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 2.460004 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ASPAdisease_causing_automatic0.999999995238027simple_aaeaffected0C152Rsingle base exchangers104894548show file
ASPAdisease_causing_automatic0.999999995238027simple_aaeaffected0C152Rsingle base exchangers104894548show file
SPATA22disease_causing_automatic1without_aaeaffected0single base exchangers104894548show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999995238027 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950102)
  • known disease mutation: rs2606 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3386814T>CN/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.454T>C
cDNA.602T>C
g.11147T>C
AA changes C152R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 152
frameshift no
known variant Reference ID: rs104894548
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2606 (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 CM950102)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
regulatory features H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9931
2.5781
(flanking)3.3731
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 increased11140wt: 0.6867 / mu: 0.7095 (marginal change - not scored)wt: TTTCAGACTTCTCTGGCTCCACTACCCTGCTACGTTTATCT
mu: TTTCAGACTTCTCTGGCTCCACTACCCCGCTACGTTTATCT		 tcca|CTAC
Acc marginally increased11143wt: 0.7975 / mu: 0.8285 (marginal change - not scored)wt: CAGACTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGAT
mu: CAGACTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGAT		 acta|CCCT
Acc marginally increased11147wt: 0.3376 / mu: 0.3384 (marginal change - not scored)wt: CTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGATTGAG
mu: CTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGATTGAG		 ccct|GCTA
Acc increased11141wt: 0.34 / mu: 0.44wt: TTCAGACTTCTCTGGCTCCACTACCCTGCTACGTTTATCTG
mu: TTCAGACTTCTCTGGCTCCACTACCCCGCTACGTTTATCTG		 ccac|TACC
Donor marginally increased11147wt: 0.9910 / mu: 0.9964 (marginal change - not scored)wt: TACCCTGCTACGTTT
mu: TACCCCGCTACGTTT		 CCCT|gcta
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      152HYIKTSLAPLPCYVYLIEHPSLKY
mutated  not conserved    152HYIKTSLAPLPRYVYLIEHPSLK
Ptroglodytes  all identical  ENSPTRG00000008568  152HYIKTSLAPLPCYVYLIEHPSLK
Mmulatta  all identical  ENSMMUG00000030388  152HYIKTSLAPLPCYVYLIEHPSLK
Fcatus  no alignment  ENSFCAG00000007919  n/a
Mmusculus  all identical  ENSMUSG00000020774  151HYIKTCMAPLPCSVYLIEHPSLK
Ggallus  not conserved  ENSGALG00000004669  153HYIKNALAPERVPVLLIEHPNLK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000005154  154HYIKKAMAPHTCSVLLNEHPQLK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005789  151NYIKTSMAPLACSVLLIEHPRLK
protein features
start (aa)end (aa)featuredetails 
152156STRANDlost
160162STRANDmight get lost (downstream of altered splice site)
164164MUTAGENY->F: Reduces activity by 99%.might get lost (downstream of altered splice site)
164168REGIONSubstrate binding.might get lost (downstream of altered splice site)
167170HELIXmight get lost (downstream of altered splice site)
168168MUTAGENR->K: Reduces activity by 99%.might get lost (downstream of altered splice site)
171180STRANDmight get lost (downstream of altered splice site)
178178MUTAGENE->D: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
178178MUTAGENE->Q: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
178178BINDINGSubstrate.might get lost (downstream of altered splice site)
178178MUTAGENE->A: Reduces activity by 99%.might get lost (downstream of altered splice site)
178178ACT_SITEmight get lost (downstream of altered splice site)
189210HELIXmight get lost (downstream of altered splice site)
218229STRANDmight get lost (downstream of altered splice site)
235237STRANDmight get lost (downstream of altered splice site)
241243STRANDmight get lost (downstream of altered splice site)
245249TURNmight get lost (downstream of altered splice site)
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 454
cDNA position
(for ins/del: last normal base / first normal base)		 602
gDNA position
(for ins/del: last normal base / first normal base)		 11147
chromosomal position
(for ins/del: last normal base / first normal base)		 3386814
original gDNA sequence snippet CTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGATTGAG
altered gDNA sequence snippet CTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGATTGAG
original cDNA sequence snippet CTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGATTGAG
altered cDNA sequence snippet CTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGATTGAG
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 PRYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD YPRDENGEIA
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*
speed 0.25 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: 0.999999995238027 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950102)
  • known disease mutation: rs2606 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3386814T>CN/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.454T>C
cDNA.612T>C
g.11147T>C
AA changes C152R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 152
frameshift no
known variant Reference ID: rs104894548
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2606 (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 CM950102)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
regulatory features H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9931
2.5781
(flanking)3.3731
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 increased11140wt: 0.6867 / mu: 0.7095 (marginal change - not scored)wt: TTTCAGACTTCTCTGGCTCCACTACCCTGCTACGTTTATCT
mu: TTTCAGACTTCTCTGGCTCCACTACCCCGCTACGTTTATCT		 tcca|CTAC
Acc marginally increased11143wt: 0.7975 / mu: 0.8285 (marginal change - not scored)wt: CAGACTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGAT
mu: CAGACTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGAT		 acta|CCCT
Acc marginally increased11147wt: 0.3376 / mu: 0.3384 (marginal change - not scored)wt: CTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGATTGAG
mu: CTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGATTGAG		 ccct|GCTA
Acc increased11141wt: 0.34 / mu: 0.44wt: TTCAGACTTCTCTGGCTCCACTACCCTGCTACGTTTATCTG
mu: TTCAGACTTCTCTGGCTCCACTACCCCGCTACGTTTATCTG		 ccac|TACC
Donor marginally increased11147wt: 0.9910 / mu: 0.9964 (marginal change - not scored)wt: TACCCTGCTACGTTT
mu: TACCCCGCTACGTTT		 CCCT|gcta
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      152HYIKTSLAPLPCYVYLIEHPSLKY
mutated  not conserved    152HYIKTSLAPLPRYVYLIEHPSLK
Ptroglodytes  all identical  ENSPTRG00000008568  152HYIKTSLAPLPCYVYLIEHPSLK
Mmulatta  all identical  ENSMMUG00000030388  152HYIKTSLAPLPCYVYLIEHPSLK
Fcatus  no alignment  ENSFCAG00000007919  n/a
Mmusculus  all identical  ENSMUSG00000020774  151HYIKTCMAPLPCSVYLIEHPSLK
Ggallus  not conserved  ENSGALG00000004669  153HYIKNALAPERVPVLLIEHPNLK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000005154  154HYIKKAMAPHTCSVLLNEHPQLK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005789  151NYIKTSMAPLACSVLLIEHPRLK
protein features
start (aa)end (aa)featuredetails 
152156STRANDlost
160162STRANDmight get lost (downstream of altered splice site)
164164MUTAGENY->F: Reduces activity by 99%.might get lost (downstream of altered splice site)
164168REGIONSubstrate binding.might get lost (downstream of altered splice site)
167170HELIXmight get lost (downstream of altered splice site)
168168MUTAGENR->K: Reduces activity by 99%.might get lost (downstream of altered splice site)
171180STRANDmight get lost (downstream of altered splice site)
178178MUTAGENE->D: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
178178MUTAGENE->Q: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
178178BINDINGSubstrate.might get lost (downstream of altered splice site)
178178MUTAGENE->A: Reduces activity by 99%.might get lost (downstream of altered splice site)
178178ACT_SITEmight get lost (downstream of altered splice site)
189210HELIXmight get lost (downstream of altered splice site)
218229STRANDmight get lost (downstream of altered splice site)
235237STRANDmight get lost (downstream of altered splice site)
241243STRANDmight get lost (downstream of altered splice site)
245249TURNmight get lost (downstream of altered splice site)
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 454
cDNA position
(for ins/del: last normal base / first normal base)		 612
gDNA position
(for ins/del: last normal base / first normal base)		 11147
chromosomal position
(for ins/del: last normal base / first normal base)		 3386814
original gDNA sequence snippet CTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGATTGAG
altered gDNA sequence snippet CTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGATTGAG
original cDNA sequence snippet CTTCTCTGGCTCCACTACCCTGCTACGTTTATCTGATTGAG
altered cDNA sequence snippet CTTCTCTGGCTCCACTACCCCGCTACGTTTATCTGATTGAG
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 PRYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD YPRDENGEIA
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*
speed 0.15 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
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 CM950102)
  • known disease mutation: rs2606 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3386814T>CN/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.30333A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894548
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2606 (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 CM950102)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
regulatory features H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9931
2.5781
(flanking)3.3731
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
Donor marginally increased30330wt: 0.9717 / mu: 0.9752 (marginal change - not scored)wt: AACGTAGCAGGGTAG
mu: AACGTAGCGGGGTAG		 CGTA|gcag
Donor marginally increased30325wt: 0.8548 / mu: 0.8559 (marginal change - not scored)wt: AGATAAACGTAGCAG
mu: AGATAAACGTAGCGG		 ATAA|acgt
Donor gained303270.98mu: ATAAACGTAGCGGGG AAAC|gtag
distance from splice site 14122
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)		 30333
chromosomal position
(for ins/del: last normal base / first normal base)		 3386814
original gDNA sequence snippet CTCAATCAGATAAACGTAGCAGGGTAGTGGAGCCAGAGAAG
altered gDNA sequence snippet CTCAATCAGATAAACGTAGCGGGGTAGTGGAGCCAGAGAAG
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 0.06 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

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