| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GPSM3 | Benign | 1|99 | 5utr | No | Single base exchange | N/A |
| ||||||
ENST00000375023(MANE Select) | NOTCH4 | Benign | 3|197 | without_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr6:32195497G>A (GRCh38) | |||||||||||||
| Gene symbol | GPSM3 | |||||||||||||
| Gene constraints | LOEUF: 1.44, LOF (oe): 0.95, misssense (oe): 0.94, synonymous (oe): 1.00 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000375043.3 | |||||||||||||
| Genbank transcript ID | NM_022107 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | 5'UTR | |||||||||||||
| DNA changes | cDNA.27C>T g.27C>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? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 6 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CGGGGATCACCTCAACTTGACTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Altered gDNA sequence snippet | CGGGGATCACCTCAACTTGATTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Original cDNA sequence snippet | CGGGGATCACCTCAACTTGACTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Altered cDNA sequence snippet | CGGGGATCACCTCAACTTGATTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Wildtype AA sequence | MEAERPQEEE DGEQGPPQDE EGWPPPNSTT RPWRSAPPSP PPPGTRHTAL GPRSASLLSL QTELLLDLVA EAQSRRLEEQ RATFYTPQNP SSLAPAPLRP LEDREQLYST ILSHQCQRME AQRSEPPLPP GGQELLELLL RVQGGGRMEE QRSRPPTHTC * | |||||||||||||
| 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 | 374 / 374 | |||||||||||||
| Last intron/exon boundary | 718 | |||||||||||||
| Theoretical NMD boundary in CDS | 294 | |||||||||||||
| Length of CDS | 483 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | 27 | |||||||||||||
| gDNA position | 27 | |||||||||||||
| Chromosomal position | 32195497 | |||||||||||||
| Speed | 0.01 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 | Chr6:32195497G>A (GRCh38) | |||||||||||||
| Gene symbol | NOTCH4 | |||||||||||||
| Gene constraints | LOEUF: 0.87, LOF (oe): 0.75, misssense (oe): 0.88, synonymous (oe): 0.92 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000375023.3 | |||||||||||||
| Genbank transcript ID | NM_004557 (exact from MANE) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.5952C>T g.28571C>T | |||||||||||||
| AA changes | no AA changes | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| 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? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | No | |||||||||||||
| Chromosome | 6 | |||||||||||||
| Strand | -1 | |||||||||||||
| Original gDNA sequence snippet | CGGGGATCACCTCAACTTGACTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Altered gDNA sequence snippet | CGGGGATCACCTCAACTTGATTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Original cDNA sequence snippet | CGGGGATCACCTCAACTTGACTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Altered cDNA sequence snippet | CGGGGATCACCTCAACTTGATTGTGGTCCCCCAGCCCTCCA | |||||||||||||
| Wildtype AA sequence | MQPPSLLLLL LLLLLLCVSV VRPRGLLCGS FPEPCANGGT CLSLSLGQGT CQCAPGFLGE TCQFPDPCQN AQLCQNGGSC QALLPAPLGL PSSPSPLTPS FLCTCLPGFT GERCQAKLED PCPPSFCSKR GRCHIQASGR PQCSCMPGWT GEQCQLRDFC SANPCVNGGV CLATYPQIQC HCPPGFEGHA CERDVNECFQ DPGPCPKGTS CHNTLGSFQC LCPVGQEGPR CELRAGPCPP RGCSNGGTCQ LMPEKDSTFH LCLCPPGFIG PDCEVNPDNC VSHQCQNGGT CQDGLDTYTC LCPETWTGWD CSEDVDECET QGPPHCRNGG TCQNSAGSFH CVCVSGWGGT SCEENLDDCI AATCAPGSTC IDRVGSFSCL CPPGRTGLLC HLEDMCLSQP CHGDAQCSTN PLTGSTLCLC QPGYSGPTCH QDLDECLMAQ QGPSPCEHGG SCLNTPGSFN CLCPPGYTGS RCEADHNECL SQPCHPGSTC LDLLATFHCL CPPGLEGQLC EVETNECASA PCLNHADCHD LLNGFQCICL PGFSGTRCEE DIDECRSSPC ANGGQCQDQP GAFHCKCLPG FEGPRCQTEV DECLSDPCPV GASCLDLPGA FFCLCPSGFT GQLCEVPLCA PNLCQPKQIC KDQKDKANCL CPDGSPGCAP PEDNCTCHHG HCQRSSCVCD VGWTGPECEA ELGGCISAPC AHGGTCYPQP SGYNCTCPTG YTGPTCSEEM TACHSGPCLN GGSCNPSPGG YYCTCPPSHT GPQCQTSTDY CVSAPCFNGG TCVNRPGTFS CLCAMGFQGP RCEGKLRPSC ADSPCRNRAT CQDSPQGPRC LCPTGYTGGS CQTLMDLCAQ KPCPRNSHCL QTGPSFHCLC LQGWTGPLCN LPLSSCQKAA LSQGIDVSSL CHNGGLCVDS GPSYFCHCPP GFQGSLCQDH VNPCESRPCQ NGATCMAQPS GYLCQCAPGY DGQNCSKELD ACQSQPCHNH GTCTPKPGGF HCACPPGFVG LRCEGDVDEC LDQPCHPTGT AACHSLANAF YCQCLPGHTG QWCEVEIDPC HSQPCFHGGT CEATAGSPLG FICHCPKGFE GPTCSHRAPS CGFHHCHHGG LCLPSPKPGF PPRCACLSGY GGPDCLTPPA PKGCGPPSPC LYNGSCSETT GLGGPGFRCS CPHSSPGPRC QKPGAKGCEG RSGDGACDAG CSGPGGNWDG GDCSLGVPDP WKGCPSHSRC WLLFRDGQCH PQCDSEECLF DGYDCETPPA CTPAYDQYCH DHFHNGHCEK GCNTAECGWD GGDCRPEDGD PEWGPSLALL VVLSPPALDQ QLFALARVLS LTLRVGLWVR KDRDGRDMVY PYPGARAEEK LGGTRDPTYQ ERAAPQTQPL GKETDSLSAG FVVVMGVDLS RCGPDHPASR CPWDPGLLLR FLAAMAAVGA LEPLLPGPLL AVHPHAGTAP PANQLPWPVL CSPVAGVILL ALGALLVLQL IRRRRREHGA LWLPPGFTRR PRTQSAPHRR RPPLGEDSIG LKALKPKAEV DEDGVVMCSG PEEGEEVGQA EETGPPSTCQ LWSLSGGCGA LPQAAMLTPP QESEMEAPDL DTRGPDGVTP LMSAVCCGEV QSGTFQGAWL GCPEPWEPLL DGGACPQAHT VGTGETPLHL AARFSRPTAA RRLLEAGANP NQPDRAGRTP LHAAVAADAR EVCQLLLRSR QTAVDARTED GTTPLMLAAR LAVEDLVEEL IAAQADVGAR DKWGKTALHW AAAVNNARAA RSLLQAGADK DAQDNREQTP LFLAAREGAV EVAQLLLGLG AARELRDQAG LAPADVAHQR NHWDLLTLLE GAGPPEARHK ATPGREAGPF PRARTVSVSV PPHGGGALPR CRTLSAGAGP RGGGACLQAR TWSVDLAARG GGAYSHCRSL SGVGAGGGPT PRGRRFSAGM RGPRPNPAIM RGRYGVAAGR GGRVSTDDWP CDWVALGACG SASNIPIPPP CLTPSPERGS PQLDCGPPAL QEMPINQGGE GKK* | |||||||||||||
| Mutated AA sequence | MQPPSLLLLL LLLLLLCVSV VRPRGLLCGS FPEPCANGGT CLSLSLGQGT CQCAPGFLGE TCQFPDPCQN AQLCQNGGSC QALLPAPLGL PSSPSPLTPS FLCTCLPGFT GERCQAKLED PCPPSFCSKR GRCHIQASGR PQCSCMPGWT GEQCQLRDFC SANPCVNGGV CLATYPQIQC HCPPGFEGHA CERDVNECFQ DPGPCPKGTS CHNTLGSFQC LCPVGQEGPR CELRAGPCPP RGCSNGGTCQ LMPEKDSTFH LCLCPPGFIG PDCEVNPDNC VSHQCQNGGT CQDGLDTYTC LCPETWTGWD CSEDVDECET QGPPHCRNGG TCQNSAGSFH CVCVSGWGGT SCEENLDDCI AATCAPGSTC IDRVGSFSCL CPPGRTGLLC HLEDMCLSQP CHGDAQCSTN PLTGSTLCLC QPGYSGPTCH QDLDECLMAQ QGPSPCEHGG SCLNTPGSFN CLCPPGYTGS RCEADHNECL SQPCHPGSTC LDLLATFHCL CPPGLEGQLC EVETNECASA PCLNHADCHD LLNGFQCICL PGFSGTRCEE DIDECRSSPC ANGGQCQDQP GAFHCKCLPG FEGPRCQTEV DECLSDPCPV GASCLDLPGA FFCLCPSGFT GQLCEVPLCA PNLCQPKQIC KDQKDKANCL CPDGSPGCAP PEDNCTCHHG HCQRSSCVCD VGWTGPECEA ELGGCISAPC AHGGTCYPQP SGYNCTCPTG YTGPTCSEEM TACHSGPCLN GGSCNPSPGG YYCTCPPSHT GPQCQTSTDY CVSAPCFNGG TCVNRPGTFS CLCAMGFQGP RCEGKLRPSC ADSPCRNRAT CQDSPQGPRC LCPTGYTGGS CQTLMDLCAQ KPCPRNSHCL QTGPSFHCLC LQGWTGPLCN LPLSSCQKAA LSQGIDVSSL CHNGGLCVDS GPSYFCHCPP GFQGSLCQDH VNPCESRPCQ NGATCMAQPS GYLCQCAPGY DGQNCSKELD ACQSQPCHNH GTCTPKPGGF HCACPPGFVG LRCEGDVDEC LDQPCHPTGT AACHSLANAF YCQCLPGHTG QWCEVEIDPC HSQPCFHGGT CEATAGSPLG FICHCPKGFE GPTCSHRAPS CGFHHCHHGG LCLPSPKPGF PPRCACLSGY GGPDCLTPPA PKGCGPPSPC LYNGSCSETT GLGGPGFRCS CPHSSPGPRC QKPGAKGCEG RSGDGACDAG CSGPGGNWDG GDCSLGVPDP WKGCPSHSRC WLLFRDGQCH PQCDSEECLF DGYDCETPPA CTPAYDQYCH DHFHNGHCEK GCNTAECGWD GGDCRPEDGD PEWGPSLALL VVLSPPALDQ QLFALARVLS LTLRVGLWVR KDRDGRDMVY PYPGARAEEK LGGTRDPTYQ ERAAPQTQPL GKETDSLSAG FVVVMGVDLS RCGPDHPASR CPWDPGLLLR FLAAMAAVGA LEPLLPGPLL AVHPHAGTAP PANQLPWPVL CSPVAGVILL ALGALLVLQL IRRRRREHGA LWLPPGFTRR PRTQSAPHRR RPPLGEDSIG LKALKPKAEV DEDGVVMCSG PEEGEEVGQA EETGPPSTCQ LWSLSGGCGA LPQAAMLTPP QESEMEAPDL DTRGPDGVTP LMSAVCCGEV QSGTFQGAWL GCPEPWEPLL DGGACPQAHT VGTGETPLHL AARFSRPTAA RRLLEAGANP NQPDRAGRTP LHAAVAADAR EVCQLLLRSR QTAVDARTED GTTPLMLAAR LAVEDLVEEL IAAQADVGAR DKWGKTALHW AAAVNNARAA RSLLQAGADK DAQDNREQTP LFLAAREGAV EVAQLLLGLG AARELRDQAG LAPADVAHQR NHWDLLTLLE GAGPPEARHK ATPGREAGPF PRARTVSVSV PPHGGGALPR CRTLSAGAGP RGGGACLQAR TWSVDLAARG GGAYSHCRSL SGVGAGGGPT PRGRRFSAGM RGPRPNPAIM RGRYGVAAGR GGRVSTDDWP CDWVALGACG SASNIPIPPP CLTPSPERGS PQLDCGPPAL QEMPINQGGE GKK* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 6012 / 6012 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2004 / 2004 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 6151 / 6151 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 140 / 140 | |||||||||||||
| Last intron/exon boundary | 5437 | |||||||||||||
| Theoretical NMD boundary in CDS | 5247 | |||||||||||||
| Length of CDS | 6012 | |||||||||||||
| Coding sequence (CDS) position | 5952 | |||||||||||||
| cDNA position | 6091 | |||||||||||||
| gDNA position | 28571 | |||||||||||||
| Chromosomal position | 32195497 | |||||||||||||
| 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