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 10 transcript(s)...
Querying Taster for transcript #1: ENST00000379825
Querying Taster for transcript #2: ENST00000397172
Querying Taster for transcript #3: ENST00000379817
Querying Taster for transcript #4: ENST00000379819
Querying Taster for transcript #5: ENST00000468275
Querying Taster for transcript #6: ENST00000463596
Querying Taster for transcript #7: ENST00000476858
Querying Taster for transcript #8: ENST00000379813
Querying Taster for transcript #9: ENST00000309615
Querying Taster for transcript #10: ENST00000436040
MT speed 0 s - this script 7.538757 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
APTXdisease_causing_automatic0.999999548353584simple_aaeaffected0H143Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999548353584simple_aaeaffected0H161Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999728021834simple_aaeaffected0H215Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999728021834simple_aaeaffected0H201Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999728021834simple_aaeaffected0H215Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999728021834simple_aaeaffected0H201Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999728021834simple_aaeaffected0H201Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999728021834simple_aaeaffected0H201Rsingle base exchangers121908133show file
APTXdisease_causing_automatic0.999999728021834simple_aaeaffected0H215Rsingle base exchangers121908133show file
APTXdisease_causing_automatic1without_aaeaffected0single base exchangers121908133show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999548353584 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000397172
Genbank transcript ID NM_001195252
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.428A>G
cDNA.431A>G
g.40370A>G
AA changes H143R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 143
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      143VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    143VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  215VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206IKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.might get lost (downstream of altered splice site)
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 855 / 855
position (AA) of stopcodon in wt / mu AA sequence 285 / 285
position of stopcodon in wt / mu cDNA 858 / 858
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 4 / 4
chromosome 9
strand -1
last intron/exon boundary 704
theoretical NMD boundary in CDS 650
length of CDS 855
coding sequence (CDS) position 428
cDNA position
(for ins/del: last normal base / first normal base)		 431
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMESLGHWS QGLKISMQDP
KMQVYKDEQV VVIKDKYPKA RYHWLVLPWT SISSLKAVAR EHLELLKHMH TVGEKVIVDF
AGSSKLRFRL GYHAIPSMSH VHLHVISQDF DSPCLKNKKH WNSFNTEYFL ESQAVIEMVQ
EAGRVTVRDG MPELLKLPLR CHECQQLLPS IPQLKEHLRK HWTQ*
mutated AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMESLGHWS QGLKISMQDP
KMQVYKDEQV VVIKDKYPKA RYRWLVLPWT SISSLKAVAR EHLELLKHMH TVGEKVIVDF
AGSSKLRFRL GYHAIPSMSH VHLHVISQDF DSPCLKNKKH WNSFNTEYFL ESQAVIEMVQ
EAGRVTVRDG MPELLKLPLR CHECQQLLPS IPQLKEHLRK HWTQ*
speed 1.31 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: 0.999999548353584 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000476858
Genbank transcript ID NM_001195250
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.482A>G
cDNA.519A>G
g.40370A>G
AA changes H161R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 161
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      161VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    161VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  215VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183RYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.might get lost (downstream of altered splice site)
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 909 / 909
position (AA) of stopcodon in wt / mu AA sequence 303 / 303
position of stopcodon in wt / mu cDNA 946 / 946
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 38 / 38
chromosome 9
strand -1
last intron/exon boundary 792
theoretical NMD boundary in CDS 704
length of CDS 909
coding sequence (CDS) position 482
cDNA position
(for ins/del: last normal base / first normal base)		 519
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQEF
EEEAKNPGLE THRKRKRSGN SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK
KESLGHWSQG LKISMQDPKM QVYKDEQVVV IKDKYPKARY HWLVLPWTSI SSLKAVAREH
LELLKHMHTV GEKVIVDFAG SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN
SFNTEYFLES QAVIEMVQEA GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW
TQ*
mutated AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQEF
EEEAKNPGLE THRKRKRSGN SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK
KESLGHWSQG LKISMQDPKM QVYKDEQVVV IKDKYPKARY RWLVLPWTSI SSLKAVAREH
LELLKHMHTV GEKVIVDFAG SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN
SFNTEYFLES QAVIEMVQEA GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW
TQ*
speed 0.91 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: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000379825
Genbank transcript ID NM_001195251
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.644A>G
cDNA.668A>G
g.40370A>G
AA changes H215R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 215
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      215VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    215VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 921 / 921
position (AA) of stopcodon in wt / mu AA sequence 307 / 307
position of stopcodon in wt / mu cDNA 945 / 945
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 25 / 25
chromosome 9
strand -1
last intron/exon boundary 941
theoretical NMD boundary in CDS 866
length of CDS 921
coding sequence (CDS) position 644
cDNA position
(for ins/del: last normal base / first normal base)		 668
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYHWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQE*
mutated AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYRWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQE*
speed 1.28 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: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000379817
Genbank transcript ID NM_001195248
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.602A>G
cDNA.799A>G
g.40370A>G
AA changes H201R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 201
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      201VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    201VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1029 / 1029
position (AA) of stopcodon in wt / mu AA sequence 343 / 343
position of stopcodon in wt / mu cDNA 1226 / 1226
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 198 / 198
chromosome 9
strand -1
last intron/exon boundary 1072
theoretical NMD boundary in CDS 824
length of CDS 1029
coding sequence (CDS) position 602
cDNA position
(for ins/del: last normal base / first normal base)		 799
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY HWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
mutated AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY RWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
speed 0.46 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: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000379819
Genbank transcript ID N/A
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.644A>G
cDNA.644A>G
g.40370A>G
AA changes H215R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 215
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      215VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    215VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1071 / 1071
position (AA) of stopcodon in wt / mu AA sequence 357 / 357
position of stopcodon in wt / mu cDNA 1071 / 1071
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 1 / 1
chromosome 9
strand -1
last intron/exon boundary 917
theoretical NMD boundary in CDS 866
length of CDS 1071
coding sequence (CDS) position 644
cDNA position
(for ins/del: last normal base / first normal base)		 644
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYHWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQAVIEM VQEAGRVTVR DGMPELLKLP LRCHECQQLL PSIPQLKEHL RKHWTQ*
mutated AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYRWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQAVIEM VQEAGRVTVR DGMPELLKLP LRCHECQQLL PSIPQLKEHL RKHWTQ*
speed 0.49 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: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000468275
Genbank transcript ID N/A
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.602A>G
cDNA.695A>G
g.40370A>G
AA changes H201R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 201
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      201VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    201VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1029 / 1029
position (AA) of stopcodon in wt / mu AA sequence 343 / 343
position of stopcodon in wt / mu cDNA 1122 / 1122
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 94 / 94
chromosome 9
strand -1
last intron/exon boundary 968
theoretical NMD boundary in CDS 824
length of CDS 1029
coding sequence (CDS) position 602
cDNA position
(for ins/del: last normal base / first normal base)		 695
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY HWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
mutated AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY RWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
speed 0.46 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: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000463596
Genbank transcript ID N/A
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.602A>G
cDNA.796A>G
g.40370A>G
AA changes H201R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 201
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      201VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    201VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1029 / 1029
position (AA) of stopcodon in wt / mu AA sequence 343 / 343
position of stopcodon in wt / mu cDNA 1223 / 1223
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 195 / 195
chromosome 9
strand -1
last intron/exon boundary 1069
theoretical NMD boundary in CDS 824
length of CDS 1029
coding sequence (CDS) position 602
cDNA position
(for ins/del: last normal base / first normal base)		 796
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY HWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
mutated AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY RWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
speed 0.48 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: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000379813
Genbank transcript ID NM_001195249
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.602A>G
cDNA.656A>G
g.40370A>G
AA changes H201R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 201
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      201VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    201VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1029 / 1029
position (AA) of stopcodon in wt / mu AA sequence 343 / 343
position of stopcodon in wt / mu cDNA 1083 / 1083
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 55 / 55
chromosome 9
strand -1
last intron/exon boundary 929
theoretical NMD boundary in CDS 824
length of CDS 1029
coding sequence (CDS) position 602
cDNA position
(for ins/del: last normal base / first normal base)		 656
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY HWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
mutated AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QVYKDEQVVV IKDKYPKARY RWLVLPWTSI SSLKAVAREH LELLKHMHTV GEKVIVDFAG
SSKLRFRLGY HAIPSMSHVH LHVISQDFDS PCLKNKKHWN SFNTEYFLES QAVIEMVQEA
GRVTVRDGMP ELLKLPLRCH ECQQLLPSIP QLKEHLRKHW TQ*
speed 0.96 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: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000309615
Genbank transcript ID NM_175069
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.644A>G
cDNA.668A>G
g.40370A>G
AA changes H215R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 215
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      215VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    215VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 921 / 921
position (AA) of stopcodon in wt / mu AA sequence 307 / 307
position of stopcodon in wt / mu cDNA 945 / 945
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 25 / 25
chromosome 9
strand -1
last intron/exon boundary 941
theoretical NMD boundary in CDS 866
length of CDS 921
coding sequence (CDS) position 644
cDNA position
(for ins/del: last normal base / first normal base)		 668
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYHWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQE*
mutated AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYRWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQE*
speed 0.48 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 CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000436040
Genbank transcript ID N/A
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region intron
DNA changes g.40370A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 1172
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.might get lost (downstream of altered splice site)
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.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 198 / 198
chromosome 9
strand -1
last intron/exon boundary 845
theoretical NMD boundary in CDS 597
length of CDS 579
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)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MMRVCWLVRQ DSRHQRIRLP HLEAVVIGRG PETKITDKKC SRQQVQLKAE CNKGYVKVKQ
VGVNPTSIDS VVIGKDQEVK LQPGQVLHMV NELYPYIVEF EEEAKNPGLE THRKRKRSGN
SDSIERDAAQ EAEAGTGLEP GSNSGQCSVP LKKGKDAPIK KESLGHWSQG LKISMQDPKM
QPCTSSCDQP GF*
mutated AA sequence N/A
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

Problems