| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RAF1 | Deleterious | 60|40 | simple_ | No | Single base exchange | Normal |
| ||||||
ENST00000251849(MANE Select) | RAF1 | Deleterious | 62|38 | simple_ | No | Single base exchange | Normal |
| |||||
| RAF1 | Deleterious | 63|37 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 63|37 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 64|36 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 64|36 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 64|36 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 64|36 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 65|35 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 65|35 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 65|35 | simple_ | No | Single base exchange | Normal |
| ||||||
| RAF1 | Deleterious | 66|34 | simple_ | No | Single base exchange | Normal |
| ||||||
| MKRN2 | Benign | 28|72 | 3utr | No | Single base exchange | N/A | |||||||
| MKRN2 | Benign | 28|72 | 3utr | No | Single base exchange | N/A |
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.37, LOF (oe): 0.25, misssense (oe): 0.70, synonymous (oe): 0.92 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000689389.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1544A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRYL HAKNIIHRDM KSNNIFLHEG LTVKIGDFGL ATVKSRWSGS QQVEQPTGSV LWMAPEVIRM QDNNPFSFQS DVYSYGIVLY ELMTGELPYS HINNRDQIIF MVGRGYASPD LSKLYKNCPK AMKRLVADCV KKVKEERPLF PQILSSIELL QHSLPKINRS ASEPSLHRAA HTEDINACTL TTSPRLPVF* | |||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRYL HAKNIIHRDM KSNNIFLHEG LTVKIGDFGL ATVKSRWSGS QQVEQPTGSV LWMAPEVIRM QDNNPFSFQS DVYSYGIVLY ELMTGELPYS HINNRDQIIF MVGRGYASPD LSKLFKNCPK AMKRLVADCV KKVKEERPLF PQILSSIELL QHSLPKINRS ASEPSLHRAA HTEDINACTL TTSPRLPVF* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1770 / 1770 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 590 / 590 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2104 / 2104 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 335 / 335 | |||||||||||||
| Last intron/exon boundary | 1960 | |||||||||||||
| Theoretical NMD boundary in CDS | 1575 | |||||||||||||
| Length of CDS | 1770 | |||||||||||||
| Coding sequence (CDS) position | 1544 | |||||||||||||
| cDNA position | 1878 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | ||||||||||||||||
| Gene symbol | RAF1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.96 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000251849.9 | ||||||||||||||||
| Genbank transcript ID | NM_002880 (exact from MANE), NM_001354692 (by similarity), NM_001354691 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | RAF1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.1721A>T g.79273A>T | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | -1 | ||||||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLYKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | ||||||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLFKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 1947 / 1947 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 649 / 649 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2278 / 2278 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 332 / 332 | ||||||||||||||||
| Last intron/exon boundary | 2134 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 1752 | ||||||||||||||||
| Length of CDS | 1947 | ||||||||||||||||
| Coding sequence (CDS) position | 1721 | ||||||||||||||||
| cDNA position | 2052 | ||||||||||||||||
| gDNA position | 79273 | ||||||||||||||||
| Chromosomal position | 12584929 | ||||||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.39, LOF (oe): 0.27, misssense (oe): 0.67, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000687923.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1610A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGDVAVKIL KVVDPTPEQF QAFRNEVAVL RKTRHVNILL FMGYMTKDNL AIVTQWCEGS SLYKHLHVQE TKFQMFQLID IARQTAQGMD YLHAKNIIHR DMKSNNIFLH EGLTVKIGDF GLATVKSRWS GSQQVEQPTG SVLWMAPEVI RMQDNNPFSF QSDVYSYGIV LYELMTGELP YSHINNRDQI IFMVGRGYAS PDLSKLYKNC PKAMKRLVAD CVKKVKEERP LFPQILSSIE LLQHSLPKIN RSASEPSLHR AAHTEDINAC TLTTSPRLPV F* | |||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGDVAVKIL KVVDPTPEQF QAFRNEVAVL RKTRHVNILL FMGYMTKDNL AIVTQWCEGS SLYKHLHVQE TKFQMFQLID IARQTAQGMD YLHAKNIIHR DMKSNNIFLH EGLTVKIGDF GLATVKSRWS GSQQVEQPTG SVLWMAPEVI RMQDNNPFSF QSDVYSYGIV LYELMTGELP YSHINNRDQI IFMVGRGYAS PDLSKLFKNC PKAMKRLVAD CVKKVKEERP LFPQILSSIE LLQHSLPKIN RSASEPSLHR AAHTEDINAC TLTTSPRLPV F* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1836 / 1836 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 612 / 612 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2161 / 2161 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 326 / 326 | |||||||||||||
| Last intron/exon boundary | 2017 | |||||||||||||
| Theoretical NMD boundary in CDS | 1641 | |||||||||||||
| Length of CDS | 1836 | |||||||||||||
| Coding sequence (CDS) position | 1610 | |||||||||||||
| cDNA position | 1935 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.37, LOF (oe): 0.25, misssense (oe): 0.67, synonymous (oe): 0.95 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000690460.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1709A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESALS SSPNNLSPTG WSQPKTPVPA QRERAPVSGT QEKNKIRPRG QRDSSYYWEI EASEVMLSTR IGSGSFGTVY KGKWHGDVAV KILKVVDPTP EQFQAFRNEV AVLRKTRHVN ILLFMGYMTK DNLAIVTQWC EGSSLYKHLH VQETKFQMFQ LIDIARQTAQ GMDYLHAKNI IHRDMKSNNI FLHEGLTVKI GDFGLATVKS RWSGSQQVEQ PTGSVLWMAP EVIRMQDNNP FSFQSDVYSY GIVLYELMTG ELPYSHINNR DQIIFMVGRG YASPDLSKLY KNCPKAMKRL VADCVKKVKE ERPLFPQILS SIELLQHSLP KINRSASEPS LHRAAHTEDI NACTLTTSPR LPVF* | |||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESALS SSPNNLSPTG WSQPKTPVPA QRERAPVSGT QEKNKIRPRG QRDSSYYWEI EASEVMLSTR IGSGSFGTVY KGKWHGDVAV KILKVVDPTP EQFQAFRNEV AVLRKTRHVN ILLFMGYMTK DNLAIVTQWC EGSSLYKHLH VQETKFQMFQ LIDIARQTAQ GMDYLHAKNI IHRDMKSNNI FLHEGLTVKI GDFGLATVKS RWSGSQQVEQ PTGSVLWMAP EVIRMQDNNP FSFQSDVYSY GIVLYELMTG ELPYSHINNR DQIIFMVGRG YASPDLSKLF KNCPKAMKRL VADCVKKVKE ERPLFPQILS SIELLQHSLP KINRSASEPS LHRAAHTEDI NACTLTTSPR LPVF* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1935 / 1935 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 645 / 645 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2266 / 2266 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 332 / 332 | |||||||||||||
| Last intron/exon boundary | 2122 | |||||||||||||
| Theoretical NMD boundary in CDS | 1740 | |||||||||||||
| Length of CDS | 1935 | |||||||||||||
| Coding sequence (CDS) position | 1709 | |||||||||||||
| cDNA position | 2040 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||||||||||
| Gene symbol | RAF1 | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.96 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000442415.7 | |||||||||||||||||||||
| Genbank transcript ID | NM_001354694 (by similarity), NM_001354689 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | RAF1_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.1781A>T g.79273A>T | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
| |||||||||||||||||||||
| Protein conservation | ||||||||||||||||||||||
| Protein features |
| |||||||||||||||||||||
| Phylogenetic conservation |
| |||||||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||||||||||
| Distance from splice site | N/A | |||||||||||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||||||||||
| poly(A) signal | N/A | |||||||||||||||||||||
| AA sequence altered | Yes | |||||||||||||||||||||
| Chromosome | 3 | |||||||||||||||||||||
| Strand | -1 | |||||||||||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIENN NLSASPRAWS RRFCLRGRDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLYKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | |||||||||||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIENN NLSASPRAWS RRFCLRGRDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLFKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 2007 / 2007 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 669 / 669 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2338 / 2338 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 332 / 332 | |||||||||||||||||||||
| Last intron/exon boundary | 2194 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 1812 | |||||||||||||||||||||
| Length of CDS | 2007 | |||||||||||||||||||||
| Coding sequence (CDS) position | 1781 | |||||||||||||||||||||
| cDNA position | 2112 | |||||||||||||||||||||
| gDNA position | 79273 | |||||||||||||||||||||
| Chromosomal position | 12584929 | |||||||||||||||||||||
| Speed | 0.10 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.37, LOF (oe): 0.25, misssense (oe): 0.66, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000690397.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1610A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESALSSSP NNLSPTGWSQ PKTPVPAQRE RAPVSGTQEK NKIRPRGQRD SSYYWEIEAS EVMLSTRIGS GSFGTVYKGK WHGDVAVKIL KVVDPTPEQF QAFRNEVAVL RKTRHVNILL FMGYMTKDNL AIVTQWCEGS SLYKHLHVQE TKFQMFQLID IARQTAQGMD YLHAKNIIHR DMKSNNIFLH EGLTVKIGDF GLATVKSRWS GSQQVEQPTG SVLWMAPEVI RMQDNNPFSF QSDVYSYGIV LYELMTGELP YSHINNRDQI IFMVGRGYAS PDLSKLYKNC PKAMKRLVAD CVKKVKEERP LFPQILSSIE LLQHSLPKIN RSASEPSLHR AAHTEDINAC TLTTSPRLPV F* | |||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESALSSSP NNLSPTGWSQ PKTPVPAQRE RAPVSGTQEK NKIRPRGQRD SSYYWEIEAS EVMLSTRIGS GSFGTVYKGK WHGDVAVKIL KVVDPTPEQF QAFRNEVAVL RKTRHVNILL FMGYMTKDNL AIVTQWCEGS SLYKHLHVQE TKFQMFQLID IARQTAQGMD YLHAKNIIHR DMKSNNIFLH EGLTVKIGDF GLATVKSRWS GSQQVEQPTG SVLWMAPEVI RMQDNNPFSF QSDVYSYGIV LYELMTGELP YSHINNRDQI IFMVGRGYAS PDLSKLFKNC PKAMKRLVAD CVKKVKEERP LFPQILSSIE LLQHSLPKIN RSASEPSLHR AAHTEDINAC TLTTSPRLPV F* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1836 / 1836 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 612 / 612 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2167 / 2167 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 332 / 332 | |||||||||||||
| Last intron/exon boundary | 2023 | |||||||||||||
| Theoretical NMD boundary in CDS | 1641 | |||||||||||||
| Length of CDS | 1836 | |||||||||||||
| Coding sequence (CDS) position | 1610 | |||||||||||||
| cDNA position | 1941 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | ||||||||||||||||
| Gene symbol | RAF1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.96 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000685653.1 | ||||||||||||||||
| Genbank transcript ID | |||||||||||||||||
| UniProt / AlphaMissense peptide | RAF1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.1721A>T g.79273A>T | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | -1 | ||||||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLYKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | ||||||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLFKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 1947 / 1947 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 649 / 649 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3652 / 3652 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 1706 / 1706 | ||||||||||||||||
| Last intron/exon boundary | 3508 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 1752 | ||||||||||||||||
| Length of CDS | 1947 | ||||||||||||||||
| Coding sequence (CDS) position | 1721 | ||||||||||||||||
| cDNA position | 3426 | ||||||||||||||||
| gDNA position | 79273 | ||||||||||||||||
| Chromosomal position | 12584929 | ||||||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | ||||||||||||||||
| Gene symbol | RAF1 | ||||||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.96 (gnomAD) | ||||||||||||||||
| Ensembl transcript ID | ENST00000691899.1 | ||||||||||||||||
| Genbank transcript ID | NM_001354690 (by similarity) | ||||||||||||||||
| UniProt / AlphaMissense peptide | RAF1_HUMAN | AlphaMissense: transcript, gene | ||||||||||||||||
| Variant type | Single base exchange | ||||||||||||||||
| Gene region | CDS | ||||||||||||||||
| DNA changes | c.1721A>T g.79273A>T | ||||||||||||||||
| AA changes |
| ||||||||||||||||
| Frameshift | No | ||||||||||||||||
| Length of protein | Normal | ||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | ||||||||||||||||
| Variant DBs |
| ||||||||||||||||
| Protein conservation | |||||||||||||||||
| Protein features |
| ||||||||||||||||
| Phylogenetic conservation |
| ||||||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | ||||||||||||||||
| Distance from splice site | N/A | ||||||||||||||||
| Kozak consensus sequence altered? | No | ||||||||||||||||
| poly(A) signal | N/A | ||||||||||||||||
| AA sequence altered | Yes | ||||||||||||||||
| Chromosome | 3 | ||||||||||||||||
| Strand | -1 | ||||||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | ||||||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLYKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | ||||||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLLLFPNST IGDSGVPALP SLTMRRMRES VSRMPVSSQH RYSTPHAFTF NTSSPSSEGS LSQRQRSTST PNVHMVSTTL PVDSRMIEDA IRSHSESASP SALSSSPNNL SPTGWSQPKT PVPAQRERAP VSGTQEKNKI RPRGQRDSSY YWEIEASEVM LSTRIGSGSF GTVYKGKWHG DVAVKILKVV DPTPEQFQAF RNEVAVLRKT RHVNILLFMG YMTKDNLAIV TQWCEGSSLY KHLHVQETKF QMFQLIDIAR QTAQGMDYLH AKNIIHRDMK SNNIFLHEGL TVKIGDFGLA TVKSRWSGSQ QVEQPTGSVL WMAPEVIRMQ DNNPFSFQSD VYSYGIVLYE LMTGELPYSH INNRDQIIFM VGRGYASPDL SKLFKNCPKA MKRLVADCVK KVKEERPLFP QILSSIELLQ HSLPKINRSA SEPSLHRAAH TEDINACTLT TSPRLPVF* | ||||||||||||||||
| Position of stopcodon in wt / mu CDS | 1947 / 1947 | ||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 649 / 649 | ||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 2113 / 2113 | ||||||||||||||||
| Position of start ATG in wt / mu cDNA | 167 / 167 | ||||||||||||||||
| Last intron/exon boundary | 1969 | ||||||||||||||||
| Theoretical NMD boundary in CDS | 1752 | ||||||||||||||||
| Length of CDS | 1947 | ||||||||||||||||
| Coding sequence (CDS) position | 1721 | ||||||||||||||||
| cDNA position | 1887 | ||||||||||||||||
| gDNA position | 79273 | ||||||||||||||||
| Chromosomal position | 12584929 | ||||||||||||||||
| Speed | 0.18 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.24, misssense (oe): 0.67, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000688543.1 | |||||||||||||
| Genbank transcript ID | NM_001354695 (by similarity), NM_001354693 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1622A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGKWHGDVA VKILKVVDPT PEQFQAFRNE VAVLRKTRHV NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATVK SRWSGSQQVE QPTGSVLWMA PEVIRMQDNN PFSFQSDVYS YGIVLYELMT GELPYSHINN RDQIIFMVGR GYASPDLSKL YKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSASEP SLHRAAHTED INACTLTTSP RLPVF* | |||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGKWHGDVA VKILKVVDPT PEQFQAFRNE VAVLRKTRHV NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATVK SRWSGSQQVE QPTGSVLWMA PEVIRMQDNN PFSFQSDVYS YGIVLYELMT GELPYSHINN RDQIIFMVGR GYASPDLSKL FKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSASEP SLHRAAHTED INACTLTTSP RLPVF* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1848 / 1848 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 616 / 616 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2249 / 2249 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 402 / 402 | |||||||||||||
| Last intron/exon boundary | 2105 | |||||||||||||
| Theoretical NMD boundary in CDS | 1653 | |||||||||||||
| Length of CDS | 1848 | |||||||||||||
| Coding sequence (CDS) position | 1622 | |||||||||||||
| cDNA position | 2023 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.24, misssense (oe): 0.67, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000692093.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1622A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGKWHGDVA VKILKVVDPT PEQFQAFRNE VAVLRKTRHV NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATVK SRWSGSQQVE QPTGSVLWMA PEVIRMQDNN PFSFQSDVYS YGIVLYELMT GELPYSHINN RDQIIFMVGR GYASPDLSKL YKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSASEP SLHRAAHTED INACTLTTSP RLPVF* | |||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGKWHGDVA VKILKVVDPT PEQFQAFRNE VAVLRKTRHV NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATVK SRWSGSQQVE QPTGSVLWMA PEVIRMQDNN PFSFQSDVYS YGIVLYELMT GELPYSHINN RDQIIFMVGR GYASPDLSKL FKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSASEP SLHRAAHTED INACTLTTSP RLPVF* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1848 / 1848 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 616 / 616 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2281 / 2281 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 434 / 434 | |||||||||||||
| Last intron/exon boundary | 2137 | |||||||||||||
| Theoretical NMD boundary in CDS | 1653 | |||||||||||||
| Length of CDS | 1848 | |||||||||||||
| Coding sequence (CDS) position | 1622 | |||||||||||||
| cDNA position | 2055 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| Speed | 0.09 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.35, LOF (oe): 0.24, misssense (oe): 0.67, synonymous (oe): 0.96 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000685437.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1622A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGKWHGDVA VKILKVVDPT PEQFQAFRNE VAVLRKTRHV NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATVK SRWSGSQQVE QPTGSVLWMA PEVIRMQDNN PFSFQSDVYS YGIVLYELMT GELPYSHINN RDQIIFMVGR GYASPDLSKL YKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSASEP SLHRAAHTED INACTLTTSP RLPVF* | |||||||||||||
| Mutated AA sequence | MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVRG LQPECCAVFR LLHEHKGKKA RLDWNTDAAS LIGEELQVDF LDHVPLTTHN FARKTFLKLA FCDICQKFLL NGFRCQTCGY KFHEHCSTKV PTMCVDWSNI RQLFSQHRYS TPHAFTFNTS SPSSEGSLSQ RQRSTSTPNV HMVSTTLPVD SRMIEDAIRS HSESASPSAL SSSPNNLSPT GWSQPKTPVP AQRERAPVSG TQEKNKIRPR GQRDSSYYWE IEASEVMLST RIGSGSFGTV YKGKWHGDVA VKILKVVDPT PEQFQAFRNE VAVLRKTRHV NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATVK SRWSGSQQVE QPTGSVLWMA PEVIRMQDNN PFSFQSDVYS YGIVLYELMT GELPYSHINN RDQIIFMVGR GYASPDLSKL FKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSASEP SLHRAAHTED INACTLTTSP RLPVF* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1848 / 1848 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 616 / 616 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2272 / 2272 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 425 / 425 | |||||||||||||
| Last intron/exon boundary | 2128 | |||||||||||||
| Theoretical NMD boundary in CDS | 1653 | |||||||||||||
| Length of CDS | 1848 | |||||||||||||
| Coding sequence (CDS) position | 1622 | |||||||||||||
| cDNA position | 2046 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | RAF1 | |||||||||||||
| Gene constraints | LOEUF: 0.36, LOF (oe): 0.24, misssense (oe): 0.64, synonymous (oe): 0.95 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000693312.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.1496A>T g.79273A>T | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| 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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered gDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Original cDNA sequence snippet | CCCAGATCTTAGTAAGCTATATAAGAACTGCCCCAAAGCAA | |||||||||||||
| Altered cDNA sequence snippet | CCCAGATCTTAGTAAGCTATTTAAGAACTGCCCCAAAGCAA | |||||||||||||
| Wildtype AA sequence | MSLHDCLMKA LKVRGLQPEC CAVFRLLHEH KGKKARLDWN TDAASLIGEE LQVDFLDHVP LTTHNFARKT FLKLAFCDIC QKFLLNGFRC QTCGYKFHEH CSTKVPTMCV DWSNIRQLLL FPNSTIGDSG VPALPSLTMR RMRESVSRMP VSSQHRYSTP HAFTFNTSSP SSEGSLSQRQ RSTSTPNVHM VSTTLPVDSR MIEDAIRSHS ESASPSALSS SPNNLSPTGW SQPKTPVPAQ RERAPVSGTQ EKNKIRPRGQ RDSSYYWEIE ASEVMLSTRI GSGSFGTVYK GKWHGDVAVK ILKVVDPTPE QFQAFRNEVA VLRKTRHVNI LLFMGYMTKD NLAIVTQWCE GSSLYKHLHV QETKFQMFQL IDIARQTAQG MDYLHAKNII HRDMKSNNIF LHEGLTVKIG DFGLATVKSR WSGSQQVEQP TGSVLWMAPE VIRMQDNNPF SFQSDVYSYG IVLYELMTGE LPYSHINNRD QIIFMVGRGY ASPDLSKLYK NCPKAMKRLV ADCVKKVKEE RPLFPQILSS IELLQHSLPK INRSASEPSL HRAAHTEDIN ACTLTTSPRL PVF* | |||||||||||||
| Mutated AA sequence | MSLHDCLMKA LKVRGLQPEC CAVFRLLHEH KGKKARLDWN TDAASLIGEE LQVDFLDHVP LTTHNFARKT FLKLAFCDIC QKFLLNGFRC QTCGYKFHEH CSTKVPTMCV DWSNIRQLLL FPNSTIGDSG VPALPSLTMR RMRESVSRMP VSSQHRYSTP HAFTFNTSSP SSEGSLSQRQ RSTSTPNVHM VSTTLPVDSR MIEDAIRSHS ESASPSALSS SPNNLSPTGW SQPKTPVPAQ RERAPVSGTQ EKNKIRPRGQ RDSSYYWEIE ASEVMLSTRI GSGSFGTVYK GKWHGDVAVK ILKVVDPTPE QFQAFRNEVA VLRKTRHVNI LLFMGYMTKD NLAIVTQWCE GSSLYKHLHV QETKFQMFQL IDIARQTAQG MDYLHAKNII HRDMKSNNIF LHEGLTVKIG DFGLATVKSR WSGSQQVEQP TGSVLWMAPE VIRMQDNNPF SFQSDVYSYG IVLYELMTGE LPYSHINNRD QIIFMVGRGY ASPDLSKLFK NCPKAMKRLV ADCVKKVKEE RPLFPQILSS IELLQHSLPK INRSASEPSL HRAAHTEDIN ACTLTTSPRL PVF* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 1722 / 1722 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 574 / 574 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 2023 / 2023 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 302 / 302 | |||||||||||||
| Last intron/exon boundary | 1879 | |||||||||||||
| Theoretical NMD boundary in CDS | 1527 | |||||||||||||
| Length of CDS | 1722 | |||||||||||||
| Coding sequence (CDS) position | 1496 | |||||||||||||
| cDNA position | 1797 | |||||||||||||
| gDNA position | 79273 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | MKRN2 | |||||||||||||
| Gene constraints | LOEUF: 0.95, LOF (oe): 0.70, misssense (oe): 0.93, synonymous (oe): 1.01 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000677142.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | 3'UTR | |||||||||||||
| DNA changes | cDNA.4158T>A g.27873T>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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | polyA signal ok | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TTGCTTTGGGGCAGTTCTTATATAGCTTACTAAGATCTGGG | |||||||||||||
| Altered gDNA sequence snippet | TTGCTTTGGGGCAGTTCTTAAATAGCTTACTAAGATCTGGG | |||||||||||||
| Original cDNA sequence snippet | TTGCTTTGGGGCAGTTCTTATATAGCTTACTAAGATCTGGG | |||||||||||||
| Altered cDNA sequence snippet | TTGCTTTGGGGCAGTTCTTAAATAGCTTACTAAGATCTGGG | |||||||||||||
| Wildtype AA sequence | MPGRCREGSG AYALTGKDLK YFMHGVCREG SQCLFSHDLA NSKPSTICKY YQKGYCAYGT RCRYDHTRPS AAAGGAVGTM AHSVPSPAFH SPHPPSEVTA SIVKTNSHEP GKREKRTLVL RDRNLSGMAE RKTQPSMVSN PGSCSDPQPS PEMKPHSYLD AIRSGLDDVE ASSSYSNEQQ LCPYAAAGEC RFGDACVYLH GEVCEICRLQ VLHPFDPEQR KAHEKICMLT FEHEMEKAFA FQASQDKVCS ICMEVILEKA SASERRFGIL SNCNHTYCLS CIRQWRCAKQ FENPIIKSCP ECRVISEFVI PSVYWVEDQN KKNELIEAFK QGMGKKACKY FEQGKGTCPF GSKCLYRHAY PDGRLAEPEK PRKQLSSQGT VRFFNSVRLW DFIENRESRH VPNNEDVDMT ELGDLFMHLS GVESSEP* | |||||||||||||
| 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 | 199 / 199 | |||||||||||||
| Last intron/exon boundary | 1344 | |||||||||||||
| Theoretical NMD boundary in CDS | 1095 | |||||||||||||
| Length of CDS | 1284 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | 4158 | |||||||||||||
| gDNA position | 27873 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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 | Chr3:12584929T>A (GRCh38) | |||||||||||||
| Gene symbol | MKRN2 | |||||||||||||
| Gene constraints | LOEUF: 0.95, LOF (oe): 0.70, misssense (oe): 0.94, synonymous (oe): 1.01 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000676541.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | 3'UTR | |||||||||||||
| DNA changes | cDNA.4328T>A g.27873T>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 | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | polyA signal ok | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 3 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | TTGCTTTGGGGCAGTTCTTATATAGCTTACTAAGATCTGGG | |||||||||||||
| Altered gDNA sequence snippet | TTGCTTTGGGGCAGTTCTTAAATAGCTTACTAAGATCTGGG | |||||||||||||
| Original cDNA sequence snippet | TTGCTTTGGGGCAGTTCTTATATAGCTTACTAAGATCTGGG | |||||||||||||
| Altered cDNA sequence snippet | TTGCTTTGGGGCAGTTCTTAAATAGCTTACTAAGATCTGGG | |||||||||||||
| Wildtype AA sequence | MRRYFMHGVC REGSQCLFSH DLANSKPSTI CKYYQKGYCA YGTRCRYDHT RPSAAAGGAV GTMAHSVPSP AFHSPHPPSE VTASIVKTNS HEPGKREKRT LVLRDRNLSG MAERKTQPSM VSNPGSCSDP QPSPEMKPHS YLDAIRSGLD DVEASSSYSN EQQLCPYAAA GECRFGDACV YLHGEVCEIC RLQVLHPFDP EQRKAHEKIC MLTFEHEMEK AFAFQASQDK VCSICMEVIL EKASASERRF GILSNCNHTY CLSCIRQWRC AKQFENPIIK SCPECRVISE FVIPSVYWVE DQNKKNELIE AFKQGMGKKA CKYFEQGKGT CPFGSKCLYR HAYPDGRLAE PEKPRKQLSS QGTVRFFNSV RLWDFIENRE SRHVPNNEDV DMTELGDLFM HLSGVESSEP * | |||||||||||||
| 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 | 420 / 420 | |||||||||||||
| Last intron/exon boundary | 1514 | |||||||||||||
| Theoretical NMD boundary in CDS | 1044 | |||||||||||||
| Length of CDS | 1233 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | 4328 | |||||||||||||
| gDNA position | 27873 | |||||||||||||
| Chromosomal position | 12584929 | |||||||||||||
| 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