| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| COL17A1 | Benign | 0|200 | without_ | No | Single base exchange | N/A |
| ||||||
ENST00000648076(MANE Select) | COL17A1 | Benign | 0|200 | without_ | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr10:104045739C>T (GRCh38) | |||||||||||||
| Gene symbol | COL17A1 | |||||||||||||
| Gene constraints | LOEUF: 0.91, LOF (oe): 0.80, misssense (oe): 0.95, synonymous (oe): 0.97 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000369733.8 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.2398+19G>A g.40142G>A | |||||||||||||
| 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 | 19 | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 10 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | AGGTAAGTGAATTTCCAAATGAGATTTCTTTCTTTTCACTG | |||||||||||||
| Altered gDNA sequence snippet | AGGTAAGTGAATTTCCAAATAAGATTTCTTTCTTTTCACTG | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MDVTKKNKRD GTEVTERIVT ETVTTRLTSL PPKGGTSNGY AKTASLGGGS RLEKQSLTHG SSGYINSTGS TRGHASTSSY RRAHSPASTL PNSPGSTFER KTHVTRHAYE GSSSGNSSPE YPRKEFASSS TRGRSQTRES EIRVRLQSAS PSTRWTELDD VKRLLKGSRS ASVSPTRNSS NTLPIPKKGT VETKIVTASS QSVSGTYDAT ILDANLPSHV WSSTLPAGSS MGTYHNNMTT QSSSLLNTNA YSAGSVFGVP NNMASCSPTL HPGLSTSSSV FGMQNNLAPS LTTLSHGTTT TSTAYGVKKN MPQSPAAVNT GVSTSAACTT SVQSDDLLHK DCKFLILEKD NTPAKKEMEL LIMTKDSGKV FTASPASIAA TSFSEDTLKK EKQAAYNADS GLKAEANGDL KTVSTKGKTT TADIHSYGSS GGGGSGGGGG VGGAGGGPWG PAPAWCPCGS CCSWWKWLLG LLLTWLLLLG LLFGLIALAE EVRKLKARVD ELERIRRSIL PYGDSMDRIE KDRLQGMAPA AGADLDKIGL HSDSQEELWM FVRKKLMMEQ ENGNLRGSPG PKGDMGSPGP KGDRGFPGTP GIPGPLGHPG PQGPKGQKGS VGDPGMEGPM GQRGREGPMG PRGEAGPPGS GEKGERGAAG EPGPHGPPGV PGSVGPKGSS GSPGPQGPPG PVGLQGLRGE VGLPGVKGDK GPMGPPGPKG DQGEKGPRGL TGEPGMRGLP GAVGEPGAKG AMGPAGPDGH QGPRGEQGLT GMPGIRGPPG PSGDPGKPGL TGPQGPQGLP GTPGRPGIKG EPGAPGKIVT SEGSSMLTVP GPPGPPGAMG PPGPPGAPGP AGPAGLPGHQ EVLNLQGPPG PPGPRGPPGP SIPGPPGPRG PPGEGLPGPP GPPGSFLSNS ETFLSGPPGP PGPPGPKGDQ GDPGVPGALG IPSGPSEGGS SSTMYVSGPP GPPGPPGPPG SISSSGQEIQ QYISEYMQSD SIRSYLSGVQ GPPGPPGPPG PVTTITGETF DYSELASHVV SYLRTSGYGV SLFSSSISSE DILAVLQRDD VRQYLRQYLM GPRGPPGPPG ASGDGSLLSL DYAELSSRIL SYMSSSGISI GLPGPPGPPG LPGTSYEELL SLLRAAGLSF IPGPPGPPGP PGPRGPPGVS GALATYAAEN SDSFRSELIS YLTSPDVRSF IVGPPGPPGP QGPPGDSRLL STDASHSRGS SSSSHSSSVR RGSSYSSSMS TGGGGAGSLG AGGAFGEAAG DRGPYGTDIG PGGGYGAAAE GGMYAGNGGL LGADFAGDLD YNELAVRVSE SMQRQGLLQG MAYTVQGPPG QPGPQGPPGI SKVFSAYSNV TADLMDFFQT YGAIQGPPGQ KGEMGTPGPK GDRGPAGPPG HPGPPGPRGH KGEKGDKGDQ VYAGRRRRRS IAVKP* | |||||||||||||
| 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 | 1 / 1 | |||||||||||||
| Last intron/exon boundary | 4192 | |||||||||||||
| Theoretical NMD boundary in CDS | 4141 | |||||||||||||
| Length of CDS | 4248 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 40142 | |||||||||||||
| Chromosomal position | 104045739 | |||||||||||||
| 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 | Chr10:104045739C>T (GRCh38) | |||||||||||||
| Gene symbol | COL17A1 | |||||||||||||
| Gene constraints | LOEUF: 0.91, LOF (oe): 0.80, misssense (oe): 0.95, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000648076.2 | |||||||||||||
| Genbank transcript ID | NM_000494 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.2398+19G>A g.40142G>A | |||||||||||||
| 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 | 19 | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 10 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | AGGTAAGTGAATTTCCAAATGAGATTTCTTTCTTTTCACTG | |||||||||||||
| Altered gDNA sequence snippet | AGGTAAGTGAATTTCCAAATAAGATTTCTTTCTTTTCACTG | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MDVTKKNKRD GTEVTERIVT ETVTTRLTSL PPKGGTSNGY AKTASLGGGS RLEKQSLTHG SSGYINSTGS TRGHASTSSY RRAHSPASTL PNSPGSTFER KTHVTRHAYE GSSSGNSSPE YPRKEFASSS TRGRSQTRES EIRVRLQSAS PSTRWTELDD VKRLLKGSRS ASVSPTRNSS NTLPIPKKGT VETKIVTASS QSVSGTYDAT ILDANLPSHV WSSTLPAGSS MGTYHNNMTT QSSSLLNTNA YSAGSVFGVP NNMASCSPTL HPGLSTSSSV FGMQNNLAPS LTTLSHGTTT TSTAYGVKKN MPQSPAAVNT GVSTSAACTT SVQSDDLLHK DCKFLILEKD NTPAKKEMEL LIMTKDSGKV FTASPASIAA TSFSEDTLKK EKQAAYNADS GLKAEANGDL KTVSTKGKTT TADIHSYGSS GGGGSGGGGG VGGAGGGPWG PAPAWCPCGS CCSWWKWLLG LLLTWLLLLG LLFGLIALAE EVRKLKARVD ELERIRRSIL PYGDSMDRIE KDRLQGMAPA AGADLDKIGL HSDSQEELWM FVRKKLMMEQ ENGNLRGSPG PKGDMGSPGP KGDRGFPGTP GIPGPLGHPG PQGPKGQKGS VGDPGMEGPM GQRGREGPMG PRGEAGPPGS GEKGERGAAG EPGPHGPPGV PGSVGPKGSS GSPGPQGPPG PVGLQGLRGE VGLPGVKGDK GPMGPPGPKG DQGEKGPRGL TGEPGMRGLP GAVGEPGAKG AMGPAGPDGH QGPRGEQGLT GMPGIRGPPG PSGDPGKPGL TGPQGPQGLP GTPGRPGIKG EPGAPGKIVT SEGSSMLTVP GPPGPPGAMG PPGPPGAPGP AGPAGLPGHQ EVLNLQGPPG PPGPRGPPGP SIPGPPGPRG PPGEGLPGPP GPPGSFLSNS ETFLSGPPGP PGPPGPKGDQ GPPGPRGHQG EQGLPGFSTS GSSSFGLNLQ GPPGPPGPQG PKGDKGDPGV PGALGIPSGP SEGGSSSTMY VSGPPGPPGP PGPPGSISSS GQEIQQYISE YMQSDSIRSY LSGVQGPPGP PGPPGPVTTI TGETFDYSEL ASHVVSYLRT SGYGVSLFSS SISSEDILAV LQRDDVRQYL RQYLMGPRGP PGPPGASGDG SLLSLDYAEL SSRILSYMSS SGISIGLPGP PGPPGLPGTS YEELLSLLRG SEFRGIVGPP GPPGPPGIPG NVWSSISVED LSSYLHTAGL SFIPGPPGPP GPPGPRGPPG VSGALATYAA ENSDSFRSEL ISYLTSPDVR SFIVGPPGPP GPQGPPGDSR LLSTDASHSR GSSSSSHSSS VRRGSSYSSS MSTGGGGAGS LGAGGAFGEA AGDRGPYGTD IGPGGGYGAA AEGGMYAGNG GLLGADFAGD LDYNELAVRV SESMQRQGLL QGMAYTVQGP PGQPGPQGPP GISKVFSAYS NVTADLMDFF QTYGAIQGPP GQKGEMGTPG PKGDRGPAGP PGHPGPPGPR GHKGEKGDKG DQVYAGRRRR RSIAVKP* | |||||||||||||
| 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 | 170 / 170 | |||||||||||||
| Last intron/exon boundary | 4607 | |||||||||||||
| Theoretical NMD boundary in CDS | 4387 | |||||||||||||
| Length of CDS | 4494 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 40142 | |||||||||||||
| Chromosomal position | 104045739 | |||||||||||||
| 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