| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000257290(MANE Select) | PDGFRA | Deleterious | 94|6 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr4:54285413G>T (GRCh38) | |||||||||||||||||||||
| Gene symbol | PDGFRA | |||||||||||||||||||||
| Gene constraints | LOEUF: 0.26, LOF (oe): 0.17, misssense (oe): 0.73, synonymous (oe): 0.89 (gnomAD) | |||||||||||||||||||||
| Ensembl transcript ID | ENST00000257290.10 | |||||||||||||||||||||
| Genbank transcript ID | NM_006206 (exact from MANE), NM_001347828 (by similarity), NM_001347829 (by similarity), NM_001347830 (by similarity) | |||||||||||||||||||||
| UniProt / AlphaMissense peptide | PGFRA_HUMAN | AlphaMissense: transcript, gene | |||||||||||||||||||||
| Variant type | Single base exchange | |||||||||||||||||||||
| Gene region | CDS | |||||||||||||||||||||
| DNA changes | c.2366G>T g.56134G>T | |||||||||||||||||||||
| AA changes |
| |||||||||||||||||||||
| Frameshift | No | |||||||||||||||||||||
| Length of protein | Normal | |||||||||||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||||||||||
| Variant DBs |
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| Protein conservation | ||||||||||||||||||||||
| Protein features |
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| Phylogenetic conservation |
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| 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 | 4 | |||||||||||||||||||||
| Strand | 1 | |||||||||||||||||||||
| Original gDNA sequence snippet | TTCAGATGATAACTCAGAAGGCCTTACTTTATTGGATTTGT | |||||||||||||||||||||
| Altered gDNA sequence snippet | TTCAGATGATAACTCAGAAGTCCTTACTTTATTGGATTTGT | |||||||||||||||||||||
| Original cDNA sequence snippet | TTCAGATGATAACTCAGAAGGCCTTACTTTATTGGATTTGT | |||||||||||||||||||||
| Altered cDNA sequence snippet | TTCAGATGATAACTCAGAAGTCCTTACTTTATTGGATTTGT | |||||||||||||||||||||
| Wildtype AA sequence | MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSSA SAAHTGLYTC YYNHTQTEEN ELEGRHIYIY VPDPDVAFVP LGMTDYLVIV EDDDSAIIPC RTTDPETPVT LHNSEGVVPA SYDSRQGFNG TFTVGPYICE ATVKGKKFQT IPFNVYALKA TSELDLEMEA LKTVYKSGET IVVTCAVFNN EVVDLQWTYP GEVKGKGITM LEEIKVPSIK LVYTLTVPEA TVKDSGDYEC AARQATREVK EMKKVTISVH EKGFIEIKPT FSQLEAVNLH EVKHFVVEVR AYPPPRISWL KNNLTLIENL TEITTDVEKI QEIRYRSKLK LIRAKEEDSG HYTIVAQNED AVKSYTFELL TQVPSSILDL VDDHHGSTGG QTVRCTAEGT PLPDIEWMIC KDIKKCNNET SWTILANNVS NIITEIHSRD RSTVEGRVTF AKVEETIAVR CLAKNLLGAE NRELKLVAPT LRSELTVAAA VLVLLVIVII SLIVLVVIWK QKPRYEIRWR VIESISPDGH EYIYVDPMQL PYDSRWEFPR DGLVLGRVLG SGAFGKVVEG TAYGLSRSQP VMKVAVKMLK PTARSSEKQA LMSELKIMTH LGPHLNIVNL LGACTKSGPI YIITEYCFYG DLVNYLHKNR DSFLSHHPEK PKKELDIFGL NPADESTRSY VILSFENNGD YMDMKQADTT QYVPMLERKE VSKYSDIQRS LYDRPASYKK KSMLDSEVKN LLSDDNSEGL TLLDLLSFTY QVARGMEFLA SKNCVHRDLA ARNVLLAQGK IVKICDFGLA RDIMHDSNYV SKGSTFLPVK WMAPESIFDN LYTTLSDVWS YGILLWEIFS LGGTPYPGMM VDSTFYNKIK SGYRMAKPDH ATSEVYEIMV KCWNSEPEKR PSFYHLSEIV ENLLPGQYKK SYEKIHLDFL KSDHPAVARM RVDSDNAYIG VTYKNEEDKL KDWEGGLDEQ RLSADSGYII PLPDIDPVPE EEDLGKRNRH SSQTSEESAI ETGSSSSTFI KREDETIEDI DMMDDIGIDS SDLVEDSFL* | |||||||||||||||||||||
| Mutated AA sequence | MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSSA SAAHTGLYTC YYNHTQTEEN ELEGRHIYIY VPDPDVAFVP LGMTDYLVIV EDDDSAIIPC RTTDPETPVT LHNSEGVVPA SYDSRQGFNG TFTVGPYICE ATVKGKKFQT IPFNVYALKA TSELDLEMEA LKTVYKSGET IVVTCAVFNN EVVDLQWTYP GEVKGKGITM LEEIKVPSIK LVYTLTVPEA TVKDSGDYEC AARQATREVK EMKKVTISVH EKGFIEIKPT FSQLEAVNLH EVKHFVVEVR AYPPPRISWL KNNLTLIENL TEITTDVEKI QEIRYRSKLK LIRAKEEDSG HYTIVAQNED AVKSYTFELL TQVPSSILDL VDDHHGSTGG QTVRCTAEGT PLPDIEWMIC KDIKKCNNET SWTILANNVS NIITEIHSRD RSTVEGRVTF AKVEETIAVR CLAKNLLGAE NRELKLVAPT LRSELTVAAA VLVLLVIVII SLIVLVVIWK QKPRYEIRWR VIESISPDGH EYIYVDPMQL PYDSRWEFPR DGLVLGRVLG SGAFGKVVEG TAYGLSRSQP VMKVAVKMLK PTARSSEKQA LMSELKIMTH LGPHLNIVNL LGACTKSGPI YIITEYCFYG DLVNYLHKNR DSFLSHHPEK PKKELDIFGL NPADESTRSY VILSFENNGD YMDMKQADTT QYVPMLERKE VSKYSDIQRS LYDRPASYKK KSMLDSEVKN LLSDDNSEVL TLLDLLSFTY QVARGMEFLA SKNCVHRDLA ARNVLLAQGK IVKICDFGLA RDIMHDSNYV SKGSTFLPVK WMAPESIFDN LYTTLSDVWS YGILLWEIFS LGGTPYPGMM VDSTFYNKIK SGYRMAKPDH ATSEVYEIMV KCWNSEPEKR PSFYHLSEIV ENLLPGQYKK SYEKIHLDFL KSDHPAVARM RVDSDNAYIG VTYKNEEDKL KDWEGGLDEQ RLSADSGYII PLPDIDPVPE EEDLGKRNRH SSQTSEESAI ETGSSSSTFI KREDETIEDI DMMDDIGIDS SDLVEDSFL* | |||||||||||||||||||||
| Position of stopcodon in wt / mu CDS | 3270 / 3270 | |||||||||||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 1090 / 1090 | |||||||||||||||||||||
| Position of stopcodon in wt / mu cDNA | 3405 / 3405 | |||||||||||||||||||||
| Position of start ATG in wt / mu cDNA | 136 / 136 | |||||||||||||||||||||
| Last intron/exon boundary | 3257 | |||||||||||||||||||||
| Theoretical NMD boundary in CDS | 3071 | |||||||||||||||||||||
| Length of CDS | 3270 | |||||||||||||||||||||
| Coding sequence (CDS) position | 2366 | |||||||||||||||||||||
| cDNA position | 2501 | |||||||||||||||||||||
| gDNA position | 56134 | |||||||||||||||||||||
| Chromosomal position | 54285413 | |||||||||||||||||||||
| 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