPG KDGLPGHPGQ RGETGFQGKT GPPGPPGVVG PQGPTGETGP MGERGHPGPP GPPGEQGLPG LAGKEGTKGD PGPAGLPGKD GPPGLRGFPG DRGLPGPVGA LGLKGNEGPP GPPGPAGSPG ERGPAGAAGP IGIPGRPGPQ GPPGPAGEKG APGEKGPQGP AGRDGLQGPV GLPGPAGPVG PPGEDGDKGE IGEPGQKGSK GDKGEQGPPG PTGPQGPIGQ PGPSGADGEP GPRGQQGLFG QKGDEGPRGF PGPPGPVGLQ GLPGPPGEKG ETGDVGQMGP PGPPGPRGPS GAPGADGPQG PPGGIGNPGA VGEKGEPGEA GEPGLPGEGG PPGPKGERGE KGESGPSGAA GPPGPKGPPG DDGPKGSPGP VGFPGDPGPP GEPGPAGQDG PPGDKGDDGE PGQTGSPGPT GEPGPSGPPG KRGPPGPAGP EGRQGEKGAK GEAGLEGPPG KTGPIGPQGA PGKPGPDGLR GIPGPVGEQG LPGSPGPDGP PGPMGPPGLP GLKGDSGPKG EKGHPGLIGL IGPPGEQGEK GDRGLPGPQG SSGPKGEQGI TGPSGPIGPP GPPGLPGPPG PKGAKGSSGP TGPKGEAGHP GPPGPPGPPG EVIQPLPIQA SRTRRNIDAS QLLDDGNGEN YVDYADGMEE IFGSLNSLKL EIEQMKRPLG TQQNPARTCK DLQLCHPDFP DGEYWVDPNQ GCSRDSFKVY CNFTAGGSTC VFPDKKSEGS KMARWPKEQP STWYSQYKRG SLLSYVDAEG NPVGVVQMTF LRLLSASAHQ NVTYHCYQSV AWQDAATGSY DKALRFLGSN DEEMSYDNNP YIRALVDGCA TKKGYQKTVL EIDTPKVEQV PIVDIMFNDF GEASQKFGFE VGPACFMG* | |||||||||||||
| 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 | 386 / 386 | |||||||||||||
| Last intron/exon boundary | 5755 | |||||||||||||
| Theoretical NMD boundary in CDS | 5319 | |||||||||||||
| Length of CDS | 5517 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 160106 | |||||||||||||
| Chromosomal position | 134801908 | |||||||||||||
| 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