Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000381884
Querying Taster for transcript #2: ENST00000545981
MT speed 2.92 s - this script 7.911099 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CENPJdisease_causing_automatic0.999999964355077simple_aaeaffected0E1235Vsingle base exchangers121434311show file
CENPJdisease_causing_automatic1without_aaeaffected0single base exchangers121434311show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999964355077 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM057325)
  • known disease mutation: rs1818 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:25458221T>AN/A show variant in all transcripts   IGV
HGNC symbol CENPJ
Ensembl transcript ID ENST00000381884
Genbank transcript ID NM_018451
UniProt peptide Q9HC77
alteration type single base exchange
alteration region CDS
DNA changes c.3704A>T
cDNA.3890A>T
g.38798A>T
AA changes E1235V Score: 121 explain score(s)
position(s) of altered AA
if AA alteration in CDS
1235
frameshift no
known variant Reference ID: rs121434311
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs1818 (pathogenic for Primary autosomal recessive microcephaly 6) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)

known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)
known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0451
4.5081
(flanking)5.4461
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 lost38797.5sequence motif lost- wt: aaca|GAAA
 mu: aaca.GTAA
Donor marginally increased38796wt: 0.9905 / mu: 0.9920 (marginal change - not scored)wt: TAAACAGAAAAACAT
mu: TAAACAGTAAAACAT
 AACA|gaaa
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1235LEVLHFSSGQIEKHYPDGRKEITF
mutated  not conserved    1235LEVLHFSSGQIVKHYPDGRKEIT
Ptroglodytes  all identical  ENSPTRG00000005715  1235LEVLHFSSGQIEKHYPDGRKEIT
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000064128  1241LEVLHFSSGQIEKHFP
Ggallus  all identical  ENSGALG00000017148  110LEVLQFSNGQIEKHYPDGKKEIT
Trubripes  all identical  ENSTRUG00000015562  894NNQTEKHFPDGRKEIT
Drerio  all identical  ENSDARG00000018121  1021MEVLQFPNNQTEKHFPDGRKEIT
Dmelanogaster  all identical  FBgn0011020  792PNGQTEHRRKDGTVEIH
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4017 / 4017
position (AA) of stopcodon in wt / mu AA sequence 1339 / 1339
position of stopcodon in wt / mu cDNA 4203 / 4203
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 187 / 187
chromosome 13
strand -1
last intron/exon boundary 4011
theoretical NMD boundary in CDS 3774
length of CDS 4017
coding sequence (CDS) position 3704
cDNA position
(for ins/del: last normal base / first normal base)
3890
gDNA position
(for ins/del: last normal base / first normal base)
38798
chromosomal position
(for ins/del: last normal base / first normal base)
25458221
original gDNA sequence snippet TGTAACAACTTTTTAAACAGAAAAACATTACCCAGATGGAA
altered gDNA sequence snippet TGTAACAACTTTTTAAACAGTAAAACATTACCCAGATGGAA
original cDNA sequence snippet TTTCTCAAGTGGACAAATAGAAAAACATTACCCAGATGGAA
altered cDNA sequence snippet TTTCTCAAGTGGACAAATAGTAAAACATTACCCAGATGGAA
wildtype AA sequence MFLMPTSSEL NSGQNFLTQW MTNPSRAGVI LNRGFPILEA DKEKRAAVDI STSFPIKGTH
FSDSFSFINE EDSLLEEQKL ESNNPYKPQS DKSETHTAFP CIKKGPQVAA CHSAPGHQEE
NKNDFIPDLA SEFKEGAYKD PLFKKLEQLK EVQQKKQEQL KRQQLEQLQR LMEEQEKLLT
MVSGQCTLPG LSLLPDDQSQ KHRSPGNTTT GERATCCFPS YVYPDPTQEE TYPSNILSHE
QSNFCRTAHG DFVLTSKRAS PNLFSEAQYQ EAPVEKNNLK EENRNHPTGE SILCWEKVTE
QIQEANDKNL QKHDDSSEVA NIEERPIKAA IGERKQTFED YLEEQIQLEE QELKQKQLKE
AEGPLPIKAK PKQPFLKRGE GLARFTNAKS KFQKGKESKL VTNQSTSEDQ PLFKMDRQQL
QRKTALKNKE LCADNPILKK DSKARTKSGS VTLSQKPKML KCSNRKSLSP SGLKIQTGKK
CDGQFRDQIK FENKVTSNNK ENVTECPKPC DTGCTGWNKT QGKDRLPLST GPASRLAAKS
PIRETMKESE SSLDVSLQKK LETWEREKEK ENLELDEFLF LEQAADEISF SSNSSFVLKI
LERDQQICKG HRMSSTPVKA VPQKTNPADP ISHCNRSEDL DHTAREKESE CEVAPKQLHS
LSSADELREQ PCKIRKAVQK STSENQTEWN ARDDEGVPNS DSSTDSEEQL DVTIKPSTED
RERGISSRED SPQVCDDKGP FKDTRTQEDK RRDVDLDLSD KDYSSDESIM ESIKHKVSEP
SRSSSLSLSK MDFDDERTWT DLEENLCNHD VVLGNESTYG TPQTCYPNNE IGILDKTIKR
KIAPVKRGED LSKSRRSRSP PTSELMMKFF PSLKPKPKSD SHLGNELKLN ISQDQPPGDN
ARSQVLREKI IELETEIEKF KAENASLAKL RIERESALEK LRKEIADFEQ QKAKELARIE
EFKKEEMRKL QKERKVFEKY TTAARTFPDK KEREEIQTLK QQIADLREDL KRKETKWSST
HSRLRSQIQM LVRENTDLRE EIKVMERFRL DAWKRAEAIE SSLEVEKKDK LANTSVRFQN
SQISSGTQVE KYKKNYLPMQ GNPPRRSKSA PPRDLGNLDK GQAASPREPL EPLNFPDPEY
KEEEEDQDIQ GEISHPDGKV EKVYKNGCRV ILFPNGTRKE VSADGKTITV TFFNGDVKQV
MPDQRVIYYY AAAQTTHTTY PEGLEVLHFS SGQIEKHYPD GRKEITFPDQ TVKNLFPDGQ
EESIFPDGTI VRVQRDGNKL IEFNNGQREL HTAQFKRREY PDGTVKTVYA NGHQETKYRS
GRIRVKDKEG NVLMDTEL*
mutated AA sequence MFLMPTSSEL NSGQNFLTQW MTNPSRAGVI LNRGFPILEA DKEKRAAVDI STSFPIKGTH
FSDSFSFINE EDSLLEEQKL ESNNPYKPQS DKSETHTAFP CIKKGPQVAA CHSAPGHQEE
NKNDFIPDLA SEFKEGAYKD PLFKKLEQLK EVQQKKQEQL KRQQLEQLQR LMEEQEKLLT
MVSGQCTLPG LSLLPDDQSQ KHRSPGNTTT GERATCCFPS YVYPDPTQEE TYPSNILSHE
QSNFCRTAHG DFVLTSKRAS PNLFSEAQYQ EAPVEKNNLK EENRNHPTGE SILCWEKVTE
QIQEANDKNL QKHDDSSEVA NIEERPIKAA IGERKQTFED YLEEQIQLEE QELKQKQLKE
AEGPLPIKAK PKQPFLKRGE GLARFTNAKS KFQKGKESKL VTNQSTSEDQ PLFKMDRQQL
QRKTALKNKE LCADNPILKK DSKARTKSGS VTLSQKPKML KCSNRKSLSP SGLKIQTGKK
CDGQFRDQIK FENKVTSNNK ENVTECPKPC DTGCTGWNKT QGKDRLPLST GPASRLAAKS
PIRETMKESE SSLDVSLQKK LETWEREKEK ENLELDEFLF LEQAADEISF SSNSSFVLKI
LERDQQICKG HRMSSTPVKA VPQKTNPADP ISHCNRSEDL DHTAREKESE CEVAPKQLHS
LSSADELREQ PCKIRKAVQK STSENQTEWN ARDDEGVPNS DSSTDSEEQL DVTIKPSTED
RERGISSRED SPQVCDDKGP FKDTRTQEDK RRDVDLDLSD KDYSSDESIM ESIKHKVSEP
SRSSSLSLSK MDFDDERTWT DLEENLCNHD VVLGNESTYG TPQTCYPNNE IGILDKTIKR
KIAPVKRGED LSKSRRSRSP PTSELMMKFF PSLKPKPKSD SHLGNELKLN ISQDQPPGDN
ARSQVLREKI IELETEIEKF KAENASLAKL RIERESALEK LRKEIADFEQ QKAKELARIE
EFKKEEMRKL QKERKVFEKY TTAARTFPDK KEREEIQTLK QQIADLREDL KRKETKWSST
HSRLRSQIQM LVRENTDLRE EIKVMERFRL DAWKRAEAIE SSLEVEKKDK LANTSVRFQN
SQISSGTQVE KYKKNYLPMQ GNPPRRSKSA PPRDLGNLDK GQAASPREPL EPLNFPDPEY
KEEEEDQDIQ GEISHPDGKV EKVYKNGCRV ILFPNGTRKE VSADGKTITV TFFNGDVKQV
MPDQRVIYYY AAAQTTHTTY PEGLEVLHFS SGQIVKHYPD GRKEITFPDQ TVKNLFPDGQ
EESIFPDGTI VRVQRDGNKL IEFNNGQREL HTAQFKRREY PDGTVKTVYA NGHQETKYRS
GRIRVKDKEG NVLMDTEL*
speed 1.49 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

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM057325)
  • known disease mutation: rs1818 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:25458221T>AN/A show variant in all transcripts   IGV
HGNC symbol CENPJ
Ensembl transcript ID ENST00000545981
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.3761A>T
g.38798A>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121434311
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs1818 (pathogenic for Primary autosomal recessive microcephaly 6) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)

known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)
known disease mutation at this position, please check HGMD for details (HGMD ID CM057325)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0451
4.5081
(flanking)5.4461
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 lost38797.5sequence motif lost- wt: aaca|GAAA
 mu: aaca.GTAA
Donor marginally increased38796wt: 0.9905 / mu: 0.9920 (marginal change - not scored)wt: TAAACAGAAAAACAT
mu: TAAACAGTAAAACAT
 AACA|gaaa
distance from splice site 2
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 signal is predicted to be ok
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 143 / 143
chromosome 13
strand -1
last intron/exon boundary 3882
theoretical NMD boundary in CDS 3689
length of CDS 3261
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
3761
gDNA position
(for ins/del: last normal base / first normal base)
38798
chromosomal position
(for ins/del: last normal base / first normal base)
25458221
original gDNA sequence snippet TGTAACAACTTTTTAAACAGAAAAACATTACCCAGATGGAA
altered gDNA sequence snippet TGTAACAACTTTTTAAACAGTAAAACATTACCCAGATGGAA
original cDNA sequence snippet TTTCTCAAGTGGACAAATAGAAAAACATTACCCAGATGGAA
altered cDNA sequence snippet TTTCTCAAGTGGACAAATAGTAAAACATTACCCAGATGGAA
wildtype AA sequence MFLMPTSSEL NSGQNFLTQW MTNPSRAGVI LNRGFPILEA DKEKRAAVDI STSFPIKGTH
FSDSFSFINE EDSLLEEQKL ESNNPYKPQS DKSETHTAFP CIKKGPQVAA CHSAPGHQEE
NKNDFIPDLA SEFKEGAYKD PLFKKLEQLK EVQQKKQEQL KRQQLEQLQR LMEEQEKLLT
MVSGQCTLPG LSLLPDDQSQ KHRSPGNTTT GERATCCFPS YVYPDPTQEE TYPSNILSHE
QSNFCRTAHG DFVLTSKRAS PNLFSEAQYQ EAPVEKNNLK EENRNHPTGE SILCWEKVTE
QIQEANDKNL QKHDDSSEVA NIEERPIKAA IGERKQTFED YLEEQIQLEE QELKQKQLKE
AEGPLPIKAK PKQPFLKRGE GLARFTNAKS KFQKGKESKL VTNQSTSEDQ PLFKMDRQQL
QRKTALKNKE LCADNPILKK DSKARTKSGS VTLSQKPKML KCSNRKSLSP SGLKIQTGKK
CDGQFRDQIK FENKVTSNNK ENVTECPKPC DTGCTGWNKT QGKDRLPLST GPASRLAAKS
PIRETMKESE SSLDVSLQKK LETWEREKEK ENLELDEFLF LEQAADEISF SSNSSFVLKI
LERDQQICKG HRMSSTPVKA VPQKTNPADP ISHCNRSEDL DHTAREKESE CEVAPKQLHS
LSSADELREQ PCKIRKAVQK STSENQTEWN ARDDEGVPNS DSSTDSEEQL DVTIKPSTED
RERGISSRED SPQVCDDKGP FKDTRTQEDK RRDVDLDLSD KDYSSDESIM ESIKHKVSEP
SRSSSLSLSK MDFDDERTWT DLEENLCNHD VVLGNESTYG TPQTCYPNNE IGILDKTIKR
KIAPVKRGED LSKSRRSRSP PTSELMMKFF PSLKPKPKSD SHLGNELKLN ISQDQPPGDN
ARSQVLREKI IELETEIEKF KAENASLAKL RIERESALEK LRKEIADFEQ QKAKELARIE
EFKKEEMRKL QKERKVFEKY TTAARTFPDK KEREEIQTLK QQIADLREDL KRKETKWSST
HSRLRSQIQM LVRENTDLRE EIKVMERFRL DAWKRAEAIE SSLEVEKKDK LAAIHLEDPS
LHLLVI*
mutated AA sequence N/A
speed 1.43 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