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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000346991
Querying Taster for transcript #2: ENST00000527044
Querying Taster for transcript #3: ENST00000399668
MT speed 0 s - this script 4.234168 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KNL1polymorphism_automatic8.58239057259791e-05simple_aaeaffectedT113Asingle base exchangers12911738show file
KNL1polymorphism_automatic8.58239057259791e-05simple_aaeaffectedT87Asingle base exchangers12911738show file
KNL1polymorphism_automatic0.00401815058154098simple_aaeaffectedT85Asingle base exchangers12911738show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999914176094274 (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) chr15:40903684A>GN/A show variant in all transcripts   IGV
HGNC symbol KNL1
Ensembl transcript ID ENST00000346991
Genbank transcript ID NM_170589
UniProt peptide Q8NG31
alteration type single base exchange
alteration region CDS
DNA changes c.337A>G
cDNA.727A>G
g.17467A>G
AA changes T113A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 113
frameshift no
known variant Reference ID: rs12911738
databasehomozygous (G/G)heterozygousallele carriers
1000G13687962164
ExAC332116875008
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0420.998
1.1820.999
(flanking)1.1370.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased17460wt: 0.35 / mu: 0.46wt: ATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATCT
mu: ATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATCT		 agaa|ACAG
Acc increased17459wt: 0.67 / mu: 0.78wt: AATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATC
mu: AATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATC		 taga|AACA
Acc marginally decreased17458wt: 0.9498 / mu: 0.9437 (marginal change - not scored)wt: TAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAAT
mu: TAATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAAT		 ttag|AAAC
Acc marginally increased17457wt: 0.9416 / mu: 0.9627 (marginal change - not scored)wt: TTAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAA
mu: TTAATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAA		 ttta|GAAA
Donor increased17461wt: 0.70 / mu: 0.99wt: TAGAAACAGAAACAG
mu: TAGAAACAGAAGCAG		 GAAA|caga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      113RFSCLSLPETETGENLLLIQNKKL
mutated  not conserved    113RFSCLSLPETEAGENLLLI
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000027326  113-------------------
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000013401  n/a
Drerio  not conserved  ENSDARG00000070239  110--SIQNLHEERPDEKIL----RF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1728REGIONInteraction with BUB1 and BUB1B.lost
205211HELIXmight get lost (downstream of altered splice site)
241250HELIXmight get lost (downstream of altered splice site)
505505MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
513513MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
539539MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
578578MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
601601MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
682682MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
765765MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
767767MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
8551201REGION2 X 104 AA approximate repeats.might get lost (downstream of altered splice site)
885989REPEAT1.might get lost (downstream of altered splice site)
954954MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
956956MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10391039MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10421042MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
10761076MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10991201REPEAT2.might get lost (downstream of altered splice site)
12321232MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
13321332CONFLICTP -> A (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
13571357CONFLICTN -> H (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
17201720MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
17561756CONFLICTN -> Y (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
17731773MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
17891803MOTIFNuclear localization signal (Potential).might get lost (downstream of altered splice site)
18181819SITEBreakpoint for translocation to form MLL- CASC5.might get lost (downstream of altered splice site)
18342316REGIONNecessary for kinetochore localization and for interaction with NSL1 and DSN1.might get lost (downstream of altered splice site)
18451845MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
18691869MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
18791879MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
19422133COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 7029 / 7029
position (AA) of stopcodon in wt / mu AA sequence 2343 / 2343
position of stopcodon in wt / mu cDNA 7419 / 7419
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 391 / 391
chromosome 15
strand 1
last intron/exon boundary 7305
theoretical NMD boundary in CDS 6864
length of CDS 7029
coding sequence (CDS) position 337
cDNA position
(for ins/del: last normal base / first normal base)		 727
gDNA position
(for ins/del: last normal base / first normal base)		 17467
chromosomal position
(for ins/del: last normal base / first normal base)		 40903684
original gDNA sequence snippet TTTTATTTTTAGAAACAGAAACAGGAGAAAATCTTCTTTTG
altered gDNA sequence snippet TTTTATTTTTAGAAACAGAAGCAGGAGAAAATCTTCTTTTG
original cDNA sequence snippet TCAGCCTCCCAGAAACAGAAACAGGAGAAAATCTTCTTTTG
altered cDNA sequence snippet TCAGCCTCCCAGAAACAGAAGCAGGAGAAAATCTTCTTTTG
wildtype AA sequence MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEGCSAMVP SQLQLLPPGF KRFSCLSLPE TETGENLLLI
QNKKLEDNYC EITGMNTLLS APIHTQMQQK EFSIIEHTRE RKHANDQTVI FSDENQMDLT
SSHTVMITKG LLDNPISEKS TKIDTTSFLA NLKLHTEDSR MKKEVNFSVD QNTSSENKID
FNDFIKRLKT GKCSAFPDVP DKENFEIPIY SKEPNSASST HQMHVSLKED ENNSNITRLF
REKDDGMNFT QCHTANIQTL IPTSSETNSR ESKGNDITIY GNDFMDLTFN HTLQILPATG
NFSEIENQTQ NAMDVTTGYG TKASGNKTVF KSKQNTAFQD LSINSADKIH ITRSHIMGAE
THIVSQTCNQ DARILAMTPE SIYSNPSIQG CKTVFYSSCN DAMEMTKCLS NMREEKNLLK
HDSNYAKMYC NPDAMSSLTE KTIYSGEENM DITKSHTVAI DNQIFKQDQS NVQIAAAPTP
EKEMMLQNLM TTSEDGKMNV NCNSVPHVSK ERIQQSLSNP LSISLTDRKT ELLSGENMDL
TESHTSNLGS QVPLAAYNLA PESTSESHSQ SKSSSDECEE ITKSRNEPFQ RSDIIAKNSL
TDTWNKDKDW VLKILPYLDK DSPQSADCNQ EIATSHNIVY CGGVLDKQIT NRNTVSWEQS
LFSTTKPLFS SGQFSMKNHD TAISSHTVKS VLGQNSKLAE PLRKSLSNPT PDYCHDKMII
CSEEEQNMDL TKSHTVVIGF GPSELQELGK TNLEHTTGQL TTMNRQIAVK VEKCGKSPIE
KSGVLKSNCI MDVLEDESVQ KPKFPKEKQN VKIWGRKSVG GPKIDKTIVF SEDDKNDMDI
TKSYTIEINH RPLLEKRDCH LVPLAGTSET ILYTCRQDDM EITRSHTTAL ECKTVSPDEI
TTRPMDKTVV FVDNHVELEM TESHTVFIDY QEKERTDRPN FELSQRKSLG TPTVICTPTE
ESVFFPGNGE SDRLVANDSQ LTPLEEWSNN RGPVEVADNM ELSKSATCKN IKDVQSPGFL
NEPLSSKSQR RKSLKLKNDK TIVFSENHKN DMDITQSCMV EIDNESALED KEDFHLAGAS
KTILYSCGQD DMEITRSHTT ALECKTLLPN EIAIRPMDKT VLFTDNYSDL EVTDSHTVFI
DCQATEKILE ENPKFGIGKG KNLGVSFPKD NSCVQEIAEK QALAVGNKIV LHTEQKQQLF
AATNRTTNEI IKFHSAAMDE KVIGKVVDQA CTLEKAQVES CQLNNRDRRN VDFTSSHATA
VCGSSDNYSC LPNVISCTDN LEGSAMLLCD KDEEKANYCP VQNDLAYAND FASEYYLESE
GQPLSAPCPL LEKEEVIQTS TKGQLDCVIT LHKDQDLIKD PRNLLANQTL VYSQDLGEMT
KLNSKRVSFK LPKDQMKVYV DDIYVIPQPH FSTDQPPLPK KGQSSINKEE VILSKAGNKS
LNIIENSSAP ICENKPKILN SEEWFAAACK KELKENIQTT NYNTALDFHS NSDVTKQVIQ
THVNAGEAPD PVITSNVPCF HSIKPNLNNL NGKTGEFLAF QTVHLPPLPE QLLELGNKAH
NDMHIVQATE IHNINIISSN AKDSRDEENK KSHNGAETTS LPPKTVFKDK VRRCSLGIFL
PRLPNKRNCS VTGIDDLEQI PADTTDINHL ETQPVSSKDS GIGSVAGKLN LSPSQYINEE
NLPVYPDEIN SSDSINIETE EKALIETYQK EISPYENKMG KTCNSQKRTW VQEEEDIHKE
KKIRKNEIKF SDTTQDREIF DHHTEEDIDK SANSVLIKNL SRTPSSCSSS LDSIKADGTS
LDFSTYRSSQ MESQFLRDTI CEESLREKLQ DGRITIREFF ILLQVHILIQ KPRQSNLPGN
FTVNTPPTPE DLMLSQYVYR PKIQIYREDC EARRQKIEEL KLSASNQDKL LVDINKNLWE
KMRHCSDKEL KAFGIYLNKI KSCFTKMTKV FTHQGKVALY GKLVQSAQNE REKLQIKIDE
MDKILKKIDN CLTEMETETK NLEDEEKNNP VEEWDSEMRA AEKELEQLKT EEEELQRNLL
ELEVQKEQTL AQIDFMQKQR NRTEELLDQL SLSEWDVVEW SDDQAVFTFV YDTIQLTITF
EESVVGFPFL DKRYRKIVDV NFQSLLDEDQ APPSSLLVHK LIFQYVEEKE SWKKTCTTQH
QLPKMLEEFS LVVHHCRLLG EEIEYLKRWG PNYNLMNIDI NNNELRLLFS SSAAFAKFEI
TLFLSAYYPS VPLPSTIQNH VGNTSQDDIA TILSKVPLEN NYLKNVVKQI YQDLFQDCHF
YH*
mutated AA sequence MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEGCSAMVP SQLQLLPPGF KRFSCLSLPE TEAGENLLLI
QNKKLEDNYC EITGMNTLLS APIHTQMQQK EFSIIEHTRE RKHANDQTVI FSDENQMDLT
SSHTVMITKG LLDNPISEKS TKIDTTSFLA NLKLHTEDSR MKKEVNFSVD QNTSSENKID
FNDFIKRLKT GKCSAFPDVP DKENFEIPIY SKEPNSASST HQMHVSLKED ENNSNITRLF
REKDDGMNFT QCHTANIQTL IPTSSETNSR ESKGNDITIY GNDFMDLTFN HTLQILPATG
NFSEIENQTQ NAMDVTTGYG TKASGNKTVF KSKQNTAFQD LSINSADKIH ITRSHIMGAE
THIVSQTCNQ DARILAMTPE SIYSNPSIQG CKTVFYSSCN DAMEMTKCLS NMREEKNLLK
HDSNYAKMYC NPDAMSSLTE KTIYSGEENM DITKSHTVAI DNQIFKQDQS NVQIAAAPTP
EKEMMLQNLM TTSEDGKMNV NCNSVPHVSK ERIQQSLSNP LSISLTDRKT ELLSGENMDL
TESHTSNLGS QVPLAAYNLA PESTSESHSQ SKSSSDECEE ITKSRNEPFQ RSDIIAKNSL
TDTWNKDKDW VLKILPYLDK DSPQSADCNQ EIATSHNIVY CGGVLDKQIT NRNTVSWEQS
LFSTTKPLFS SGQFSMKNHD TAISSHTVKS VLGQNSKLAE PLRKSLSNPT PDYCHDKMII
CSEEEQNMDL TKSHTVVIGF GPSELQELGK TNLEHTTGQL TTMNRQIAVK VEKCGKSPIE
KSGVLKSNCI MDVLEDESVQ KPKFPKEKQN VKIWGRKSVG GPKIDKTIVF SEDDKNDMDI
TKSYTIEINH RPLLEKRDCH LVPLAGTSET ILYTCRQDDM EITRSHTTAL ECKTVSPDEI
TTRPMDKTVV FVDNHVELEM TESHTVFIDY QEKERTDRPN FELSQRKSLG TPTVICTPTE
ESVFFPGNGE SDRLVANDSQ LTPLEEWSNN RGPVEVADNM ELSKSATCKN IKDVQSPGFL
NEPLSSKSQR RKSLKLKNDK TIVFSENHKN DMDITQSCMV EIDNESALED KEDFHLAGAS
KTILYSCGQD DMEITRSHTT ALECKTLLPN EIAIRPMDKT VLFTDNYSDL EVTDSHTVFI
DCQATEKILE ENPKFGIGKG KNLGVSFPKD NSCVQEIAEK QALAVGNKIV LHTEQKQQLF
AATNRTTNEI IKFHSAAMDE KVIGKVVDQA CTLEKAQVES CQLNNRDRRN VDFTSSHATA
VCGSSDNYSC LPNVISCTDN LEGSAMLLCD KDEEKANYCP VQNDLAYAND FASEYYLESE
GQPLSAPCPL LEKEEVIQTS TKGQLDCVIT LHKDQDLIKD PRNLLANQTL VYSQDLGEMT
KLNSKRVSFK LPKDQMKVYV DDIYVIPQPH FSTDQPPLPK KGQSSINKEE VILSKAGNKS
LNIIENSSAP ICENKPKILN SEEWFAAACK KELKENIQTT NYNTALDFHS NSDVTKQVIQ
THVNAGEAPD PVITSNVPCF HSIKPNLNNL NGKTGEFLAF QTVHLPPLPE QLLELGNKAH
NDMHIVQATE IHNINIISSN AKDSRDEENK KSHNGAETTS LPPKTVFKDK VRRCSLGIFL
PRLPNKRNCS VTGIDDLEQI PADTTDINHL ETQPVSSKDS GIGSVAGKLN LSPSQYINEE
NLPVYPDEIN SSDSINIETE EKALIETYQK EISPYENKMG KTCNSQKRTW VQEEEDIHKE
KKIRKNEIKF SDTTQDREIF DHHTEEDIDK SANSVLIKNL SRTPSSCSSS LDSIKADGTS
LDFSTYRSSQ MESQFLRDTI CEESLREKLQ DGRITIREFF ILLQVHILIQ KPRQSNLPGN
FTVNTPPTPE DLMLSQYVYR PKIQIYREDC EARRQKIEEL KLSASNQDKL LVDINKNLWE
KMRHCSDKEL KAFGIYLNKI KSCFTKMTKV FTHQGKVALY GKLVQSAQNE REKLQIKIDE
MDKILKKIDN CLTEMETETK NLEDEEKNNP VEEWDSEMRA AEKELEQLKT EEEELQRNLL
ELEVQKEQTL AQIDFMQKQR NRTEELLDQL SLSEWDVVEW SDDQAVFTFV YDTIQLTITF
EESVVGFPFL DKRYRKIVDV NFQSLLDEDQ APPSSLLVHK LIFQYVEEKE SWKKTCTTQH
QLPKMLEEFS LVVHHCRLLG EEIEYLKRWG PNYNLMNIDI NNNELRLLFS SSAAFAKFEI
TLFLSAYYPS VPLPSTIQNH VGNTSQDDIA TILSKVPLEN NYLKNVVKQI YQDLFQDCHF
YH*
speed 0.96 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: 0.999914176094274 (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) chr15:40903684A>GN/A show variant in all transcripts   IGV
HGNC symbol KNL1
Ensembl transcript ID ENST00000399668
Genbank transcript ID NM_144508
UniProt peptide Q8NG31
alteration type single base exchange
alteration region CDS
DNA changes c.259A>G
cDNA.420A>G
g.17467A>G
AA changes T87A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 87
frameshift no
known variant Reference ID: rs12911738
databasehomozygous (G/G)heterozygousallele carriers
1000G13687962164
ExAC332116875008
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0420.998
1.1820.999
(flanking)1.1370.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased17460wt: 0.35 / mu: 0.46wt: ATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATCT
mu: ATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATCT		 agaa|ACAG
Acc increased17459wt: 0.67 / mu: 0.78wt: AATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATC
mu: AATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATC		 taga|AACA
Acc marginally decreased17458wt: 0.9498 / mu: 0.9437 (marginal change - not scored)wt: TAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAAT
mu: TAATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAAT		 ttag|AAAC
Acc marginally increased17457wt: 0.9416 / mu: 0.9627 (marginal change - not scored)wt: TTAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAA
mu: TTAATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAA		 ttta|GAAA
Donor increased17461wt: 0.70 / mu: 0.99wt: TAGAAACAGAAACAG
mu: TAGAAACAGAAGCAG		 GAAA|caga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      87IVRKSEMEETETGENLLLIQNKKL
mutated  not conserved    87IVRKSEMEETEAGENLLLIQNKK
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000027326  87TERNSE-----------------
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000013401  n/a
Drerio  not conserved  ENSDARG00000070239  86LGSIQNLHEERPDEKIL----RF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1728REGIONInteraction with BUB1 and BUB1B.lost
205211HELIXmight get lost (downstream of altered splice site)
241250HELIXmight get lost (downstream of altered splice site)
505505MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
513513MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
539539MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
578578MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
601601MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
682682MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
765765MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
767767MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
8551201REGION2 X 104 AA approximate repeats.might get lost (downstream of altered splice site)
885989REPEAT1.might get lost (downstream of altered splice site)
954954MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
956956MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10391039MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10421042MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
10761076MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10991201REPEAT2.might get lost (downstream of altered splice site)
12321232MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
13321332CONFLICTP -> A (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
13571357CONFLICTN -> H (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
17201720MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
17561756CONFLICTN -> Y (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
17731773MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
17891803MOTIFNuclear localization signal (Potential).might get lost (downstream of altered splice site)
18181819SITEBreakpoint for translocation to form MLL- CASC5.might get lost (downstream of altered splice site)
18342316REGIONNecessary for kinetochore localization and for interaction with NSL1 and DSN1.might get lost (downstream of altered splice site)
18451845MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
18691869MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
18791879MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
19422133COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6951 / 6951
position (AA) of stopcodon in wt / mu AA sequence 2317 / 2317
position of stopcodon in wt / mu cDNA 7112 / 7112
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 162 / 162
chromosome 15
strand 1
last intron/exon boundary 6998
theoretical NMD boundary in CDS 6786
length of CDS 6951
coding sequence (CDS) position 259
cDNA position
(for ins/del: last normal base / first normal base)		 420
gDNA position
(for ins/del: last normal base / first normal base)		 17467
chromosomal position
(for ins/del: last normal base / first normal base)		 40903684
original gDNA sequence snippet TTTTATTTTTAGAAACAGAAACAGGAGAAAATCTTCTTTTG
altered gDNA sequence snippet TTTTATTTTTAGAAACAGAAGCAGGAGAAAATCTTCTTTTG
original cDNA sequence snippet CAGAAATGGAAGAAACAGAAACAGGAGAAAATCTTCTTTTG
altered cDNA sequence snippet CAGAAATGGAAGAAACAGAAGCAGGAGAAAATCTTCTTTTG
wildtype AA sequence MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEETETGEN LLLIQNKKLE DNYCEITGMN TLLSAPIHTQ
MQQKEFSIIE HTRERKHAND QTVIFSDENQ MDLTSSHTVM ITKGLLDNPI SEKSTKIDTT
SFLANLKLHT EDSRMKKEVN FSVDQNTSSE NKIDFNDFIK RLKTGKCSAF PDVPDKENFE
IPIYSKEPNS ASSTHQMHVS LKEDENNSNI TRLFREKDDG MNFTQCHTAN IQTLIPTSSE
TNSRESKGND ITIYGNDFMD LTFNHTLQIL PATGNFSEIE NQTQNAMDVT TGYGTKASGN
KTVFKSKQNT AFQDLSINSA DKIHITRSHI MGAETHIVSQ TCNQDARILA MTPESIYSNP
SIQGCKTVFY SSCNDAMEMT KCLSNMREEK NLLKHDSNYA KMYCNPDAMS SLTEKTIYSG
EENMDITKSH TVAIDNQIFK QDQSNVQIAA APTPEKEMML QNLMTTSEDG KMNVNCNSVP
HVSKERIQQS LSNPLSISLT DRKTELLSGE NMDLTESHTS NLGSQVPLAA YNLAPESTSE
SHSQSKSSSD ECEEITKSRN EPFQRSDIIA KNSLTDTWNK DKDWVLKILP YLDKDSPQSA
DCNQEIATSH NIVYCGGVLD KQITNRNTVS WEQSLFSTTK PLFSSGQFSM KNHDTAISSH
TVKSVLGQNS KLAEPLRKSL SNPTPDYCHD KMIICSEEEQ NMDLTKSHTV VIGFGPSELQ
ELGKTNLEHT TGQLTTMNRQ IAVKVEKCGK SPIEKSGVLK SNCIMDVLED ESVQKPKFPK
EKQNVKIWGR KSVGGPKIDK TIVFSEDDKN DMDITKSYTI EINHRPLLEK RDCHLVPLAG
TSETILYTCR QDDMEITRSH TTALECKTVS PDEITTRPMD KTVVFVDNHV ELEMTESHTV
FIDYQEKERT DRPNFELSQR KSLGTPTVIC TPTEESVFFP GNGESDRLVA NDSQLTPLEE
WSNNRGPVEV ADNMELSKSA TCKNIKDVQS PGFLNEPLSS KSQRRKSLKL KNDKTIVFSE
NHKNDMDITQ SCMVEIDNES ALEDKEDFHL AGASKTILYS CGQDDMEITR SHTTALECKT
LLPNEIAIRP MDKTVLFTDN YSDLEVTDSH TVFIDCQATE KILEENPKFG IGKGKNLGVS
FPKDNSCVQE IAEKQALAVG NKIVLHTEQK QQLFAATNRT TNEIIKFHSA AMDEKVIGKV
VDQACTLEKA QVESCQLNNR DRRNVDFTSS HATAVCGSSD NYSCLPNVIS CTDNLEGSAM
LLCDKDEEKA NYCPVQNDLA YANDFASEYY LESEGQPLSA PCPLLEKEEV IQTSTKGQLD
CVITLHKDQD LIKDPRNLLA NQTLVYSQDL GEMTKLNSKR VSFKLPKDQM KVYVDDIYVI
PQPHFSTDQP PLPKKGQSSI NKEEVILSKA GNKSLNIIEN SSAPICENKP KILNSEEWFA
AACKKELKEN IQTTNYNTAL DFHSNSDVTK QVIQTHVNAG EAPDPVITSN VPCFHSIKPN
LNNLNGKTGE FLAFQTVHLP PLPEQLLELG NKAHNDMHIV QATEIHNINI ISSNAKDSRD
EENKKSHNGA ETTSLPPKTV FKDKVRRCSL GIFLPRLPNK RNCSVTGIDD LEQIPADTTD
INHLETQPVS SKDSGIGSVA GKLNLSPSQY INEENLPVYP DEINSSDSIN IETEEKALIE
TYQKEISPYE NKMGKTCNSQ KRTWVQEEED IHKEKKIRKN EIKFSDTTQD REIFDHHTEE
DIDKSANSVL IKNLSRTPSS CSSSLDSIKA DGTSLDFSTY RSSQMESQFL RDTICEESLR
EKLQDGRITI REFFILLQVH ILIQKPRQSN LPGNFTVNTP PTPEDLMLSQ YVYRPKIQIY
REDCEARRQK IEELKLSASN QDKLLVDINK NLWEKMRHCS DKELKAFGIY LNKIKSCFTK
MTKVFTHQGK VALYGKLVQS AQNEREKLQI KIDEMDKILK KIDNCLTEME TETKNLEDEE
KNNPVEEWDS EMRAAEKELE QLKTEEEELQ RNLLELEVQK EQTLAQIDFM QKQRNRTEEL
LDQLSLSEWD VVEWSDDQAV FTFVYDTIQL TITFEESVVG FPFLDKRYRK IVDVNFQSLL
DEDQAPPSSL LVHKLIFQYV EEKESWKKTC TTQHQLPKML EEFSLVVHHC RLLGEEIEYL
KRWGPNYNLM NIDINNNELR LLFSSSAAFA KFEITLFLSA YYPSVPLPST IQNHVGNTSQ
DDIATILSKV PLENNYLKNV VKQIYQDLFQ DCHFYH*
mutated AA sequence MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEETEAGEN LLLIQNKKLE DNYCEITGMN TLLSAPIHTQ
MQQKEFSIIE HTRERKHAND QTVIFSDENQ MDLTSSHTVM ITKGLLDNPI SEKSTKIDTT
SFLANLKLHT EDSRMKKEVN FSVDQNTSSE NKIDFNDFIK RLKTGKCSAF PDVPDKENFE
IPIYSKEPNS ASSTHQMHVS LKEDENNSNI TRLFREKDDG MNFTQCHTAN IQTLIPTSSE
TNSRESKGND ITIYGNDFMD LTFNHTLQIL PATGNFSEIE NQTQNAMDVT TGYGTKASGN
KTVFKSKQNT AFQDLSINSA DKIHITRSHI MGAETHIVSQ TCNQDARILA MTPESIYSNP
SIQGCKTVFY SSCNDAMEMT KCLSNMREEK NLLKHDSNYA KMYCNPDAMS SLTEKTIYSG
EENMDITKSH TVAIDNQIFK QDQSNVQIAA APTPEKEMML QNLMTTSEDG KMNVNCNSVP
HVSKERIQQS LSNPLSISLT DRKTELLSGE NMDLTESHTS NLGSQVPLAA YNLAPESTSE
SHSQSKSSSD ECEEITKSRN EPFQRSDIIA KNSLTDTWNK DKDWVLKILP YLDKDSPQSA
DCNQEIATSH NIVYCGGVLD KQITNRNTVS WEQSLFSTTK PLFSSGQFSM KNHDTAISSH
TVKSVLGQNS KLAEPLRKSL SNPTPDYCHD KMIICSEEEQ NMDLTKSHTV VIGFGPSELQ
ELGKTNLEHT TGQLTTMNRQ IAVKVEKCGK SPIEKSGVLK SNCIMDVLED ESVQKPKFPK
EKQNVKIWGR KSVGGPKIDK TIVFSEDDKN DMDITKSYTI EINHRPLLEK RDCHLVPLAG
TSETILYTCR QDDMEITRSH TTALECKTVS PDEITTRPMD KTVVFVDNHV ELEMTESHTV
FIDYQEKERT DRPNFELSQR KSLGTPTVIC TPTEESVFFP GNGESDRLVA NDSQLTPLEE
WSNNRGPVEV ADNMELSKSA TCKNIKDVQS PGFLNEPLSS KSQRRKSLKL KNDKTIVFSE
NHKNDMDITQ SCMVEIDNES ALEDKEDFHL AGASKTILYS CGQDDMEITR SHTTALECKT
LLPNEIAIRP MDKTVLFTDN YSDLEVTDSH TVFIDCQATE KILEENPKFG IGKGKNLGVS
FPKDNSCVQE IAEKQALAVG NKIVLHTEQK QQLFAATNRT TNEIIKFHSA AMDEKVIGKV
VDQACTLEKA QVESCQLNNR DRRNVDFTSS HATAVCGSSD NYSCLPNVIS CTDNLEGSAM
LLCDKDEEKA NYCPVQNDLA YANDFASEYY LESEGQPLSA PCPLLEKEEV IQTSTKGQLD
CVITLHKDQD LIKDPRNLLA NQTLVYSQDL GEMTKLNSKR VSFKLPKDQM KVYVDDIYVI
PQPHFSTDQP PLPKKGQSSI NKEEVILSKA GNKSLNIIEN SSAPICENKP KILNSEEWFA
AACKKELKEN IQTTNYNTAL DFHSNSDVTK QVIQTHVNAG EAPDPVITSN VPCFHSIKPN
LNNLNGKTGE FLAFQTVHLP PLPEQLLELG NKAHNDMHIV QATEIHNINI ISSNAKDSRD
EENKKSHNGA ETTSLPPKTV FKDKVRRCSL GIFLPRLPNK RNCSVTGIDD LEQIPADTTD
INHLETQPVS SKDSGIGSVA GKLNLSPSQY INEENLPVYP DEINSSDSIN IETEEKALIE
TYQKEISPYE NKMGKTCNSQ KRTWVQEEED IHKEKKIRKN EIKFSDTTQD REIFDHHTEE
DIDKSANSVL IKNLSRTPSS CSSSLDSIKA DGTSLDFSTY RSSQMESQFL RDTICEESLR
EKLQDGRITI REFFILLQVH ILIQKPRQSN LPGNFTVNTP PTPEDLMLSQ YVYRPKIQIY
REDCEARRQK IEELKLSASN QDKLLVDINK NLWEKMRHCS DKELKAFGIY LNKIKSCFTK
MTKVFTHQGK VALYGKLVQS AQNEREKLQI KIDEMDKILK KIDNCLTEME TETKNLEDEE
KNNPVEEWDS EMRAAEKELE QLKTEEEELQ RNLLELEVQK EQTLAQIDFM QKQRNRTEEL
LDQLSLSEWD VVEWSDDQAV FTFVYDTIQL TITFEESVVG FPFLDKRYRK IVDVNFQSLL
DEDQAPPSSL LVHKLIFQYV EEKESWKKTC TTQHQLPKML EEFSLVVHHC RLLGEEIEYL
KRWGPNYNLM NIDINNNELR LLFSSSAAFA KFEITLFLSA YYPSVPLPST IQNHVGNTSQ
DDIATILSKV PLENNYLKNV VKQIYQDLFQ DCHFYH*
speed 1.22 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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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.995981849418459 (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) chr15:40903684A>GN/A show variant in all transcripts   IGV
HGNC symbol KNL1
Ensembl transcript ID ENST00000527044
Genbank transcript ID N/A
UniProt peptide Q8NG31
alteration type single base exchange
alteration region CDS
DNA changes c.253A>G
cDNA.628A>G
g.17467A>G
AA changes T85A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 85
frameshift no
known variant Reference ID: rs12911738
databasehomozygous (G/G)heterozygousallele carriers
1000G13687962164
ExAC332116875008
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0420.998
1.1820.999
(flanking)1.1370.998
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 lost17464sequence motif lost- wt: acag|AAAC
 mu: acag.AAGC
Acc increased17460wt: 0.35 / mu: 0.46wt: ATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATCT
mu: ATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATCT		 agaa|ACAG
Acc increased17459wt: 0.67 / mu: 0.78wt: AATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAATC
mu: AATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAATC		 taga|AACA
Acc marginally increased17457wt: 0.9416 / mu: 0.9627 (marginal change - not scored)wt: TTAATTTTAATTTTATTTTTAGAAACAGAAACAGGAGAAAA
mu: TTAATTTTAATTTTATTTTTAGAAACAGAAGCAGGAGAAAA		 ttta|GAAA
Donor increased17461wt: 0.70 / mu: 0.99wt: TAGAAACAGAAACAG
mu: TAGAAACAGAAGCAG		 GAAA|caga
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      85MKIVRKSEMEETGENLLLIQNKKL
mutated  not conserved    85MKIVRKSEMEEAGENLLLIQNKK
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000027326  85MKTERNSEI--SGMNTLL
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000013401  n/a
Drerio  all identical  ENSDARG00000070239  366YFSEEDNAMEMTGVSDISVRNKD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1728REGIONInteraction with BUB1 and BUB1B.lost
205211HELIXmight get lost (downstream of altered splice site)
241250HELIXmight get lost (downstream of altered splice site)
505505MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
513513MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
539539MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
578578MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
601601MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
682682MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
765765MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
767767MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
8551201REGION2 X 104 AA approximate repeats.might get lost (downstream of altered splice site)
885989REPEAT1.might get lost (downstream of altered splice site)
954954MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
956956MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10391039MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10421042MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
10761076MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10991201REPEAT2.might get lost (downstream of altered splice site)
12321232MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
13321332CONFLICTP -> A (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
13571357CONFLICTN -> H (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
17201720MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
17561756CONFLICTN -> Y (in Ref. 2; BAC05691).might get lost (downstream of altered splice site)
17731773MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
17891803MOTIFNuclear localization signal (Potential).might get lost (downstream of altered splice site)
18181819SITEBreakpoint for translocation to form MLL- CASC5.might get lost (downstream of altered splice site)
18342316REGIONNecessary for kinetochore localization and for interaction with NSL1 and DSN1.might get lost (downstream of altered splice site)
18451845MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
18691869MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
18791879MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
19422133COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 342 / 342
position (AA) of stopcodon in wt / mu AA sequence 114 / 114
position of stopcodon in wt / mu cDNA 717 / 717
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 376 / 376
chromosome 15
strand 1
last intron/exon boundary 692
theoretical NMD boundary in CDS 266
length of CDS 342
coding sequence (CDS) position 253
cDNA position
(for ins/del: last normal base / first normal base)		 628
gDNA position
(for ins/del: last normal base / first normal base)		 17467
chromosomal position
(for ins/del: last normal base / first normal base)		 40903684
original gDNA sequence snippet TTTTATTTTTAGAAACAGAAACAGGAGAAAATCTTCTTTTG
altered gDNA sequence snippet TTTTATTTTTAGAAACAGAAGCAGGAGAAAATCTTCTTTTG
original cDNA sequence snippet GAAAGTCAGAAATGGAAGAAACAGGAGAAAATCTTCTTTTG
altered cDNA sequence snippet GAAAGTCAGAAATGGAAGAAGCAGGAGAAAATCTTCTTTTG
wildtype AA sequence MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEETGENLL LIQNKKLEDN YCEITVFNYR TYP*
mutated AA sequence MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEEAGENLL LIQNKKLEDN YCEITVFNYR TYP*
speed 0.87 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