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: ENST00000260630
Querying Taster for transcript #2: ENST00000407341
MT speed 0 s - this script 3.023422 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CYP1B1polymorphism_automatic2.10773953845944e-10simple_aaeaffectedA119Ssingle base exchangers1056827show file
CYP1B1polymorphism_automatic2.10773953845944e-10simple_aaeaffectedA119Ssingle base exchangers1056827show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999789226 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM003809)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:38302177C>AN/A show variant in all transcripts   IGV
HGNC symbol CYP1B1
Ensembl transcript ID ENST00000260630
Genbank transcript ID NM_000104
UniProt peptide Q16678
alteration type single base exchange
alteration region CDS
DNA changes c.355G>T
cDNA.757G>T
g.34868G>T
AA changes A119S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 119
frameshift no
known variant Reference ID: rs1056827
databasehomozygous (A/A)heterozygousallele carriers
1000G38110531434
ExAC49101998924899

known disease mutation at this position, please check HGMD for details (HGMD ID CM003809)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7780.616
-0.2430.312
(flanking)-0.090.333
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased34859wt: 0.7094 / mu: 0.7102 (marginal change - not scored)wt: AGCAGGGCTCGGCCTTCGCCGACCGGCCGGCCTTCGCCTCC
mu: AGCAGGGCTCGGCCTTCGCCGACCGGCCGTCCTTCGCCTCC		 gccg|ACCG
Acc increased34878wt: 0.21 / mu: 0.57wt: CGACCGGCCGGCCTTCGCCTCCTTCCGTGTGGTGTCCGGCG
mu: CGACCGGCCGTCCTTCGCCTCCTTCCGTGTGGTGTCCGGCG		 cctc|CTTC
Acc increased34877wt: 0.31 / mu: 0.89wt: CCGACCGGCCGGCCTTCGCCTCCTTCCGTGTGGTGTCCGGC
mu: CCGACCGGCCGTCCTTCGCCTCCTTCCGTGTGGTGTCCGGC		 gcct|CCTT
Acc gained348750.39mu: CGCCGACCGGCCGTCCTTCGCCTCCTTCCGTGTGGTGTCCG tcgc|CTCC
distance from splice site 356
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      119VQQGSAFADRPAFASFRVVSGGRS
mutated  all conserved    119VQQGSAFADRPSFASFRVVSGGR
Ptroglodytes  all conserved  ENSPTRG00000011843  119VQQGSAFADRPSFASFRVVSGGR
Mmulatta  all conserved  ENSMMUG00000013945  119VQQGSAFADRPSFASFRVISGGR
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000024087  119VQQGSIFADRPPFASFRVVSGGR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000068934  105VKKATDFAGRPDFASFRFVSNGK
Dmelanogaster  not conserved  FBgn0086917  122NKNGKYFGGRPDFFRYHKLFGGDRNN
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121125HELIXmight get lost (downstream of altered splice site)
126129HELIXmight get lost (downstream of altered splice site)
132135STRANDmight get lost (downstream of altered splice site)
139154HELIXmight get lost (downstream of altered splice site)
162183HELIXmight get lost (downstream of altered splice site)
184188HELIXmight get lost (downstream of altered splice site)
194209HELIXmight get lost (downstream of altered splice site)
219224HELIXmight get lost (downstream of altered splice site)
228235HELIXmight get lost (downstream of altered splice site)
241243TURNmight get lost (downstream of altered splice site)
245249HELIXmight get lost (downstream of altered splice site)
253282HELIXmight get lost (downstream of altered splice site)
292304HELIXmight get lost (downstream of altered splice site)
317319HELIXmight get lost (downstream of altered splice site)
320348HELIXmight get lost (downstream of altered splice site)
350363HELIXmight get lost (downstream of altered splice site)
372377HELIXmight get lost (downstream of altered splice site)
379392HELIXmight get lost (downstream of altered splice site)
407409STRANDmight get lost (downstream of altered splice site)
412414STRANDmight get lost (downstream of altered splice site)
419424STRANDmight get lost (downstream of altered splice site)
425428HELIXmight get lost (downstream of altered splice site)
431433TURNmight get lost (downstream of altered splice site)
435439STRANDmight get lost (downstream of altered splice site)
442445HELIXmight get lost (downstream of altered splice site)
454457HELIXmight get lost (downstream of altered splice site)
470470METALIron (heme axial ligand) (By similarity).might get lost (downstream of altered splice site)
473490HELIXmight get lost (downstream of altered splice site)
491495STRANDmight get lost (downstream of altered splice site)
505513STRANDmight get lost (downstream of altered splice site)
518524STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1632 / 1632
position (AA) of stopcodon in wt / mu AA sequence 544 / 544
position of stopcodon in wt / mu cDNA 2034 / 2034
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 403 / 403
chromosome 2
strand -1
last intron/exon boundary 1446
theoretical NMD boundary in CDS 993
length of CDS 1632
coding sequence (CDS) position 355
cDNA position
(for ins/del: last normal base / first normal base)		 757
gDNA position
(for ins/del: last normal base / first normal base)		 34868
chromosomal position
(for ins/del: last normal base / first normal base)		 38302177
original gDNA sequence snippet CGGCCTTCGCCGACCGGCCGGCCTTCGCCTCCTTCCGTGTG
altered gDNA sequence snippet CGGCCTTCGCCGACCGGCCGTCCTTCGCCTCCTTCCGTGTG
original cDNA sequence snippet CGGCCTTCGCCGACCGGCCGGCCTTCGCCTCCTTCCGTGTG
altered cDNA sequence snippet CGGCCTTCGCCGACCGGCCGTCCTTCGCCTCCTTCCGTGTG
wildtype AA sequence MGTSLSPNDP WPLNPLSIQQ TTLLLLLSVL ATVHVGQRLL RQRRRQLRSA PPGPFAWPLI
GNAAAVGQAA HLSFARLARR YGDVFQIRLG SCPIVVLNGE RAIHQALVQQ GSAFADRPAF
ASFRVVSGGR SMAFGHYSEH WKVQRRAAHS MMRNFFTRQP RSRQVLEGHV LSEARELVAL
LVRGSADGAF LDPRPLTVVA VANVMSAVCF GCRYSHDDPE FRELLSHNEE FGRTVGAGSL
VDVMPWLQYF PNPVRTVFRE FEQLNRNFSN FILDKFLRHC ESLRPGAAPR DMMDAFILSA
EKKAAGDSHG GGARLDLENV PATITDIFGA SQDTLSTALQ WLLLLFTRYP DVQTRVQAEL
DQVVGRDRLP CMGDQPNLPY VLAFLYEAMR FSSFVPVTIP HATTANTSVL GYHIPKDTVV
FVNQWSVNHD PVKWPNPENF DPARFLDKDG LINKDLTSRV MIFSVGKRRC IGEELSKMQL
FLFISILAHQ CDFRANPNEP AKMNFSYGLT IKPKSFKVNV TLRESMELLD SAVQNLQAKE
TCQ*
mutated AA sequence MGTSLSPNDP WPLNPLSIQQ TTLLLLLSVL ATVHVGQRLL RQRRRQLRSA PPGPFAWPLI
GNAAAVGQAA HLSFARLARR YGDVFQIRLG SCPIVVLNGE RAIHQALVQQ GSAFADRPSF
ASFRVVSGGR SMAFGHYSEH WKVQRRAAHS MMRNFFTRQP RSRQVLEGHV LSEARELVAL
LVRGSADGAF LDPRPLTVVA VANVMSAVCF GCRYSHDDPE FRELLSHNEE FGRTVGAGSL
VDVMPWLQYF PNPVRTVFRE FEQLNRNFSN FILDKFLRHC ESLRPGAAPR DMMDAFILSA
EKKAAGDSHG GGARLDLENV PATITDIFGA SQDTLSTALQ WLLLLFTRYP DVQTRVQAEL
DQVVGRDRLP CMGDQPNLPY VLAFLYEAMR FSSFVPVTIP HATTANTSVL GYHIPKDTVV
FVNQWSVNHD PVKWPNPENF DPARFLDKDG LINKDLTSRV MIFSVGKRRC IGEELSKMQL
FLFISILAHQ CDFRANPNEP AKMNFSYGLT IKPKSFKVNV TLRESMELLD SAVQNLQAKE
TCQ*
speed 0.64 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: 0.999999999789226 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM003809)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:38302177C>AN/A show variant in all transcripts   IGV
HGNC symbol CYP1B1
Ensembl transcript ID ENST00000407341
Genbank transcript ID N/A
UniProt peptide Q16678
alteration type single base exchange
alteration region CDS
DNA changes c.355G>T
cDNA.656G>T
g.34868G>T
AA changes A119S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 119
frameshift no
known variant Reference ID: rs1056827
databasehomozygous (A/A)heterozygousallele carriers
1000G38110531434
ExAC49101998924899

known disease mutation at this position, please check HGMD for details (HGMD ID CM003809)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7780.616
-0.2430.312
(flanking)-0.090.333
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased34859wt: 0.7094 / mu: 0.7102 (marginal change - not scored)wt: AGCAGGGCTCGGCCTTCGCCGACCGGCCGGCCTTCGCCTCC
mu: AGCAGGGCTCGGCCTTCGCCGACCGGCCGTCCTTCGCCTCC		 gccg|ACCG
Acc increased34878wt: 0.21 / mu: 0.57wt: CGACCGGCCGGCCTTCGCCTCCTTCCGTGTGGTGTCCGGCG
mu: CGACCGGCCGTCCTTCGCCTCCTTCCGTGTGGTGTCCGGCG		 cctc|CTTC
Acc increased34877wt: 0.31 / mu: 0.89wt: CCGACCGGCCGGCCTTCGCCTCCTTCCGTGTGGTGTCCGGC
mu: CCGACCGGCCGTCCTTCGCCTCCTTCCGTGTGGTGTCCGGC		 gcct|CCTT
Acc gained348750.39mu: CGCCGACCGGCCGTCCTTCGCCTCCTTCCGTGTGGTGTCCG tcgc|CTCC
distance from splice site 356
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      119VQQGSAFADRPAFASFRVVSGGRS
mutated  all conserved    119VQQGSAFADRPSFASFRVVSGGR
Ptroglodytes  all conserved  ENSPTRG00000011843  119VQQGSAFADRPSFASFRVVSGGR
Mmulatta  all conserved  ENSMMUG00000013945  119VQQGSAFADRPSFASFRVISGGR
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000024087  119VQQGSIFADRPPFASFRVVSGGR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000068934  105VKKATDFAGRPDFASFRFVSNGK
Dmelanogaster  not conserved  FBgn0086917  122NKNGKYFGGRPDFFRYHKLFGGDRNN
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
121125HELIXmight get lost (downstream of altered splice site)
126129HELIXmight get lost (downstream of altered splice site)
132135STRANDmight get lost (downstream of altered splice site)
139154HELIXmight get lost (downstream of altered splice site)
162183HELIXmight get lost (downstream of altered splice site)
184188HELIXmight get lost (downstream of altered splice site)
194209HELIXmight get lost (downstream of altered splice site)
219224HELIXmight get lost (downstream of altered splice site)
228235HELIXmight get lost (downstream of altered splice site)
241243TURNmight get lost (downstream of altered splice site)
245249HELIXmight get lost (downstream of altered splice site)
253282HELIXmight get lost (downstream of altered splice site)
292304HELIXmight get lost (downstream of altered splice site)
317319HELIXmight get lost (downstream of altered splice site)
320348HELIXmight get lost (downstream of altered splice site)
350363HELIXmight get lost (downstream of altered splice site)
372377HELIXmight get lost (downstream of altered splice site)
379392HELIXmight get lost (downstream of altered splice site)
407409STRANDmight get lost (downstream of altered splice site)
412414STRANDmight get lost (downstream of altered splice site)
419424STRANDmight get lost (downstream of altered splice site)
425428HELIXmight get lost (downstream of altered splice site)
431433TURNmight get lost (downstream of altered splice site)
435439STRANDmight get lost (downstream of altered splice site)
442445HELIXmight get lost (downstream of altered splice site)
454457HELIXmight get lost (downstream of altered splice site)
470470METALIron (heme axial ligand) (By similarity).might get lost (downstream of altered splice site)
473490HELIXmight get lost (downstream of altered splice site)
491495STRANDmight get lost (downstream of altered splice site)
505513STRANDmight get lost (downstream of altered splice site)
518524STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1632 / 1632
position (AA) of stopcodon in wt / mu AA sequence 544 / 544
position of stopcodon in wt / mu cDNA 1933 / 1933
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 302 / 302
chromosome 2
strand -1
last intron/exon boundary 1345
theoretical NMD boundary in CDS 993
length of CDS 1632
coding sequence (CDS) position 355
cDNA position
(for ins/del: last normal base / first normal base)		 656
gDNA position
(for ins/del: last normal base / first normal base)		 34868
chromosomal position
(for ins/del: last normal base / first normal base)		 38302177
original gDNA sequence snippet CGGCCTTCGCCGACCGGCCGGCCTTCGCCTCCTTCCGTGTG
altered gDNA sequence snippet CGGCCTTCGCCGACCGGCCGTCCTTCGCCTCCTTCCGTGTG
original cDNA sequence snippet CGGCCTTCGCCGACCGGCCGGCCTTCGCCTCCTTCCGTGTG
altered cDNA sequence snippet CGGCCTTCGCCGACCGGCCGTCCTTCGCCTCCTTCCGTGTG
wildtype AA sequence MGTSLSPNDP WPLNPLSIQQ TTLLLLLSVL ATVHVGQRLL RQRRRQLRSA PPGPFAWPLI
GNAAAVGQAA HLSFARLARR YGDVFQIRLG SCPIVVLNGE RAIHQALVQQ GSAFADRPAF
ASFRVVSGGR SMAFGHYSEH WKVQRRAAHS MMRNFFTRQP RSRQVLEGHV LSEARELVAL
LVRGSADGAF LDPRPLTVVA VANVMSAVCF GCRYSHDDPE FRELLSHNEE FGRTVGAGSL
VDVMPWLQYF PNPVRTVFRE FEQLNRNFSN FILDKFLRHC ESLRPGAAPR DMMDAFILSA
EKKAAGDSHG GGARLDLENV PATITDIFGA SQDTLSTALQ WLLLLFTRYP DVQTRVQAEL
DQVVGRDRLP CMGDQPNLPY VLAFLYEAMR FSSFVPVTIP HATTANTSVL GYHIPKDTVV
FVNQWSVNHD PVKWPNPENF DPARFLDKDG LINKDLTSRV MIFSVGKRRC IGEELSKMQL
FLFISILAHQ CDFRANPNEP AKMNFSYGLT IKPKSFKVNV TLRESMELLD SAVQNLQAKE
TCQ*
mutated AA sequence MGTSLSPNDP WPLNPLSIQQ TTLLLLLSVL ATVHVGQRLL RQRRRQLRSA PPGPFAWPLI
GNAAAVGQAA HLSFARLARR YGDVFQIRLG SCPIVVLNGE RAIHQALVQQ GSAFADRPSF
ASFRVVSGGR SMAFGHYSEH WKVQRRAAHS MMRNFFTRQP RSRQVLEGHV LSEARELVAL
LVRGSADGAF LDPRPLTVVA VANVMSAVCF GCRYSHDDPE FRELLSHNEE FGRTVGAGSL
VDVMPWLQYF PNPVRTVFRE FEQLNRNFSN FILDKFLRHC ESLRPGAAPR DMMDAFILSA
EKKAAGDSHG GGARLDLENV PATITDIFGA SQDTLSTALQ WLLLLFTRYP DVQTRVQAEL
DQVVGRDRLP CMGDQPNLPY VLAFLYEAMR FSSFVPVTIP HATTANTSVL GYHIPKDTVV
FVNQWSVNHD PVKWPNPENF DPARFLDKDG LINKDLTSRV MIFSVGKRRC IGEELSKMQL
FLFISILAHQ CDFRANPNEP AKMNFSYGLT IKPKSFKVNV TLRESMELLD SAVQNLQAKE
TCQ*
speed 0.66 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