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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000266041
Querying Taster for transcript #2: ENST00000485816
Querying Taster for transcript #3: ENST00000406595
Querying Taster for transcript #4: ENST00000346281
Querying Taster for transcript #5: ENST00000434759
MT speed 2.76 s - this script 3.875693 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ITIH4polymorphism_automatic0.841809606784767simple_aaeaffectedI85Nsingle base exchangers13072536show file
ITIH4polymorphism_automatic0.841809606784767simple_aaeaffectedI85Nsingle base exchangers13072536show file
ITIH4polymorphism_automatic0.841809606784767simple_aaeaffectedI85Nsingle base exchangers13072536show file
ITIH4polymorphism_automatic0.841809606784767simple_aaeaffectedI85Nsingle base exchangers13072536show file
ITIH4polymorphism_automatic0.999999999995479without_aaeaffectedsingle base exchangers13072536show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.158190393215233 (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
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:52861211A>TN/A show variant in all transcripts   IGV
HGNC symbol ITIH4
Ensembl transcript ID ENST00000266041
Genbank transcript ID NM_002218
UniProt peptide Q14624
alteration type single base exchange
alteration region CDS
DNA changes c.254T>A
cDNA.351T>A
g.4285T>A
AA changes I85N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 85
frameshift no
known variant Reference ID: rs13072536
databasehomozygous (T/T)heterozygousallele carriers
1000G1668961062
ExAC43082144525753
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9660.991
0.6060.979
(flanking)-0.1150.967
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost4282.5sequence motif lost- wt: ccca|GGAT
 mu: ccca.GGAA
Acc marginally increased4281wt: 0.8712 / mu: 0.8733 (marginal change - not scored)wt: ACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACC
mu: ACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACC		 ccca|GGAT
Acc marginally increased4275wt: 0.2184 / mu: 0.2264 (marginal change - not scored)wt: TCAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGC
mu: TCAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGC		 tctg|CCCC
Acc marginally increased4276wt: 0.5850 / mu: 0.5963 (marginal change - not scored)wt: CAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCA
mu: CAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCA		 ctgc|CCCC
Acc marginally increased4280wt: 0.6087 / mu: 0.6576 (marginal change - not scored)wt: AACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGAC
mu: AACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGAC		 cccc|AGGA
Acc marginally increased4282wt: 0.9638 / mu: 0.9676 (marginal change - not scored)wt: CTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCT
mu: CTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCT		 ccag|GATC
Donor increased4281wt: 0.26 / mu: 0.92wt: CCCCCAGGATCATCG
mu: CCCCCAGGAACATCG		 CCCA|ggat
Donor increased4287wt: 0.37 / mu: 0.47wt: GGATCATCGATGGCA
mu: GGAACATCGATGGCA		 ATCA|tcga
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      85PKKAFITNFSMIIDGMTYPGIIKE
mutated  not conserved    85PKKAFITNFSMNIDGMTYPGIIK
Ptroglodytes  all identical  ENSPTRG00000034152  85PKKAFITNFSMIIDGMTYPGIIK
Mmulatta  all identical  ENSMMUG00000014523  85PKKAFITNFSMIIDGVTYPGIIK
Fcatus  all identical  ENSFCAG00000015724  84PKRAFITNFSMIIDGVTYPGNIK
Mmusculus  all identical  ENSMUSG00000021922  85PRKAFITNFSMIIDGVTYPGVVK
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013605  85PKNAFITKFKMVIDGQEYDGIVK
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
29148DOMAINVIT.lost
8585CONFLICTI -> K (in Ref. 3; AAD05198).lost
114114CONFLICTS -> N (in Ref. 2; BAA07602).might get lost (downstream of altered splice site)
207207CONFLICTN -> F (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
207207CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
221221CONFLICTQ -> E (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
272432DOMAINVWFA.might get lost (downstream of altered splice site)
307307CONFLICTR -> V (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
322322CONFLICTW -> Y (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
517517CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
577577CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
662688PROPEPPotentially active peptide. /FTId=PRO_0000016542.might get lost (downstream of altered splice site)
696696CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
701701CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
702702CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
719725REGIONO-glycosylated at three sites.might get lost (downstream of altered splice site)
720720CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
747747DISULFIDProbable.might get lost (downstream of altered splice site)
816817CONFLICTET -> QR (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
925925DISULFIDProbable.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2793 / 2793
position (AA) of stopcodon in wt / mu AA sequence 931 / 931
position of stopcodon in wt / mu cDNA 2890 / 2890
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 98 / 98
chromosome 3
strand -1
last intron/exon boundary 2821
theoretical NMD boundary in CDS 2673
length of CDS 2793
coding sequence (CDS) position 254
cDNA position
(for ins/del: last normal base / first normal base)		 351
gDNA position
(for ins/del: last normal base / first normal base)		 4285
chromosomal position
(for ins/del: last normal base / first normal base)		 52861211
original gDNA sequence snippet CCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCTACC
altered gDNA sequence snippet CCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCTACC
original cDNA sequence snippet CATCACCAACTTCTCCATGATCATCGATGGCATGACCTACC
altered cDNA sequence snippet CATCACCAACTTCTCCATGAACATCGATGGCATGACCTACC
wildtype AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMIIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS GSTFFKYYLQ GAKIPKPEAS FSPRRGWNRQ AGAAGSRMNF
RPGVLSSRQL GLPGPPDVPD HAAYHPFRRL AILPASAPPA TSNPDPAVSR VMNMKIEETT
MTTQTPAPIQ APSAILPLPG QSVERLCVDP RHRQGPVNLL SDPEQGVEVT GQYEREKAGF
SWIEVTFKNP LVWVHASPEH VVVTRNRRSS AYKWKETLFS VMPGLKMTMD KTGLLLLSDP
DKVTIGLLFW DGRGEGLRLL LRDTDRFSSH VGGTLGQFYQ EVLWGSPAAS DDGRRTLRVQ
GNDHSATRER RLDYQEGPPG VEISCWSVEL *
mutated AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMNIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS GSTFFKYYLQ GAKIPKPEAS FSPRRGWNRQ AGAAGSRMNF
RPGVLSSRQL GLPGPPDVPD HAAYHPFRRL AILPASAPPA TSNPDPAVSR VMNMKIEETT
MTTQTPAPIQ APSAILPLPG QSVERLCVDP RHRQGPVNLL SDPEQGVEVT GQYEREKAGF
SWIEVTFKNP LVWVHASPEH VVVTRNRRSS AYKWKETLFS VMPGLKMTMD KTGLLLLSDP
DKVTIGLLFW DGRGEGLRLL LRDTDRFSSH VGGTLGQFYQ EVLWGSPAAS DDGRRTLRVQ
GNDHSATRER RLDYQEGPPG VEISCWSVEL *
speed 0.86 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: simple_aae, prob: 0.158190393215233 (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
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:52861211A>TN/A show variant in all transcripts   IGV
HGNC symbol ITIH4
Ensembl transcript ID ENST00000485816
Genbank transcript ID N/A
UniProt peptide Q14624
alteration type single base exchange
alteration region CDS
DNA changes c.254T>A
cDNA.285T>A
g.4285T>A
AA changes I85N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 85
frameshift no
known variant Reference ID: rs13072536
databasehomozygous (T/T)heterozygousallele carriers
1000G1668961062
ExAC43082144525753
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9660.991
0.6060.979
(flanking)-0.1150.967
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost4282.5sequence motif lost- wt: ccca|GGAT
 mu: ccca.GGAA
Acc marginally increased4281wt: 0.8712 / mu: 0.8733 (marginal change - not scored)wt: ACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACC
mu: ACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACC		 ccca|GGAT
Acc marginally increased4275wt: 0.2184 / mu: 0.2264 (marginal change - not scored)wt: TCAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGC
mu: TCAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGC		 tctg|CCCC
Acc marginally increased4276wt: 0.5850 / mu: 0.5963 (marginal change - not scored)wt: CAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCA
mu: CAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCA		 ctgc|CCCC
Acc marginally increased4280wt: 0.6087 / mu: 0.6576 (marginal change - not scored)wt: AACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGAC
mu: AACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGAC		 cccc|AGGA
Acc marginally increased4282wt: 0.9638 / mu: 0.9676 (marginal change - not scored)wt: CTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCT
mu: CTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCT		 ccag|GATC
Donor increased4281wt: 0.26 / mu: 0.92wt: CCCCCAGGATCATCG
mu: CCCCCAGGAACATCG		 CCCA|ggat
Donor increased4287wt: 0.37 / mu: 0.47wt: GGATCATCGATGGCA
mu: GGAACATCGATGGCA		 ATCA|tcga
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      85PKKAFITNFSMIIDGMTYPGIIKE
mutated  not conserved    85PKKAFITNFSMNIDGMTYPGIIK
Ptroglodytes  all identical  ENSPTRG00000034152  85PKKAFITNFSMIIDGMTYPGIIK
Mmulatta  all identical  ENSMMUG00000014523  85PKKAFITNFSMIIDGVTYPGIIK
Fcatus  all identical  ENSFCAG00000015724  84PKRAFITNFSMIIDGVTYPGNIK
Mmusculus  all identical  ENSMUSG00000021922  85PRKAFITNFSMIIDGVTYPGVVK
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013605  85PKNAFITKFKMVIDGQEYDGIVK
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
29148DOMAINVIT.lost
8585CONFLICTI -> K (in Ref. 3; AAD05198).lost
114114CONFLICTS -> N (in Ref. 2; BAA07602).might get lost (downstream of altered splice site)
207207CONFLICTN -> F (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
207207CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
221221CONFLICTQ -> E (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
272432DOMAINVWFA.might get lost (downstream of altered splice site)
307307CONFLICTR -> V (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
322322CONFLICTW -> Y (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
517517CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
577577CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
662688PROPEPPotentially active peptide. /FTId=PRO_0000016542.might get lost (downstream of altered splice site)
696696CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
701701CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
702702CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
719725REGIONO-glycosylated at three sites.might get lost (downstream of altered splice site)
720720CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
747747DISULFIDProbable.might get lost (downstream of altered splice site)
816817CONFLICTET -> QR (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
925925DISULFIDProbable.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2808 / 2808
position (AA) of stopcodon in wt / mu AA sequence 936 / 936
position of stopcodon in wt / mu cDNA 2839 / 2839
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 32 / 32
chromosome 3
strand -1
last intron/exon boundary 2770
theoretical NMD boundary in CDS 2688
length of CDS 2808
coding sequence (CDS) position 254
cDNA position
(for ins/del: last normal base / first normal base)		 285
gDNA position
(for ins/del: last normal base / first normal base)		 4285
chromosomal position
(for ins/del: last normal base / first normal base)		 52861211
original gDNA sequence snippet CCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCTACC
altered gDNA sequence snippet CCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCTACC
original cDNA sequence snippet CATCACCAACTTCTCCATGATCATCGATGGCATGACCTACC
altered cDNA sequence snippet CATCACCAACTTCTCCATGAACATCGATGGCATGACCTACC
wildtype AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMIIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS GSTFFKYYLQ GAKIPKPGLD HTEASFSPRR GWNRQAGAAG
SRMNFRPGVL SSRQLGLPGP PDVPDHAAYH PFRRLAILPA SAPPATSNPD PAVSRVMNMK
IEETTMTTQT PAPIQAPSAI LPLPGQSVER LCVDPRHRQG PVNLLSDPEQ GVEVTGQYER
EKAGFSWIEV TFKNPLVWVH ASPEHVVVTR NRRSSAYKWK ETLFSVMPGL KMTMDKTGLL
LLSDPDKVTI GLLFWDGRGE GLRLLLRDTD RFSSHVGGTL GQFYQEVLWG SPAASDDGRR
TLRVQGNDHS ATRERRLDYQ EGPPGVEISC WSVEL*
mutated AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMNIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS GSTFFKYYLQ GAKIPKPGLD HTEASFSPRR GWNRQAGAAG
SRMNFRPGVL SSRQLGLPGP PDVPDHAAYH PFRRLAILPA SAPPATSNPD PAVSRVMNMK
IEETTMTTQT PAPIQAPSAI LPLPGQSVER LCVDPRHRQG PVNLLSDPEQ GVEVTGQYER
EKAGFSWIEV TFKNPLVWVH ASPEHVVVTR NRRSSAYKWK ETLFSVMPGL KMTMDKTGLL
LLSDPDKVTI GLLFWDGRGE GLRLLLRDTD RFSSHVGGTL GQFYQEVLWG SPAASDDGRR
TLRVQGNDHS ATRERRLDYQ EGPPGVEISC WSVEL*
speed 0.90 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: simple_aae, prob: 0.158190393215233 (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
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:52861211A>TN/A show variant in all transcripts   IGV
HGNC symbol ITIH4
Ensembl transcript ID ENST00000406595
Genbank transcript ID NM_001166449
UniProt peptide Q14624
alteration type single base exchange
alteration region CDS
DNA changes c.254T>A
cDNA.284T>A
g.4285T>A
AA changes I85N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 85
frameshift no
known variant Reference ID: rs13072536
databasehomozygous (T/T)heterozygousallele carriers
1000G1668961062
ExAC43082144525753
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9660.991
0.6060.979
(flanking)-0.1150.967
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost4282.5sequence motif lost- wt: ccca|GGAT
 mu: ccca.GGAA
Acc marginally increased4281wt: 0.8712 / mu: 0.8733 (marginal change - not scored)wt: ACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACC
mu: ACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACC		 ccca|GGAT
Acc marginally increased4275wt: 0.2184 / mu: 0.2264 (marginal change - not scored)wt: TCAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGC
mu: TCAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGC		 tctg|CCCC
Acc marginally increased4276wt: 0.5850 / mu: 0.5963 (marginal change - not scored)wt: CAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCA
mu: CAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCA		 ctgc|CCCC
Acc marginally increased4280wt: 0.6087 / mu: 0.6576 (marginal change - not scored)wt: AACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGAC
mu: AACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGAC		 cccc|AGGA
Acc marginally increased4282wt: 0.9638 / mu: 0.9676 (marginal change - not scored)wt: CTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCT
mu: CTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCT		 ccag|GATC
Donor increased4281wt: 0.26 / mu: 0.92wt: CCCCCAGGATCATCG
mu: CCCCCAGGAACATCG		 CCCA|ggat
Donor increased4287wt: 0.37 / mu: 0.47wt: GGATCATCGATGGCA
mu: GGAACATCGATGGCA		 ATCA|tcga
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      85PKKAFITNFSMIIDGMTYPGIIKE
mutated  not conserved    85PKKAFITNFSMNIDGMTYPGIIK
Ptroglodytes  all identical  ENSPTRG00000034152  85PKKAFITNFSMIIDGMTYPGIIK
Mmulatta  all identical  ENSMMUG00000014523  85PKKAFITNFSMIIDGVTYPGIIK
Fcatus  all identical  ENSFCAG00000015724  84PKRAFITNFSMIIDGVTYPGNIK
Mmusculus  all identical  ENSMUSG00000021922  85PRKAFITNFSMIIDGVTYPGVVK
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013605  85PKNAFITKFKMVIDGQEYDGIVK
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
29148DOMAINVIT.lost
8585CONFLICTI -> K (in Ref. 3; AAD05198).lost
114114CONFLICTS -> N (in Ref. 2; BAA07602).might get lost (downstream of altered splice site)
207207CONFLICTN -> F (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
207207CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
221221CONFLICTQ -> E (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
272432DOMAINVWFA.might get lost (downstream of altered splice site)
307307CONFLICTR -> V (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
322322CONFLICTW -> Y (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
517517CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
577577CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
662688PROPEPPotentially active peptide. /FTId=PRO_0000016542.might get lost (downstream of altered splice site)
696696CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
701701CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
702702CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
719725REGIONO-glycosylated at three sites.might get lost (downstream of altered splice site)
720720CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
747747DISULFIDProbable.might get lost (downstream of altered splice site)
816817CONFLICTET -> QR (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
925925DISULFIDProbable.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2703 / 2703
position (AA) of stopcodon in wt / mu AA sequence 901 / 901
position of stopcodon in wt / mu cDNA 2733 / 2733
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 31 / 31
chromosome 3
strand -1
last intron/exon boundary 2664
theoretical NMD boundary in CDS 2583
length of CDS 2703
coding sequence (CDS) position 254
cDNA position
(for ins/del: last normal base / first normal base)		 284
gDNA position
(for ins/del: last normal base / first normal base)		 4285
chromosomal position
(for ins/del: last normal base / first normal base)		 52861211
original gDNA sequence snippet CCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCTACC
altered gDNA sequence snippet CCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCTACC
original cDNA sequence snippet CATCACCAACTTCTCCATGATCATCGATGGCATGACCTACC
altered cDNA sequence snippet CATCACCAACTTCTCCATGAACATCGATGGCATGACCTACC
wildtype AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMIIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS AGAAGSRMNF RPGVLSSRQL GLPGPPDVPD HAAYHPFRRL
AILPASAPPA TSNPDPAVSR VMNMKIEETT MTTQTPAPIQ APSAILPLPG QSVERLCVDP
RHRQGPVNLL SDPEQGVEVT GQYEREKAGF SWIEVTFKNP LVWVHASPEH VVVTRNRRSS
AYKWKETLFS VMPGLKMTMD KTGLLLLSDP DKVTIGLLFW DGRGEGLRLL LRDTDRFSSH
VGGTLGQFYQ EVLWGSPAAS DDGRRTLRVQ GNDHSATRER RLDYQEGPPG VEISCWSVEL
*
mutated AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMNIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS AGAAGSRMNF RPGVLSSRQL GLPGPPDVPD HAAYHPFRRL
AILPASAPPA TSNPDPAVSR VMNMKIEETT MTTQTPAPIQ APSAILPLPG QSVERLCVDP
RHRQGPVNLL SDPEQGVEVT GQYEREKAGF SWIEVTFKNP LVWVHASPEH VVVTRNRRSS
AYKWKETLFS VMPGLKMTMD KTGLLLLSDP DKVTIGLLFW DGRGEGLRLL LRDTDRFSSH
VGGTLGQFYQ EVLWGSPAAS DDGRRTLRVQ GNDHSATRER RLDYQEGPPG VEISCWSVEL
*
speed 0.09 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: simple_aae, prob: 0.158190393215233 (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
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:52861211A>TN/A show variant in all transcripts   IGV
HGNC symbol ITIH4
Ensembl transcript ID ENST00000346281
Genbank transcript ID N/A
UniProt peptide Q14624
alteration type single base exchange
alteration region CDS
DNA changes c.254T>A
cDNA.313T>A
g.4285T>A
AA changes I85N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 85
frameshift no
known variant Reference ID: rs13072536
databasehomozygous (T/T)heterozygousallele carriers
1000G1668961062
ExAC43082144525753
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9660.991
0.6060.979
(flanking)-0.1150.967
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost4282.5sequence motif lost- wt: ccca|GGAT
 mu: ccca.GGAA
Acc marginally increased4281wt: 0.8712 / mu: 0.8733 (marginal change - not scored)wt: ACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACC
mu: ACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACC		 ccca|GGAT
Acc marginally increased4275wt: 0.2184 / mu: 0.2264 (marginal change - not scored)wt: TCAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGC
mu: TCAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGC		 tctg|CCCC
Acc marginally increased4276wt: 0.5850 / mu: 0.5963 (marginal change - not scored)wt: CAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCA
mu: CAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCA		 ctgc|CCCC
Acc marginally increased4280wt: 0.6087 / mu: 0.6576 (marginal change - not scored)wt: AACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGAC
mu: AACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGAC		 cccc|AGGA
Acc marginally increased4282wt: 0.9638 / mu: 0.9676 (marginal change - not scored)wt: CTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCT
mu: CTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCT		 ccag|GATC
Donor increased4281wt: 0.26 / mu: 0.92wt: CCCCCAGGATCATCG
mu: CCCCCAGGAACATCG		 CCCA|ggat
Donor increased4287wt: 0.37 / mu: 0.47wt: GGATCATCGATGGCA
mu: GGAACATCGATGGCA		 ATCA|tcga
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      85PKKAFITNFSMIIDGMTYPGIIKE
mutated  not conserved    85PKKAFITNFSMNIDGMTYPGIIK
Ptroglodytes  all identical  ENSPTRG00000034152  85PKKAFITNFSMIIDGMTYPGIIK
Mmulatta  all identical  ENSMMUG00000014523  85PKKAFITNFSMIIDGVTYPGIIK
Fcatus  all identical  ENSFCAG00000015724  84PKRAFITNFSMIIDGVTYPGNIK
Mmusculus  all identical  ENSMUSG00000021922  85PRKAFITNFSMIIDGVTYPGVVK
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013605  85PKNAFITKFKMVIDGQEYDGIVK
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
29148DOMAINVIT.lost
8585CONFLICTI -> K (in Ref. 3; AAD05198).lost
114114CONFLICTS -> N (in Ref. 2; BAA07602).might get lost (downstream of altered splice site)
207207CONFLICTN -> F (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
207207CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
221221CONFLICTQ -> E (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
272432DOMAINVWFA.might get lost (downstream of altered splice site)
307307CONFLICTR -> V (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
322322CONFLICTW -> Y (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
517517CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
577577CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
662688PROPEPPotentially active peptide. /FTId=PRO_0000016542.might get lost (downstream of altered splice site)
696696CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
701701CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
702702CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
719725REGIONO-glycosylated at three sites.might get lost (downstream of altered splice site)
720720CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
747747DISULFIDProbable.might get lost (downstream of altered splice site)
816817CONFLICTET -> QR (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
925925DISULFIDProbable.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2745 / 2745
position (AA) of stopcodon in wt / mu AA sequence 915 / 915
position of stopcodon in wt / mu cDNA 2804 / 2804
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 60 / 60
chromosome 3
strand -1
last intron/exon boundary 2735
theoretical NMD boundary in CDS 2625
length of CDS 2745
coding sequence (CDS) position 254
cDNA position
(for ins/del: last normal base / first normal base)		 313
gDNA position
(for ins/del: last normal base / first normal base)		 4285
chromosomal position
(for ins/del: last normal base / first normal base)		 52861211
original gDNA sequence snippet CCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCTACC
altered gDNA sequence snippet CCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCTACC
original cDNA sequence snippet CATCACCAACTTCTCCATGATCATCGATGGCATGACCTACC
altered cDNA sequence snippet CATCACCAACTTCTCCATGAACATCGATGGCATGACCTACC
wildtype AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMIIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS AGAAGSRMNF RPGVLSSRQL GLPGPPDVPD HAAYHPFRRL
AILPASAPPA TSNPDPAVSR VMNMKIEETT MTTQTPACPS CSRSRAPAVP APIQAPSAIL
PLPGQSVERL CVDPRHRQGP VNLLSDPEQG VEVTGQYERE KAGFSWIEVT FKNPLVWVHA
SPEHVVVTRN RRSSAYKWKE TLFSVMPGLK MTMDKTGLLL LSDPDKVTIG LLFWDGRGEG
LRLLLRDTDR FSSHVGGTLG QFYQEVLWGS PAASDDGRRT LRVQGNDHSA TRERRLDYQE
GPPGVEISCW SVEL*
mutated AA sequence MKPPRPVRTC SKVLVLLSLL AIHQTTTAEK NGIDIYSLTV DSRVSSRFAH TVVTSRVVNR
ANTVQEATFQ MELPKKAFIT NFSMNIDGMT YPGIIKEKAE AQAQYSAAVA KGKSAGLVKA
TGRNMEQFQV SVSVAPNAKI TFELVYEELL KRRLGVYELL LKVRPQQLVK HLQMDIHIFE
PQGISFLETE STFMTNQLVD ALTTWQNKTK AHIRFKPTLS QQQKSPEQQE TVLDGNLIIR
YDVDRAISGG SIQIENGYFV HYFAPEGLTT MPKNVVFVID KSGSMSGRKI QQTREALIKI
LDDLSPRDQF NLIVFSTEAT QWRPSLVPAS AENVNKARSF AAGIQALGGT NINDAMLMAV
QLLDSSNQEE RLPEGSVSLI ILLTDGDPTV GETNPRSIQN NVREAVSGRY SLFCLGFGFD
VSYAFLEKLA LDNGGLARRI HEDSDSALQL QDFYQEVANP LLTAVTFEYP SNAVEEVTQN
NFRLLFKGSE MVVAGKLQDR GPDVLTATVS GKLPTQNITF QTESSVAEQE AEFQSPKYIF
HNFMERLWAY LTIQQLLEQT VSASDADQQA LRNQALNLSL AYSFVTPLTS MVVTKPDDQE
QSQVAEKPME GESRNRNVHS AGAAGSRMNF RPGVLSSRQL GLPGPPDVPD HAAYHPFRRL
AILPASAPPA TSNPDPAVSR VMNMKIEETT MTTQTPACPS CSRSRAPAVP APIQAPSAIL
PLPGQSVERL CVDPRHRQGP VNLLSDPEQG VEVTGQYERE KAGFSWIEVT FKNPLVWVHA
SPEHVVVTRN RRSSAYKWKE TLFSVMPGLK MTMDKTGLLL LSDPDKVTIG LLFWDGRGEG
LRLLLRDTDR FSSHVGGTLG QFYQEVLWGS PAASDDGRRT LRVQGNDHSA TRERRLDYQE
GPPGVEISCW SVEL*
speed 0.84 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: 4.52057899848994e-12 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:52861211A>TN/A show variant in all transcripts   IGV
HGNC symbol ITIH4
Ensembl transcript ID ENST00000434759
Genbank transcript ID N/A
UniProt peptide Q14624
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.139T>A
g.4285T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs13072536
databasehomozygous (T/T)heterozygousallele carriers
1000G1668961062
ExAC43082144525753
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9660.991
0.6060.979
(flanking)-0.1150.967
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
splice site change before start ATG (at aa -3) | splice site change before start ATG (at aa -1) |
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost4282.5sequence motif lost- wt: ccca|GGAT
 mu: ccca.GGAA
Acc marginally increased4281wt: 0.8712 / mu: 0.8733 (marginal change - not scored)wt: ACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACC
mu: ACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACC		 ccca|GGAT
Acc marginally increased4275wt: 0.2184 / mu: 0.2264 (marginal change - not scored)wt: TCAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGC
mu: TCAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGC		 tctg|CCCC
Acc marginally increased4276wt: 0.5850 / mu: 0.5963 (marginal change - not scored)wt: CAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCA
mu: CAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCA		 ctgc|CCCC
Acc marginally increased4280wt: 0.6087 / mu: 0.6576 (marginal change - not scored)wt: AACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGAC
mu: AACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGAC		 cccc|AGGA
Acc marginally increased4282wt: 0.9638 / mu: 0.9676 (marginal change - not scored)wt: CTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCT
mu: CTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCT		 ccag|GATC
Donor increased4281wt: 0.26 / mu: 0.92wt: CCCCCAGGATCATCG
mu: CCCCCAGGAACATCG		 CCCA|ggat
Donor increased4287wt: 0.37 / mu: 0.47wt: GGATCATCGATGGCA
mu: GGAACATCGATGGCA		 ATCA|tcga
distance from splice site 3
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
128SIGNALmight get lost (downstream of altered splice site)
29148DOMAINVIT.might get lost (downstream of altered splice site)
8181CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
8585CONFLICTI -> K (in Ref. 3; AAD05198).might get lost (downstream of altered splice site)
114114CONFLICTS -> N (in Ref. 2; BAA07602).might get lost (downstream of altered splice site)
207207CONFLICTN -> F (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
207207CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
221221CONFLICTQ -> E (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
272432DOMAINVWFA.might get lost (downstream of altered splice site)
307307CONFLICTR -> V (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
322322CONFLICTW -> Y (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
517517CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
577577CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
662688PROPEPPotentially active peptide. /FTId=PRO_0000016542.might get lost (downstream of altered splice site)
696696CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
701701CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
702702CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
719725REGIONO-glycosylated at three sites.might get lost (downstream of altered splice site)
720720CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
747747DISULFIDProbable.might get lost (downstream of altered splice site)
816817CONFLICTET -> QR (in Ref. 5; AA sequence).might get lost (downstream of altered splice site)
925925DISULFIDProbable.might get lost (downstream of altered splice site)
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 150 / 150
chromosome 3
strand -1
last intron/exon boundary 1984
theoretical NMD boundary in CDS 1784
length of CDS 1683
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 139
gDNA position
(for ins/del: last normal base / first normal base)		 4285
chromosomal position
(for ins/del: last normal base / first normal base)		 52861211
original gDNA sequence snippet CCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCTACC
altered gDNA sequence snippet CCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCTACC
original cDNA sequence snippet ACTACTACTGCCGAAAAGGATCATCGATGGCATGACCTACC
altered cDNA sequence snippet ACTACTACTGCCGAAAAGGAACATCGATGGCATGACCTACC
wildtype AA sequence MTYPGIIKEK AEAQAQYSAA VAKGKSAGLV KATGRNMEQF QVSVSVAPNA KITFELVYEE
LLKRRLGVYE LLLKVRPQQL VKHLQMDIHI FEPQGISFLE TESTFMTNQL VDALTTWQNK
TKAHIRFKPT LSQQQKSPEQ QETVLDGNLI IRYDVDRAIS GGSIQIENGY FVHYFAPEGL
TTMPKNVVFV IDKSGSMSGR KIQQTREALI KILDDLSPRD QFNLIVFSTE ATQWRPSLVP
ASAENVNKAR SFAAGIQALG GTNINDAMLM AVQLLDSSNQ EERLPEGSVS LIILLTDGDP
TVGETNPRSI QNNVREAVSG RYSLFCLGFG FDVSYAFLEK LALDNGGLAR RIHEDSDSAL
QLQDFYQEVA NPLLTAVTFE YPSNAVEEVT QNNFRLLFKG SEMVVAGKLQ DRGPDVLTAT
VSGKLPTQNI TFQTESSVAE QEAEFQSPKY IFHNFMERLW AYLTIQQLLE QTVSASDADQ
QALRNQALNL SLAYSFVTPL TSMVVTKPDD QEQSQVAEKP MEGESRNRNV HSGSTFFKYY
LQGAKIPKPG DKVGGGGRGD *
mutated AA sequence N/A
speed 0.07 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
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Problems