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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000573597
Querying Taster for transcript #2: ENST00000456349
Querying Taster for transcript #3: ENST00000263080
Querying Taster for transcript #4: ENST00000541913
MT speed 0 s - this script 4.115877 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ASPAdisease_causing_automatic0.999999999999816simple_aaeaffected0D249Vsingle base exchangers104894552show file
ASPAdisease_causing_automatic0.999999999999816simple_aaeaffected0D249Vsingle base exchangers104894552show file
SPATA22disease_causing_automatic1without_aaeaffected0single base exchangers104894552show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999816 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM023015)
  • known disease mutation: rs2615 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402186A>TN/A show variant in all transcripts   IGV
HGNC symbol ASPA
Ensembl transcript ID ENST00000456349
Genbank transcript ID N/A
UniProt peptide P45381
alteration type single base exchange
alteration region CDS
DNA changes c.746A>T
cDNA.894A>T
g.26519A>T
AA changes D249V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 249
frameshift no
known variant Reference ID: rs104894552
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01515

known disease mutation: rs2615 (pathogenic for Spongy degeneration of central nervous system) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6511
4.6821
(flanking)2.171
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 lost26517sequence motif lost- wt: agag|GATC
 mu: agag.GTTC
Acc marginally increased26511wt: 0.6064 / mu: 0.6434 (marginal change - not scored)wt: ATATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAA
mu: ATATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAA		 ttcc|TGAG
Acc marginally increased26510wt: 0.7562 / mu: 0.7921 (marginal change - not scored)wt: TATATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGA
mu: TATATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGA		 tttc|CTGA
Acc marginally increased26513wt: 0.9195 / mu: 0.9254 (marginal change - not scored)wt: ATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAAAC
mu: ATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAAC		 cctg|AGAG
Acc increased26516wt: 0.58 / mu: 0.66wt: TATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAAACCAC
mu: TATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAACCAC		 gaga|GGAT
Acc marginally increased26509wt: 0.8168 / mu: 0.8441 (marginal change - not scored)wt: ATATATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGG
mu: ATATATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGG		 gttt|CCTG
Acc marginally increased26512wt: 0.8284 / mu: 0.8375 (marginal change - not scored)wt: TATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAAA
mu: TATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAA		 tcct|GAGA
Donor marginally increased26512wt: 0.9410 / mu: 0.9756 (marginal change - not scored)wt: TTTCCTGAGAGGATC
mu: TTTCCTGAGAGGTTC		 TCCT|gaga
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      249EIAAIIHPNLQDQDWKPLHPGDPM
mutated  not conserved    249AIIHPNLQVQDWKPLHPGDP
Ptroglodytes  all identical  ENSPTRG00000008568  249AIIHPNLQDQDWKPLHPGDP
Mmulatta  all identical  ENSMMUG00000030388  249AVIHPNLQDQDWKPLHPGDP
Fcatus  all identical  ENSFCAG00000007919  249DIAAIIHPNLQDQDWKPLHPRDP
Mmusculus  all identical  ENSMUSG00000020774  248AVIHPNLQDQDWKPLHPGDP
Ggallus  all identical  ENSGALG00000004669  250IAIIHPNLQDQDWQPLNNGDP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000005154  251DCDWEPLNRGDP
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005789  248DCTAIIHNNLQDQDWKELKPGDP
protein features
start (aa)end (aa)featuredetails 
245249TURNlost
259263STRANDmight get lost (downstream of altered splice site)
269271STRANDmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
278282STRANDmight get lost (downstream of altered splice site)
285285MUTAGENE->D: 5-fold decrease in activity.might get lost (downstream of altered splice site)
286288HELIXmight get lost (downstream of altered splice site)
288288BINDINGSubstrate.might get lost (downstream of altered splice site)
288288MUTAGENY->F: Reduces activity by 99%.might get lost (downstream of altered splice site)
289292TURNmight get lost (downstream of altered splice site)
294305STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 942 / 942
position (AA) of stopcodon in wt / mu AA sequence 314 / 314
position of stopcodon in wt / mu cDNA 1090 / 1090
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 149 / 149
chromosome 17
strand 1
last intron/exon boundary 893
theoretical NMD boundary in CDS 694
length of CDS 942
coding sequence (CDS) position 746
cDNA position
(for ins/del: last normal base / first normal base)		 894
gDNA position
(for ins/del: last normal base / first normal base)		 26519
chromosomal position
(for ins/del: last normal base / first normal base)		 3402186
original gDNA sequence snippet TTTGATTGTTTCCTGAGAGGATCAAGACTGGAAACCACTGC
altered gDNA sequence snippet TTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAACCACTGC
original cDNA sequence snippet CATCCATCCTAATCTGCAGGATCAAGACTGGAAACCACTGC
altered cDNA sequence snippet CATCCATCCTAATCTGCAGGTTCAAGACTGGAAACCACTGC
wildtype AA sequence MTSCHIAEEH IQKVAIFGGT HGNELTGVFL VKHWLENGAE IQRTGLEVKP FITNPRAVKK
CTRYIDCDLN RIFDLENLGK KMSEDLPYEV RRAQEINHLF GPKDSEDSYD IIFDLHNTTS
NMGCTLILED SRNNFLIQMF HYIKTSLAPL PCYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD YPRDENGEIA
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*
mutated AA sequence MTSCHIAEEH IQKVAIFGGT HGNELTGVFL VKHWLENGAE IQRTGLEVKP FITNPRAVKK
CTRYIDCDLN RIFDLENLGK KMSEDLPYEV RRAQEINHLF GPKDSEDSYD IIFDLHNTTS
NMGCTLILED SRNNFLIQMF HYIKTSLAPL PCYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD YPRDENGEIA
AIIHPNLQVQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*
speed 1.27 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: simple_aae, prob: 0.999999999999816 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM023015)
  • known disease mutation: rs2615 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402186A>TN/A show variant in all transcripts   IGV
HGNC symbol ASPA
Ensembl transcript ID ENST00000263080
Genbank transcript ID NM_000049
UniProt peptide P45381
alteration type single base exchange
alteration region CDS
DNA changes c.746A>T
cDNA.904A>T
g.26519A>T
AA changes D249V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 249
frameshift no
known variant Reference ID: rs104894552
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01515

known disease mutation: rs2615 (pathogenic for Spongy degeneration of central nervous system) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6511
4.6821
(flanking)2.171
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 lost26517sequence motif lost- wt: agag|GATC
 mu: agag.GTTC
Acc marginally increased26511wt: 0.6064 / mu: 0.6434 (marginal change - not scored)wt: ATATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAA
mu: ATATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAA		 ttcc|TGAG
Acc marginally increased26510wt: 0.7562 / mu: 0.7921 (marginal change - not scored)wt: TATATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGA
mu: TATATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGA		 tttc|CTGA
Acc marginally increased26513wt: 0.9195 / mu: 0.9254 (marginal change - not scored)wt: ATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAAAC
mu: ATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAAC		 cctg|AGAG
Acc increased26516wt: 0.58 / mu: 0.66wt: TATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAAACCAC
mu: TATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAACCAC		 gaga|GGAT
Acc marginally increased26509wt: 0.8168 / mu: 0.8441 (marginal change - not scored)wt: ATATATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGG
mu: ATATATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGG		 gttt|CCTG
Acc marginally increased26512wt: 0.8284 / mu: 0.8375 (marginal change - not scored)wt: TATTTATTTTGATTGTTTCCTGAGAGGATCAAGACTGGAAA
mu: TATTTATTTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAA		 tcct|GAGA
Donor marginally increased26512wt: 0.9410 / mu: 0.9756 (marginal change - not scored)wt: TTTCCTGAGAGGATC
mu: TTTCCTGAGAGGTTC		 TCCT|gaga
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      249EIAAIIHPNLQDQDWKPLHPGDPM
mutated  not conserved    249AIIHPNLQVQDWKPLHPGDP
Ptroglodytes  all identical  ENSPTRG00000008568  249AIIHPNLQDQDWKPLHPGDP
Mmulatta  all identical  ENSMMUG00000030388  249AVIHPNLQDQDWKPLHPGDP
Fcatus  all identical  ENSFCAG00000007919  249DIAAIIHPNLQDQDWKPLHPRDP
Mmusculus  all identical  ENSMUSG00000020774  248AVIHPNLQDQDWKPLHPGDP
Ggallus  all identical  ENSGALG00000004669  250IAIIHPNLQDQDWQPLNNGDP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000005154  251DCDWEPLNRGDP
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005789  248DCTAIIHNNLQDQDWKELKPGDP
protein features
start (aa)end (aa)featuredetails 
245249TURNlost
259263STRANDmight get lost (downstream of altered splice site)
269271STRANDmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
278282STRANDmight get lost (downstream of altered splice site)
285285MUTAGENE->D: 5-fold decrease in activity.might get lost (downstream of altered splice site)
286288HELIXmight get lost (downstream of altered splice site)
288288BINDINGSubstrate.might get lost (downstream of altered splice site)
288288MUTAGENY->F: Reduces activity by 99%.might get lost (downstream of altered splice site)
289292TURNmight get lost (downstream of altered splice site)
294305STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 942 / 942
position (AA) of stopcodon in wt / mu AA sequence 314 / 314
position of stopcodon in wt / mu cDNA 1100 / 1100
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 159 / 159
chromosome 17
strand 1
last intron/exon boundary 903
theoretical NMD boundary in CDS 694
length of CDS 942
coding sequence (CDS) position 746
cDNA position
(for ins/del: last normal base / first normal base)		 904
gDNA position
(for ins/del: last normal base / first normal base)		 26519
chromosomal position
(for ins/del: last normal base / first normal base)		 3402186
original gDNA sequence snippet TTTGATTGTTTCCTGAGAGGATCAAGACTGGAAACCACTGC
altered gDNA sequence snippet TTTGATTGTTTCCTGAGAGGTTCAAGACTGGAAACCACTGC
original cDNA sequence snippet CATCCATCCTAATCTGCAGGATCAAGACTGGAAACCACTGC
altered cDNA sequence snippet CATCCATCCTAATCTGCAGGTTCAAGACTGGAAACCACTGC
wildtype AA sequence MTSCHIAEEH IQKVAIFGGT HGNELTGVFL VKHWLENGAE IQRTGLEVKP FITNPRAVKK
CTRYIDCDLN RIFDLENLGK KMSEDLPYEV RRAQEINHLF GPKDSEDSYD IIFDLHNTTS
NMGCTLILED SRNNFLIQMF HYIKTSLAPL PCYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD YPRDENGEIA
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*
mutated AA sequence MTSCHIAEEH IQKVAIFGGT HGNELTGVFL VKHWLENGAE IQRTGLEVKP FITNPRAVKK
CTRYIDCDLN RIFDLENLGK KMSEDLPYEV RRAQEINHLF GPKDSEDSYD IIFDLHNTTS
NMGCTLILED SRNNFLIQMF HYIKTSLAPL PCYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD YPRDENGEIA
AIIHPNLQVQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*
speed 0.47 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 CM023015)
  • known disease mutation: rs2615 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402186A>TN/A show variant in all transcripts   IGV
HGNC symbol SPATA22
Ensembl transcript ID ENST00000541913
Genbank transcript ID N/A
UniProt peptide Q8NHS9
alteration type single base exchange
alteration region intron
DNA changes g.14961T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894552
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01515

known disease mutation: rs2615 (pathogenic for Spongy degeneration of central nervous system) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6511
4.6821
(flanking)2.171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -23) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased14960wt: 0.37 / mu: 0.57wt: TGCAGTGGTTTCCAGTCTTGATCCTCTCAGGAAACAATCAA
mu: TGCAGTGGTTTCCAGTCTTGAACCTCTCAGGAAACAATCAA		 ttga|TCCT
Donor increased14953wt: 0.62 / mu: 0.86wt: TTTCCAGTCTTGATC
mu: TTTCCAGTCTTGAAC		 TCCA|gtct
distance from splice site 14520
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
66CONFLICTN -> S (in Ref. 1; AAK51120/AAK53408/ AAK61373/AAK61374).might get lost (downstream of altered splice site)
8484CONFLICTV -> A (in Ref. 1; AAK53408/AAK61373/ AAK61374).might get lost (downstream of altered splice site)
279279MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
280280MOD_RESPhosphotyrosine.might 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 515 / 515
chromosome 17
strand -1
last intron/exon boundary 1367
theoretical NMD boundary in CDS 802
length of CDS 1044
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)		 14961
chromosomal position
(for ins/del: last normal base / first normal base)		 3402186
original gDNA sequence snippet GCAGTGGTTTCCAGTCTTGATCCTCTCAGGAAACAATCAAA
altered gDNA sequence snippet GCAGTGGTTTCCAGTCTTGAACCTCTCAGGAAACAATCAAA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MKRSLNENSA RSTAGCLPVP LFNQKKRNRQ PLTSNPLKDD SDWAWEAVNP ELAPVMKTVD
TGQIPHSVSR PLRSQDSVFN SIQSNTGRSQ GGWSYRDGNK NTSLKTWNKN DFKPQCKRTN
LVANDGKNSC PVSSGAQQQK QLRIPEPPNL SRNKETELLR QTHSSKISGC TMRGLDKNSA
LQTLKPNFQQ NQYKKQMLDD IPEDNTLKET SLYQLQFKEK ASSLRIISAV IESMKYWREH
AQKTVLLFEV LAVLDSAVTP GPYYSKTFLM RDGKNTLPCV FYEIDRELPR LIRGRVHRCV
GNYDQKKNIF QCVSVRPASV SEQKTFQAFV KIADVEMQYY INVMNET*
mutated AA sequence N/A
speed 0.38 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

data problem

back to results table