Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000306534
Querying Taster for transcript #2: ENST00000533054
MT speed 2.25 s - this script 4.704581 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ROBO4polymorphism_automatic9.96902560501667e-12simple_aaeQ54Rsingle base exchangers59648931show file
ROBO4polymorphism_automatic0.00288478030625705without_aaesingle base exchangers59648931show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999990031 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:124767067T>CN/A show variant in all transcripts   IGV
HGNC symbol ROBO4
Ensembl transcript ID ENST00000306534
Genbank transcript ID NM_019055
UniProt peptide Q8WZ75
alteration type single base exchange
alteration region CDS
DNA changes c.161A>G
cDNA.647A>G
g.1330A>G
AA changes Q54R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS
54
frameshift no
known variant Reference ID: rs59648931
databasehomozygous (C/C)heterozygousallele carriers
1000G44810301478
ExAC44961909523591
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5810.165
-0.0520.172
(flanking)0.4960.518
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      54FQGPGPARMSCQASGQPPPTIRWL
mutated  all conserved    54FQGPGPARMSCRASGQPP
Ptroglodytes  all conserved  ENSPTRG00000004434  54FQGPGPARMSCRASGQPP
Mmulatta  all conserved  ENSMMUG00000021578  54FQGPGPARMSCRASGQPP
Fcatus  all conserved  ENSFCAG00000006753  54LQGPGPAKMSCRASGQPP
Mmusculus  all conserved  ENSMUSG00000032125  64LQGSGPAKMRCRSSGQPP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all conserved  FBgn0005631  108VKKNEPATLNCKVEGKPEPTIEW
Celegans  not conserved  ZK377.2  53VSRGSPATLNC---GAKPSTAKITW
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
32131DOMAINIg-like C2-type 1.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3024 / 3024
position (AA) of stopcodon in wt / mu AA sequence 1008 / 1008
position of stopcodon in wt / mu cDNA 3510 / 3510
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 487 / 487
chromosome 11
strand -1
last intron/exon boundary 3488
theoretical NMD boundary in CDS 2951
length of CDS 3024
coding sequence (CDS) position 161
cDNA position
(for ins/del: last normal base / first normal base)
647
gDNA position
(for ins/del: last normal base / first normal base)
1330
chromosomal position
(for ins/del: last normal base / first normal base)
124767067
original gDNA sequence snippet CCCTGCCAGGATGAGCTGCCAAGCCTCAGGCCAGCCACCTC
altered gDNA sequence snippet CCCTGCCAGGATGAGCTGCCGAGCCTCAGGCCAGCCACCTC
original cDNA sequence snippet CCCTGCCAGGATGAGCTGCCAAGCCTCAGGCCAGCCACCTC
altered cDNA sequence snippet CCCTGCCAGGATGAGCTGCCGAGCCTCAGGCCAGCCACCTC
wildtype AA sequence MGSGGDSLLG GRGSLPLLLL LIMGGMAQDS PPQILVHPQD QLFQGPGPAR MSCQASGQPP
PTIRWLLNGQ PLSMVPPDPH HLLPDGTLLL LQPPARGHAH DGQALSTDLG VYTCEASNRL
GTAVSRGARL SVAVLREDFQ IQPRDMVAVV GEQFTLECGP PWGHPEPTVS WWKDGKPLAL
QPGRHTVSGG SLLMARAEKS DEGTYMCVAT NSAGHRESRA ARVSIQEPQD YTEPVELLAV
RIQLENVTLL NPDPAEGPKP RPAVWLSWKV SGPAAPAQSY TALFRTQTAP GGQGAPWAEE
LLAGWQSAEL GGLHWGQDYE FKVRPSSGRA RGPDSNVLLL RLPEKVPSAP PQEVTLKPGN
GTVFVSWVPP PAENHNGIIR GYQVWSLGNT SLPPANWTVV GEQTQLEIAT HMPGSYCVQV
AAVTGAGAGE PSRPVCLLLE QAMERATQEP SEHGPWTLEQ LRATLKRPEV IATCGVALWL
LLLGTAVCIH RRRRARVHLG PGLYRYTSED AILKHRMDHS DSQWLADTWR STSGSRDLSS
SSSLSSRLGA DARDPLDCRR SLLSWDSRSP GVPLLPDTST FYGSLIAELP SSTPARPSPQ
VPAVRRLPPQ LAQLSSPCSS SDSLCSRRGL SSPRLSLAPA EAWKAKKKQE LQHANSSPLL
RGSHSLELRA CELGNRGSKN LSQSPGAVPQ ALVAWRALGP KLLSSSNELV TRHLPPAPLF
PHETPPTQSQ QTQPPVAPQA PSSILLPAAP IPILSPCSPP SPQASSLSGP SPASSRLSSS
SLSSLGEDQD SVLTPEEVAL CLELSEGEET PRNSVSPMPR APSPPTTYGY ISVPTASEFT
DMGRTGGGVG PKGGVLLCPP RPCLTPTPSE GSLANGWGSA SEDNAASARA SLVSSSDGSF
LADAHFARAL AVAVDSFGFG LEPREADCVF IDASSPPSPR DEIFLTPNLS LPLWEWRPDW
LEDMEVSHTQ RLGRGMPPWP PDSQISSQRS QLHCRMPKAG ASPVDYS*
mutated AA sequence MGSGGDSLLG GRGSLPLLLL LIMGGMAQDS PPQILVHPQD QLFQGPGPAR MSCRASGQPP
PTIRWLLNGQ PLSMVPPDPH HLLPDGTLLL LQPPARGHAH DGQALSTDLG VYTCEASNRL
GTAVSRGARL SVAVLREDFQ IQPRDMVAVV GEQFTLECGP PWGHPEPTVS WWKDGKPLAL
QPGRHTVSGG SLLMARAEKS DEGTYMCVAT NSAGHRESRA ARVSIQEPQD YTEPVELLAV
RIQLENVTLL NPDPAEGPKP RPAVWLSWKV SGPAAPAQSY TALFRTQTAP GGQGAPWAEE
LLAGWQSAEL GGLHWGQDYE FKVRPSSGRA RGPDSNVLLL RLPEKVPSAP PQEVTLKPGN
GTVFVSWVPP PAENHNGIIR GYQVWSLGNT SLPPANWTVV GEQTQLEIAT HMPGSYCVQV
AAVTGAGAGE PSRPVCLLLE QAMERATQEP SEHGPWTLEQ LRATLKRPEV IATCGVALWL
LLLGTAVCIH RRRRARVHLG PGLYRYTSED AILKHRMDHS DSQWLADTWR STSGSRDLSS
SSSLSSRLGA DARDPLDCRR SLLSWDSRSP GVPLLPDTST FYGSLIAELP SSTPARPSPQ
VPAVRRLPPQ LAQLSSPCSS SDSLCSRRGL SSPRLSLAPA EAWKAKKKQE LQHANSSPLL
RGSHSLELRA CELGNRGSKN LSQSPGAVPQ ALVAWRALGP KLLSSSNELV TRHLPPAPLF
PHETPPTQSQ QTQPPVAPQA PSSILLPAAP IPILSPCSPP SPQASSLSGP SPASSRLSSS
SLSSLGEDQD SVLTPEEVAL CLELSEGEET PRNSVSPMPR APSPPTTYGY ISVPTASEFT
DMGRTGGGVG PKGGVLLCPP RPCLTPTPSE GSLANGWGSA SEDNAASARA SLVSSSDGSF
LADAHFARAL AVAVDSFGFG LEPREADCVF IDASSPPSPR DEIFLTPNLS LPLWEWRPDW
LEDMEVSHTQ RLGRGMPPWP PDSQISSQRS QLHCRMPKAG ASPVDYS*
speed 1.10 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.997115219693743 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:124767067T>CN/A show variant in all transcripts   IGV
HGNC symbol ROBO4
Ensembl transcript ID ENST00000533054
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.1330A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs59648931
databasehomozygous (C/C)heterozygousallele carriers
1000G44810301478
ExAC44961909523591
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5810.165
-0.0520.172
(flanking)0.4960.518
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 116
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
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
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 303 / 303
chromosome 11
strand -1
last intron/exon boundary 2869
theoretical NMD boundary in CDS 2516
length of CDS 2589
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
1330
chromosomal position
(for ins/del: last normal base / first normal base)
124767067
original gDNA sequence snippet CCCTGCCAGGATGAGCTGCCAAGCCTCAGGCCAGCCACCTC
altered gDNA sequence snippet CCCTGCCAGGATGAGCTGCCGAGCCTCAGGCCAGCCACCTC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVAVVGEQFT LECGPPWGHP EPTVSWWKDG KPLALQPGRH TVSGGSLLMA RAEKSDEGTY
MCVATNSAGH RESRAARVSI QEPQDYTEPV ELLAVRIQLE NVTLLNPDPA EGPKPRPAVW
LSWKVSGPAA PAQSYTALFR TQTAPGGQGA PWAEELLAGW QSAELGGLHW GQDYEFKVRP
SSGRARGPDS NVLLLRLPEK VPSAPPQEVT LKPGNGTVFV SWVPPPAENH NGIIRGYQVW
SLGNTSLPPA NWTVVGEQTQ LEIATHMPGS YCVQVAAVTG AGAGEPSRPV CLLLEQAMER
ATQEPSEHGP WTLEQLRATL KRPEVIATCG VALWLLLLGT AVCIHRRRRA RVHLGPGLYR
YTSEDAILKH RMDHSDSQWL ADTWRSTSGS RDLSSSSSLS SRLGADARDP LDCRRSLLSW
DSRSPGVPLL PDTSTFYGSL IAELPSSTPA RPSPQVPAVR RLPPQLAQLS SPCSSSDSLC
SRRGLSSPRL SLAPAEAWKA KKKQELQHAN SSPLLRGSHS LELRACELGN RGSKNLSQSP
GAVPQALVAW RALGPKLLSS SNELVTRHLP PAPLFPHETP PTQSQQTQPP VAPQAPSSIL
LPAAPIPILS PCSPPSPQAS SLSGPSPASS RLSSSSLSSL GEDQDSVLTP EEVALCLELS
EGEETPRNSV SPMPRAPSPP TTYGYISVPT ASEFTDMGRT GGGVGPKGGV LLCPPRPCLT
PTPSEGSLAN GWGSASEDNA ASARASLVSS SDGSFLADAH FARALAVAVD SFGFGLEPRE
ADCVFIDASS PPSPRDEIFL TPNLSLPLWE WRPDWLEDME VSHTQRLGRG MPPWPPDSQI
SSQRSQLHCR MPKAGASPVD YS*
mutated AA sequence N/A
speed 1.15 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

Problems