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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000342412
Querying Taster for transcript #2: ENST00000217169
Querying Taster for transcript #3: ENST00000395306
MT speed 0 s - this script 2.637133 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BIRC7polymorphism_automatic9.99200722162641e-16simple_aaeaffectedE223Qsingle base exchangers1077019show file
BIRC7polymorphism_automatic1.6324985796512e-07without_aaeaffectedsingle base exchangers1077019show file
BIRC7polymorphism_automatic1.6324985796512e-07without_aaeaffectedsingle base exchangers1077019show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999999 (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) chr20:61870727G>CN/A show variant in all transcripts   IGV
HGNC symbol BIRC7
Ensembl transcript ID ENST00000217169
Genbank transcript ID NM_139317
UniProt peptide Q96CA5
alteration type single base exchange
alteration region CDS
DNA changes c.667G>C
cDNA.881G>C
g.3493G>C
AA changes E223Q Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 223
frameshift no
known variant Reference ID: rs1077019
databasehomozygous (C/C)heterozygousallele carriers
1000G1688991067
ExAC23091786220171
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.130.005
0.1020.008
(flanking)0.7380.015
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased3497wt: 0.53 / mu: 0.61wt: CGAGGCCCAGAGGGC
mu: CCAGGCCCAGAGGGC		 AGGC|ccag
Donor marginally increased3484wt: 0.9371 / mu: 0.9728 (marginal change - not scored)wt: GGGTCAGTCCAGCCG
mu: GGGTCAGTCCAGCCC		 GTCA|gtcc
Donor gained34950.36mu: GCCCAGGCCCAGAGG CCAG|gccc
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      223SAQEPGGVSPAEAQRAWWVLEPPG
mutated  all conserved    223SAQEPGGVSPAQAQRAWWVLEPP
Ptroglodytes  not conserved  ENSPTRG00000013731  180--------------P
Mmulatta  all conserved  ENSMMUG00000009229  223SAQEPGGASPAQAQSGWWVLEPP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000038840  228DVSE------------------P
Ggallus  not conserved  ENSGALG00000005762  249F------VSSIFTDECL
Trubripes  not conserved  ENSTRUG00000004995  290RARAPQSTVPSRSRASAHFSPPP
Drerio  not conserved  ENSDARG00000058082  307EERQTGDTRSETVETQRTPRTTRTRTQVSSRE
Dmelanogaster  not conserved  FBgn0015247  416AAEAVANISKITDEIQKMSVATPN
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000013316  306SVSVPR--APTQRERPEPPKEPA
protein features
start (aa)end (aa)featuredetails 
243249HELIXmight get lost (downstream of altered splice site)
252286ZN_FINGRING-type.might get lost (downstream of altered splice site)
253255TURNmight get lost (downstream of altered splice site)
256259STRANDmight get lost (downstream of altered splice site)
262265STRANDmight get lost (downstream of altered splice site)
273275TURNmight get lost (downstream of altered splice site)
276278HELIXmight get lost (downstream of altered splice site)
283285TURNmight get lost (downstream of altered splice site)
291294STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 897 / 897
position (AA) of stopcodon in wt / mu AA sequence 299 / 299
position of stopcodon in wt / mu cDNA 1111 / 1111
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 215 / 215
chromosome 20
strand 1
last intron/exon boundary 1117
theoretical NMD boundary in CDS 852
length of CDS 897
coding sequence (CDS) position 667
cDNA position
(for ins/del: last normal base / first normal base)		 881
gDNA position
(for ins/del: last normal base / first normal base)		 3493
chromosomal position
(for ins/del: last normal base / first normal base)		 61870727
original gDNA sequence snippet TAGGAGGGGTCAGTCCAGCCGAGGCCCAGAGGGCGTGGTGG
altered gDNA sequence snippet TAGGAGGGGTCAGTCCAGCCCAGGCCCAGAGGGCGTGGTGG
original cDNA sequence snippet CAGGAGGGGTCAGTCCAGCCGAGGCCCAGAGGGCGTGGTGG
altered cDNA sequence snippet CAGGAGGGGTCAGTCCAGCCCAGGCCCAGAGGGCGTGGTGG
wildtype AA sequence MGPKDSAKCL HRGPQPSHWA AGDGPTQERC GPRSLGSPVL GLDTCRAWDH VDGQILGQLR
PLTEEEEEEG AGATLSRGPA FPGMGSEELR LASFYDWPLT AEVPPELLAA AGFFHTGHQD
KVRCFFCYGG LQSWKRGDDP WTEHAKWFPS CQFLLRSKGR DFVHSVQETH SQLLGSWDPW
EEPEDAAPVA PSVPASGYPE LPTPRREVQS ESAQEPGGVS PAEAQRAWWV LEPPGARDVE
AQLRRLQEER TCKVCLDRAV SIVFVPCGHL VCAECAPGLQ LCPICRAPVR SRVRTFLS*
mutated AA sequence MGPKDSAKCL HRGPQPSHWA AGDGPTQERC GPRSLGSPVL GLDTCRAWDH VDGQILGQLR
PLTEEEEEEG AGATLSRGPA FPGMGSEELR LASFYDWPLT AEVPPELLAA AGFFHTGHQD
KVRCFFCYGG LQSWKRGDDP WTEHAKWFPS CQFLLRSKGR DFVHSVQETH SQLLGSWDPW
EEPEDAAPVA PSVPASGYPE LPTPRREVQS ESAQEPGGVS PAQAQRAWWV LEPPGARDVE
AQLRRLQEER TCKVCLDRAV SIVFVPCGHL VCAECAPGLQ LCPICRAPVR SRVRTFLS*
speed 0.36 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999836750142 (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) chr20:61870727G>CN/A show variant in all transcripts   IGV
HGNC symbol BIRC7
Ensembl transcript ID ENST00000342412
Genbank transcript ID NM_022161
UniProt peptide Q96CA5
alteration type single base exchange
alteration region intron
DNA changes g.3493G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs1077019
databasehomozygous (C/C)heterozygousallele carriers
1000G1688991067
ExAC23091786220171
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.130.005
0.1020.008
(flanking)0.7380.015
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased3497wt: 0.53 / mu: 0.61wt: CGAGGCCCAGAGGGC
mu: CCAGGCCCAGAGGGC		 AGGC|ccag
Donor marginally increased3484wt: 0.9371 / mu: 0.9728 (marginal change - not scored)wt: GGGTCAGTCCAGCCG
mu: GGGTCAGTCCAGCCC		 GTCA|gtcc
Donor gained34950.36mu: GCCCAGGCCCAGAGG CCAG|gccc
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
243249HELIXmight get lost (downstream of altered splice site)
252286ZN_FINGRING-type.might get lost (downstream of altered splice site)
253255TURNmight get lost (downstream of altered splice site)
256259STRANDmight get lost (downstream of altered splice site)
262265STRANDmight get lost (downstream of altered splice site)
273275TURNmight get lost (downstream of altered splice site)
276278HELIXmight get lost (downstream of altered splice site)
283285TURNmight get lost (downstream of altered splice site)
291294STRANDmight 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 215 / 215
chromosome 20
strand 1
last intron/exon boundary 1063
theoretical NMD boundary in CDS 798
length of CDS 843
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 3493
chromosomal position
(for ins/del: last normal base / first normal base)		 61870727
original gDNA sequence snippet TAGGAGGGGTCAGTCCAGCCGAGGCCCAGAGGGCGTGGTGG
altered gDNA sequence snippet TAGGAGGGGTCAGTCCAGCCCAGGCCCAGAGGGCGTGGTGG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGPKDSAKCL HRGPQPSHWA AGDGPTQERC GPRSLGSPVL GLDTCRAWDH VDGQILGQLR
PLTEEEEEEG AGATLSRGPA FPGMGSEELR LASFYDWPLT AEVPPELLAA AGFFHTGHQD
KVRCFFCYGG LQSWKRGDDP WTEHAKWFPS CQFLLRSKGR DFVHSVQETH SQLLGSWDPW
EEPEDAAPVA PSVPASGYPE LPTPRREVQS ESAQEPGARD VEAQLRRLQE ERTCKVCLDR
AVSIVFVPCG HLVCAECAPG LQLCPICRAP VRSRVRTFLS *
mutated AA sequence N/A
speed 0.30 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999836750142 (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) chr20:61870727G>CN/A show variant in all transcripts   IGV
HGNC symbol BIRC7
Ensembl transcript ID ENST00000395306
Genbank transcript ID N/A
UniProt peptide Q96CA5
alteration type single base exchange
alteration region intron
DNA changes g.3493G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs1077019
databasehomozygous (C/C)heterozygousallele carriers
1000G1688991067
ExAC23091786220171
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.130.005
0.1020.008
(flanking)0.7380.015
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased3497wt: 0.53 / mu: 0.61wt: CGAGGCCCAGAGGGC
mu: CCAGGCCCAGAGGGC		 AGGC|ccag
Donor marginally increased3484wt: 0.9371 / mu: 0.9728 (marginal change - not scored)wt: GGGTCAGTCCAGCCG
mu: GGGTCAGTCCAGCCC		 GTCA|gtcc
Donor gained34950.36mu: GCCCAGGCCCAGAGG CCAG|gccc
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
90155REPEATBIR.might get lost (downstream of altered splice site)
130132STRANDmight get lost (downstream of altered splice site)
138138MUTAGEND->A: Abolishes inhibition of caspases, SMAC binding and anti-apoptotic activity.might get lost (downstream of altered splice site)
140147HELIXmight get lost (downstream of altered splice site)
144144METALZinc.might get lost (downstream of altered splice site)
151151METALZinc.might get lost (downstream of altered splice site)
152158HELIXmight get lost (downstream of altered splice site)
160168HELIXmight get lost (downstream of altered splice site)
243249HELIXmight get lost (downstream of altered splice site)
252286ZN_FINGRING-type.might get lost (downstream of altered splice site)
253255TURNmight get lost (downstream of altered splice site)
256259STRANDmight get lost (downstream of altered splice site)
262265STRANDmight get lost (downstream of altered splice site)
273275TURNmight get lost (downstream of altered splice site)
276278HELIXmight get lost (downstream of altered splice site)
283285TURNmight get lost (downstream of altered splice site)
291294STRANDmight 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 7 / 7
chromosome 20
strand 1
last intron/exon boundary 395
theoretical NMD boundary in CDS 338
length of CDS 582
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 3493
chromosomal position
(for ins/del: last normal base / first normal base)		 61870727
original gDNA sequence snippet TAGGAGGGGTCAGTCCAGCCGAGGCCCAGAGGGCGTGGTGG
altered gDNA sequence snippet TAGGAGGGGTCAGTCCAGCCCAGGCCCAGAGGGCGTGGTGG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MPLPWDYPEA PWRRLHSSPP RPCPRALQGG GRRGPNPDPR GSKGLKQTVG ALNPNLHLWG
ICSCQFLLRS KGRDFVHSVQ ETHSQLLGSW DPWEEPEDAA PVAPSVPASG YPELPTPRRE
VQSESAQEPG ARDVEAQLRR LQEERTCKVC LDRAVSIVFV PCGHLVCAEC APGLQLCPIC
RAPVRSRVRT FLS*
mutated AA sequence N/A
speed 0.26 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