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: ENST00000382771
Querying Taster for transcript #2: ENST00000489441
MT speed 0 s - this script 3.359347 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SERPINB5polymorphism_automatic5.09353556360503e-05simple_aaeaffectedS176Psingle base exchangers2289519show file
SERPINB5polymorphism_automatic5.09353556360503e-05simple_aaeaffectedS176Psingle base exchangers2289519show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999949064644364 (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 CM083559)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:61160287T>CN/A show variant in all transcripts   IGV
HGNC symbol SERPINB5
Ensembl transcript ID ENST00000382771
Genbank transcript ID NM_002639
UniProt peptide P36952
alteration type single base exchange
alteration region CDS
DNA changes c.526T>C
cDNA.818T>C
g.16294T>C
AA changes S176P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 176
frameshift no
known variant Reference ID: rs2289519
databasehomozygous (C/C)heterozygousallele carriers
1000G13009832283
ExAC27750-227335017

known disease mutation at this position, please check HGMD for details (HGMD ID CM083559)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2390.999
2.261
(flanking)3.1470.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased16285wt: 0.50 / mu: 0.63wt: GGATGAAGAAATTTT
mu: GGATGAAGAAATTTC		 ATGA|agaa
Donor increased16286wt: 0.78 / mu: 0.97wt: GATGAAGAAATTTTC
mu: GATGAAGAAATTTCC		 TGAA|gaaa
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      176AYFVGKWMKKFSESETKECPFRVN
mutated  not conserved    176AYFVGKWMKKFPESET
Ptroglodytes  not conserved  ENSPTRG00000029287  176AYFVGKWMKKFPESET
Mmulatta  not conserved  ENSMMUG00000014182  176AYFVGKWMKKFPES
Fcatus  not conserved  ENSFCAG00000008379  176AYFVGKWMKKFPESET
Mmusculus  not conserved  ENSMUSG00000067006  176AYFVGKWMKKFPESET
Ggallus  not conserved  ENSGALG00000012873  176AYFVTNWMKKFPEAEI
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000027590  176ASFKGKWVYTFNKSET
protein features
start (aa)end (aa)featuredetails 
171173STRANDmight get lost (downstream of altered splice site)
177179HELIXmight get lost (downstream of altered splice site)
181190STRANDmight get lost (downstream of altered splice site)
188188CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
192209STRANDmight get lost (downstream of altered splice site)
210213TURNmight get lost (downstream of altered splice site)
214221STRANDmight get lost (downstream of altered splice site)
222224HELIXmight get lost (downstream of altered splice site)
225235STRANDmight get lost (downstream of altered splice site)
239249HELIXmight get lost (downstream of altered splice site)
245245CONFLICTK -> Q (in Ref. 5; CAE45703).might get lost (downstream of altered splice site)
252258HELIXmight get lost (downstream of altered splice site)
261263HELIXmight get lost (downstream of altered splice site)
265274STRANDmight get lost (downstream of altered splice site)
276282STRANDmight get lost (downstream of altered splice site)
284291HELIXmight get lost (downstream of altered splice site)
295297TURNmight get lost (downstream of altered splice site)
299301TURNmight get lost (downstream of altered splice site)
305307TURNmight get lost (downstream of altered splice site)
315326STRANDmight get lost (downstream of altered splice site)
337341TURNmight get lost (downstream of altered splice site)
340341SITEReactive bond homolog (By similarity).might get lost (downstream of altered splice site)
344349STRANDmight get lost (downstream of altered splice site)
354360STRANDmight get lost (downstream of altered splice site)
361361CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
361364TURNmight get lost (downstream of altered splice site)
365372STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1128 / 1128
position (AA) of stopcodon in wt / mu AA sequence 376 / 376
position of stopcodon in wt / mu cDNA 1420 / 1420
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 293 / 293
chromosome 18
strand 1
last intron/exon boundary 1028
theoretical NMD boundary in CDS 685
length of CDS 1128
coding sequence (CDS) position 526
cDNA position
(for ins/del: last normal base / first normal base)		 818
gDNA position
(for ins/del: last normal base / first normal base)		 16294
chromosomal position
(for ins/del: last normal base / first normal base)		 61160287
original gDNA sequence snippet GCAAGTGGATGAAGAAATTTTCTGAATCAGAAACAAAAGAA
altered gDNA sequence snippet GCAAGTGGATGAAGAAATTTCCTGAATCAGAAACAAAAGAA
original cDNA sequence snippet GCAAGTGGATGAAGAAATTTTCTGAATCAGAAACAAAAGAA
altered cDNA sequence snippet GCAAGTGGATGAAGAAATTTCCTGAATCAGAAACAAAAGAA
wildtype AA sequence MDALQLANSA FAVDLFKQLC EKEPLGNVLF SPICLSTSLS LAQVGAKGDT ANEIGQVLHF
ENVKDVPFGF QTVTSDVNKL SSFYSLKLIK RLYVDKSLNL STEFISSTKR PYAKELETVD
FKDKLEETKG QINNSIKDLT DGHFENILAD NSVNDQTKIL VVNAAYFVGK WMKKFSESET
KECPFRVNKT DTKPVQMMNM EATFCMGNID SINCKIIELP FQNKHLSMFI LLPKDVEDES
TGLEKIEKQL NSESLSQWTN PSTMANAKVK LSIPKFKVEK MIDPKACLEN LGLKHIFSED
TSDFSGMSET KGVALSNVIH KVCLEITEDG GDSIEVPGAR ILQHKDELNA DHPFIYIIRH
NKTRNIIFFG KFCSP*
mutated AA sequence MDALQLANSA FAVDLFKQLC EKEPLGNVLF SPICLSTSLS LAQVGAKGDT ANEIGQVLHF
ENVKDVPFGF QTVTSDVNKL SSFYSLKLIK RLYVDKSLNL STEFISSTKR PYAKELETVD
FKDKLEETKG QINNSIKDLT DGHFENILAD NSVNDQTKIL VVNAAYFVGK WMKKFPESET
KECPFRVNKT DTKPVQMMNM EATFCMGNID SINCKIIELP FQNKHLSMFI LLPKDVEDES
TGLEKIEKQL NSESLSQWTN PSTMANAKVK LSIPKFKVEK MIDPKACLEN LGLKHIFSED
TSDFSGMSET KGVALSNVIH KVCLEITEDG GDSIEVPGAR ILQHKDELNA DHPFIYIIRH
NKTRNIIFFG KFCSP*
speed 0.21 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: 0.999949064644364 (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 CM083559)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:61160287T>CN/A show variant in all transcripts   IGV
HGNC symbol SERPINB5
Ensembl transcript ID ENST00000489441
Genbank transcript ID N/A
UniProt peptide P36952
alteration type single base exchange
alteration region CDS
DNA changes c.526T>C
cDNA.621T>C
g.16294T>C
AA changes S176P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 176
frameshift no
known variant Reference ID: rs2289519
databasehomozygous (C/C)heterozygousallele carriers
1000G13009832283
ExAC27750-227335017

known disease mutation at this position, please check HGMD for details (HGMD ID CM083559)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2390.999
2.261
(flanking)3.1470.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased16285wt: 0.50 / mu: 0.63wt: GGATGAAGAAATTTT
mu: GGATGAAGAAATTTC		 ATGA|agaa
Donor increased16286wt: 0.78 / mu: 0.97wt: GATGAAGAAATTTTC
mu: GATGAAGAAATTTCC		 TGAA|gaaa
distance from splice site 102
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      176AYFVGKWMKKFSESETKECPFRVN
mutated  not conserved    176AYFVGKWMKKFPESET
Ptroglodytes  not conserved  ENSPTRG00000029287  176AYFVGKWMKKFPESET
Mmulatta  not conserved  ENSMMUG00000014182  176AYFVGKWMKKFPES
Fcatus  not conserved  ENSFCAG00000008379  176AYFVGKWMKKFPESET
Mmusculus  not conserved  ENSMUSG00000067006  176AYFVGKWMKKFPESET
Ggallus  not conserved  ENSGALG00000012873  176AYFVTNWMKKFPEAEI
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000027590  176ASFKGKWVYTFNKSET
protein features
start (aa)end (aa)featuredetails 
171173STRANDmight get lost (downstream of altered splice site)
177179HELIXmight get lost (downstream of altered splice site)
181190STRANDmight get lost (downstream of altered splice site)
188188CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
192209STRANDmight get lost (downstream of altered splice site)
210213TURNmight get lost (downstream of altered splice site)
214221STRANDmight get lost (downstream of altered splice site)
222224HELIXmight get lost (downstream of altered splice site)
225235STRANDmight get lost (downstream of altered splice site)
239249HELIXmight get lost (downstream of altered splice site)
245245CONFLICTK -> Q (in Ref. 5; CAE45703).might get lost (downstream of altered splice site)
252258HELIXmight get lost (downstream of altered splice site)
261263HELIXmight get lost (downstream of altered splice site)
265274STRANDmight get lost (downstream of altered splice site)
276282STRANDmight get lost (downstream of altered splice site)
284291HELIXmight get lost (downstream of altered splice site)
295297TURNmight get lost (downstream of altered splice site)
299301TURNmight get lost (downstream of altered splice site)
305307TURNmight get lost (downstream of altered splice site)
315326STRANDmight get lost (downstream of altered splice site)
337341TURNmight get lost (downstream of altered splice site)
340341SITEReactive bond homolog (By similarity).might get lost (downstream of altered splice site)
344349STRANDmight get lost (downstream of altered splice site)
354360STRANDmight get lost (downstream of altered splice site)
361361CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
361364TURNmight get lost (downstream of altered splice site)
365372STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 696 / 696
position (AA) of stopcodon in wt / mu AA sequence 232 / 232
position of stopcodon in wt / mu cDNA 791 / 791
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 96 / 96
chromosome 18
strand 1
last intron/exon boundary 520
theoretical NMD boundary in CDS 374
length of CDS 696
coding sequence (CDS) position 526
cDNA position
(for ins/del: last normal base / first normal base)		 621
gDNA position
(for ins/del: last normal base / first normal base)		 16294
chromosomal position
(for ins/del: last normal base / first normal base)		 61160287
original gDNA sequence snippet GCAAGTGGATGAAGAAATTTTCTGAATCAGAAACAAAAGAA
altered gDNA sequence snippet GCAAGTGGATGAAGAAATTTCCTGAATCAGAAACAAAAGAA
original cDNA sequence snippet GCAAGTGGATGAAGAAATTTTCTGAATCAGAAACAAAAGAA
altered cDNA sequence snippet GCAAGTGGATGAAGAAATTTCCTGAATCAGAAACAAAAGAA
wildtype AA sequence MDALQLANSA FAVDLFKQLC EKEPLGNVLF SPICLSTSLS LAQVGAKGDT ANEIGQVLHF
ENVKDVPFGF QTVTSDVNKL SSFYSLKLIK RLYVDKSLNL STEFISSTKR PYAKELETVD
FKDKLEETKG QINNSIKDLT DGHFENILAD NSVNDQTKIL VVNAAYFVGK WMKKFSESET
KECPFRVNKV CGAACSSKRS PIIDVKNDRD RVGHKSIPMR NLRARPAKCL S*
mutated AA sequence MDALQLANSA FAVDLFKQLC EKEPLGNVLF SPICLSTSLS LAQVGAKGDT ANEIGQVLHF
ENVKDVPFGF QTVTSDVNKL SSFYSLKLIK RLYVDKSLNL STEFISSTKR PYAKELETVD
FKDKLEETKG QINNSIKDLT DGHFENILAD NSVNDQTKIL VVNAAYFVGK WMKKFPESET
KECPFRVNKV CGAACSSKRS PIIDVKNDRD RVGHKSIPMR NLRARPAKCL S*
speed 1.15 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