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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 2.78 s - this script 6.571027 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ASPAdisease_causing_automatic0.99999999828482simple_aaeaffected0A305Esingle base exchangers28940574show file
ASPAdisease_causing_automatic0.99999999828482simple_aaeaffected0A305Esingle base exchangers28940574show file
SPATA22disease_causing_automatic1without_aaeaffected0single base exchangers28940574show file

some transcripts had annotation problems and are not shown

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999828482 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940124)
  • known disease mutation: rs2607 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402354C>AN/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.914C>A
cDNA.1062C>A
g.26687C>A
AA changes A305E Score: 107 explain score(s)
position(s) of altered AA
if AA alteration in CDS
305
frameshift no
known variant Reference ID: rs28940574
databasehomozygous (A/A)heterozygousallele carriers
1000G022
ExAC02727

known disease mutation: rs2607 (pathogenic for Spongy degeneration of central nervous system|Canavan Disease, Familial Form|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3390.998
5.3390.998
(flanking)0.3490.486
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased26687wt: 0.9761 / mu: 0.9936 (marginal change - not scored)wt: CAATGCAAAAAGTAT
mu: CAATGAAAAAAGTAT
 ATGC|aaaa
Donor increased26684wt: 0.42 / mu: 0.54wt: GCTCAATGCAAAAAG
mu: GCTCAATGAAAAAAG
 TCAA|tgca
Donor gained266830.68mu: CGCTCAATGAAAAAA CTCA|atga
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      305AFAKTTKLTLNAKSIRCCLH*
mutated  not conserved    305LTLNEKSIRCCLH
Ptroglodytes  all identical  ENSPTRG00000008568  305LTLNAKSIRCCLH
Mmulatta  all identical  ENSMMUG00000030388  305LMLNAKSIRCSVH
Fcatus  all identical  ENSFCAG00000007919  305KATKLTLNARSIRSSL
Mmusculus  all identical  ENSMUSG00000020774  304LTLSAKSIRSTLH
Ggallus  all identical  ENSGALG00000004669  306KMELTAGHIR
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000005154  307AFVTTCREILAANAI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005789  304AFTTTQKMTLCAQAIRC
protein features
start (aa)end (aa)featuredetails 
294305STRANDlost
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 914
cDNA position
(for ins/del: last normal base / first normal base)
1062
gDNA position
(for ins/del: last normal base / first normal base)
26687
chromosomal position
(for ins/del: last normal base / first normal base)
3402354
original gDNA sequence snippet AACTAAACTAACGCTCAATGCAAAAAGTATTCGCTGCTGTT
altered gDNA sequence snippet AACTAAACTAACGCTCAATGAAAAAAGTATTCGCTGCTGTT
original cDNA sequence snippet AACTAAACTAACGCTCAATGCAAAAAGTATTCGCTGCTGTT
altered cDNA sequence snippet AACTAAACTAACGCTCAATGAAAAAAGTATTCGCTGCTGTT
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
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNEKSIRC CLH*
speed 0.87 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: 0.99999999828482 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940124)
  • known disease mutation: rs2607 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402354C>AN/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.914C>A
cDNA.1072C>A
g.26687C>A
AA changes A305E Score: 107 explain score(s)
position(s) of altered AA
if AA alteration in CDS
305
frameshift no
known variant Reference ID: rs28940574
databasehomozygous (A/A)heterozygousallele carriers
1000G022
ExAC02727

known disease mutation: rs2607 (pathogenic for Spongy degeneration of central nervous system|Canavan Disease, Familial Form|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3390.998
5.3390.998
(flanking)0.3490.486
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased26687wt: 0.9761 / mu: 0.9936 (marginal change - not scored)wt: CAATGCAAAAAGTAT
mu: CAATGAAAAAAGTAT
 ATGC|aaaa
Donor increased26684wt: 0.42 / mu: 0.54wt: GCTCAATGCAAAAAG
mu: GCTCAATGAAAAAAG
 TCAA|tgca
Donor gained266830.68mu: CGCTCAATGAAAAAA CTCA|atga
distance from splice site 170
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      305AFAKTTKLTLNAKSIRCCLH*
mutated  not conserved    305LTLNEKSIRCCLH
Ptroglodytes  all identical  ENSPTRG00000008568  305LTLNAKSIRCCLH
Mmulatta  all identical  ENSMMUG00000030388  305LMLNAKSIRCSVH
Fcatus  all identical  ENSFCAG00000007919  305KATKLTLNARSIRSSL
Mmusculus  all identical  ENSMUSG00000020774  304LTLSAKSIRSTLH
Ggallus  all identical  ENSGALG00000004669  306KMELTAGHIR
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000005154  307AFVTTCREILAANAI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005789  304AFTTTQKMTLCAQAIRC
protein features
start (aa)end (aa)featuredetails 
294305STRANDlost
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 914
cDNA position
(for ins/del: last normal base / first normal base)
1072
gDNA position
(for ins/del: last normal base / first normal base)
26687
chromosomal position
(for ins/del: last normal base / first normal base)
3402354
original gDNA sequence snippet AACTAAACTAACGCTCAATGCAAAAAGTATTCGCTGCTGTT
altered gDNA sequence snippet AACTAAACTAACGCTCAATGAAAAAAGTATTCGCTGCTGTT
original cDNA sequence snippet AACTAAACTAACGCTCAATGCAAAAAGTATTCGCTGCTGTT
altered cDNA sequence snippet AACTAAACTAACGCTCAATGAAAAAAGTATTCGCTGCTGTT
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
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNEKSIRC CLH*
speed 1.18 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 CM940124)
  • known disease mutation: rs2607 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402354C>AN/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.14793G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs28940574
databasehomozygous (A/A)heterozygousallele carriers
1000G022
ExAC02727

known disease mutation: rs2607 (pathogenic for Spongy degeneration of central nervous system|Canavan Disease, Familial Form|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3390.998
5.3390.998
(flanking)0.3490.486
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 marginally increased14794wt: 0.6617 / mu: 0.6802 (marginal change - not scored)wt: ACAGCAGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTTG
mu: ACAGCAGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTTG
 ttgc|ATTG
Acc increased14801wt: 0.51 / mu: 0.87wt: CGAATACTTTTTGCATTGAGCGTTAGTTTAGTTGTCTTTGC
mu: CGAATACTTTTTTCATTGAGCGTTAGTTTAGTTGTCTTTGC
 gagc|GTTA
Acc increased14798wt: 0.47 / mu: 0.93wt: CAGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTTGTCTT
mu: CAGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTTGTCTT
 attg|AGCG
Acc increased14799wt: 0.56 / mu: 0.95wt: AGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTTGTCTTT
mu: AGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTTGTCTTT
 ttga|GCGT
distance from splice site 14352
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)
14793
chromosomal position
(for ins/del: last normal base / first normal base)
3402354
original gDNA sequence snippet AACAGCAGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTT
altered gDNA sequence snippet AACAGCAGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTT
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 0.73 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