| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000380518(MANE Select) | COL2A1 | Benign | 0|200 | without_ | No | Single base exchange | N/A |
| |||||
| COL2A1 | Benign | 1|199 | without_ | No | Single base exchange | N/A |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr12:47995550C>G (GRCh38) | |||||||||||||
| Gene symbol | COL2A1 | |||||||||||||
| Gene constraints | LOEUF: 0.18, LOF (oe): 0.13, misssense (oe): 0.67, synonymous (oe): 0.98 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000380518.8 | |||||||||||||
| Genbank transcript ID | NM_001844 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.708+160G>C g.9005G>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 | 12 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCTAGCTGTGGAGGAACTCTGACAGACAGCCCAATGTGGCA | |||||||||||||
| Altered gDNA sequence snippet | CCTAGCTGTGGAGGAACTCTCACAGACAGCCCAATGTGGCA | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MIRLGAPQTL VLLTLLVAAV LRCQGQDVQE AGSCVQDGQR YNDKDVWKPE PCRICVCDTG TVLCDDIICE DVKDCLSPEI PFGECCPICP TDLATASGQP GPKGQKGEPG DIKDIVGPKG PPGPQGPAGE QGPRGDRGDK GEKGAPGPRG RDGEPGTPGN PGPPGPPGPP GPPGLGGNFA AQMAGGFDEK AGGAQLGVMQ GPMGPMGPRG PPGPAGAPGP QGFQGNPGEP GEPGVSGPMG PRGPPGPPGK PGDDGEAGKP GKAGERGPPG PQGARGFPGT PGLPGVKGHR GYPGLDGAKG EAGAPGVKGE SGSPGENGSP GPMGPRGLPG ERGRTGPAGA AGARGNDGQP GPAGPPGPVG PAGGPGFPGA PGAKGEAGPT GARGPEGAQG PRGEPGTPGS PGPAGASGNP GTDGIPGAKG SAGAPGIAGA PGFPGPRGPP GPQGATGPLG PKGQTGEPGI AGFKGEQGPK GEPGPAGPQG APGPAGEEGK RGARGEPGGV GPIGPPGERG APGNRGFPGQ DGLAGPKGAP GERGPSGLAG PKGANGDPGR PGEPGLPGAR GLTGRPGDAG PQGKVGPSGA PGEDGRPGPP GPQGARGQPG VMGFPGPKGA NGEPGKAGEK GLPGAPGLRG LPGKDGETGA AGPPGPAGPA GERGEQGAPG PSGFQGLPGP PGPPGEGGKP GDQGVPGEAG APGLVGPRGE RGFPGERGSP GAQGLQGPRG LPGTPGTDGP KGASGPAGPP GAQGPPGLQG MPGERGAAGI AGPKGDRGDV GEKGPEGAPG KDGGRGLTGP IGPPGPAGAN GEKGEVGPPG PAGSAGARGA PGERGETGPP GPAGFAGPPG ADGQPGAKGE QGEAGQKGDA GAPGPQGPSG APGPQGPTGV TGPKGARGAQ GPPGATGFPG AAGRVGPPGS NGNPGPPGPP GPSGKDGPKG ARGDSGPPGR AGEPGLQGPA GPPGEKGEPG DDGPSGAEGP PGPQGLAGQR GIVGLPGQRG ERGFPGLPGP SGEPGKQGAP GASGDRGPPG PVGPPGLTGP AGEPGREGSP GADGPPGRDG AAGVKGDRGE TGAVGAPGAP GPPGSPGPAG PTGKQGDRGE AGAQGPMGPS GPAGARGIQG PQGPRGDKGE AGEPGERGLK GHRGFTGLQG LPGPPGPSGD QGASGPAGPS GPRGPPGPVG PSGKDGANGI PGPIGPPGPR GRSGETGPAG PPGNPGPPGP PGPPGPGIDM SAFAGLGPRE KGPDPLQYMR ADQAAGGLRQ HDAEVDATLK SLNNQIESIR SPEGSRKNPA RTCRDLKLCH PEWKSGDYWI DPNQGCTLDA MKVFCNMETG ETCVYPNPAN VPKKNWWSSK SKEKKHIWFG ETINGGFHFS YGDDNLAPNT ANVQMTFLRL LSTEGSQNIT YHCKNSIAYL DEAAGNLKKA LLIQGSNDVE IRAEGNSRFT YTALKDGCTK HTGKWGKTVI EYRSQKTSRL PIIDIAPMDI GGPEQEFGVD IGPVCFL* | |||||||||||||
| 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 | 156 / 156 | |||||||||||||
| Last intron/exon boundary | 4472 | |||||||||||||
| Theoretical NMD boundary in CDS | 4266 | |||||||||||||
| Length of CDS | 4464 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 9005 | |||||||||||||
| Chromosomal position | 47995550 | |||||||||||||
| 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 | Chr12:47995550C>G (GRCh38) | |||||||||||||
| Gene symbol | COL2A1 | |||||||||||||
| Gene constraints | LOEUF: 0.19, LOF (oe): 0.14, misssense (oe): 0.68, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000337299.7 | |||||||||||||
| Genbank transcript ID | NM_033150 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | intron | |||||||||||||
| DNA changes | c.501+160G>C g.9005G>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 | 12 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCTAGCTGTGGAGGAACTCTGACAGACAGCCCAATGTGGCA | |||||||||||||
| Altered gDNA sequence snippet | CCTAGCTGTGGAGGAACTCTCACAGACAGCCCAATGTGGCA | |||||||||||||
| Original cDNA sequence snippet | N/A | |||||||||||||
| Altered cDNA sequence snippet | N/A | |||||||||||||
| Wildtype AA sequence | MIRLGAPQTL VLLTLLVAAV LRCQGQDVRQ PGPKGQKGEP GDIKDIVGPK GPPGPQGPAG EQGPRGDRGD KGEKGAPGPR GRDGEPGTPG NPGPPGPPGP PGPPGLGGNF AAQMAGGFDE KAGGAQLGVM QGPMGPMGPR GPPGPAGAPG PQGFQGNPGE PGEPGVSGPM GPRGPPGPPG KPGDDGEAGK PGKAGERGPP GPQGARGFPG TPGLPGVKGH RGYPGLDGAK GEAGAPGVKG ESGSPGENGS PGPMGPRGLP GERGRTGPAG AAGARGNDGQ PGPAGPPGPV GPAGGPGFPG APGAKGEAGP TGARGPEGAQ GPRGEPGTPG SPGPAGASGN PGTDGIPGAK GSAGAPGIAG APGFPGPRGP PGPQGATGPL GPKGQTGEPG IAGFKGEQGP KGEPGPAGPQ GAPGPAGEEG KRGARGEPGG VGPIGPPGER GAPGNRGFPG QDGLAGPKGA PGERGPSGLA GPKGANGDPG RPGEPGLPGA RGLTGRPGDA GPQGKVGPSG APGEDGRPGP PGPQGARGQP GVMGFPGPKG ANGEPGKAGE KGLPGAPGLR GLPGKDGETG AAGPPGPAGP AGERGEQGAP GPSGFQGLPG PPGPPGEGGK PGDQGVPGEA GAPGLVGPRG ERGFPGERGS PGAQGLQGPR GLPGTPGTDG PKGASGPAGP PGAQGPPGLQ GMPGERGAAG IAGPKGDRGD VGEKGPEGAP GKDGGRGLTG PIGPPGPAGA NGEKGEVGPP GPAGSAGARG APGERGETGP PGPAGFAGPP GADGQPGAKG EQGEAGQKGD AGAPGPQGPS GAPGPQGPTG VTGPKGARGA QGPPGATGFP GAAGRVGPPG SNGNPGPPGP PGPSGKDGPK GARGDSGPPG RAGEPGLQGP AGPPGEKGEP GDDGPSGAEG PPGPQGLAGQ RGIVGLPGQR GERGFPGLPG PSGEPGKQGA PGASGDRGPP GPVGPPGLTG PAGEPGREGS PGADGPPGRD GAAGVKGDRG ETGAVGAPGA PGPPGSPGPA GPTGKQGDRG EAGAQGPMGP SGPAGARGIQ GPQGPRGDKG EAGEPGERGL KGHRGFTGLQ GLPGPPGPSG DQGASGPAGP SGPRGPPGPV GPSGKDGANG IPGPIGPPGP RGRSGETGPA GPPGNPGPPG PPGPPGPGID MSAFAGLGPR EKGPDPLQYM RADQAAGGLR QHDAEVDATL KSLNNQIESI RSPEGSRKNP ARTCRDLKLC HPEWKSGDYW IDPNQGCTLD AMKVFCNMET GETCVYPNPA NVPKKNWWSS KSKEKKHIWF GETINGGFHF SYGDDNLAPN TANVQMTFLR LLSTEGSQNI TYHCKNSIAY LDEAAGNLKK ALLIQGSNDV EIRAEGNSRF TYTALKDGCT KHTGKWGKTV IEYRSQKTSR LPIIDIAPMD IGGPEQEFGV DIGPVCFL* | |||||||||||||
| 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 | 186 / 186 | |||||||||||||
| Last intron/exon boundary | 4295 | |||||||||||||
| Theoretical NMD boundary in CDS | 4059 | |||||||||||||
| Length of CDS | 4257 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | N/A | |||||||||||||
| gDNA position | 9005 | |||||||||||||
| Chromosomal position | 47995550 | |||||||||||||
| 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