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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000268251
Querying Taster for transcript #2: ENST00000567812
Querying Taster for transcript #3: ENST00000425191
Querying Taster for transcript #4: ENST00000569156
Querying Taster for transcript #5: ENST00000396600
MT speed 0 s - this script 4.689832 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABATdisease_causing_automatic0.999999999593777simple_aae0R220Ksingle base exchangers121434578show file
ABATdisease_causing_automatic0.999999999593777simple_aae0R235Ksingle base exchangers121434578show file
ABATdisease_causing_automatic0.999999999593777simple_aae0R220Ksingle base exchangers121434578show file
ABATdisease_causing_automatic0.999999999593777simple_aae0R220Ksingle base exchangers121434578show file
ABATdisease_causing_automatic0.999999999593777simple_aae0R220Ksingle base exchangers121434578show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999593777 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980002)
  • known disease mutation: rs16216 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:8862105G>AN/A show variant in all transcripts   IGV
HGNC symbol ABAT
Ensembl transcript ID ENST00000268251
Genbank transcript ID NM_001127448
UniProt peptide P80404
alteration type single base exchange
alteration region CDS
DNA changes c.659G>A
cDNA.847G>A
g.93684G>A
AA changes R220K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 220
frameshift no
known variant Reference ID: rs121434578
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16216 (pathogenic for Gamma-aminobutyric acid transaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2241
5.9321
(flanking)0.6141
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 increased93681wt: 0.7211 / mu: 0.7348 (marginal change - not scored)wt: CTTCATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGG
mu: CTTCATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGG		 atgg|GAGG
Donor marginally increased93679wt: 0.9578 / mu: 0.9984 (marginal change - not scored)wt: TTCCATGGGAGGACC
mu: TTCCATGGGAAGACC		 CCAT|ggga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      220SILSFMGAFHGRTMGCLATTHSKA
mutated  all conserved    220SILSFMGAFHGKTMGCLATTHSK
Ptroglodytes  all identical  ENSPTRG00000007746  220SILSFMGAFHGRTMGCLATTHSK
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000001435  220SILSFMGAFHGRTLGCLATTHSK
Mmusculus  all identical  ENSMUSG00000057880  220SILSFMGAFHGRTMGCLATTHSK
Ggallus  all identical  ENSGALG00000007334  220AMLSFMGGFHGRTFGCLATTHSK
Trubripes  all identical  ENSTRUG00000010349  202SILSFMGAFHGRTMGCLATTHSK
Drerio  all identical  ENSDARG00000006031  220SILSFMGAFHGRTLGCLATTHSK
Dmelanogaster  all identical  FBgn0036927  208SILSFKGAFHGRTL
Celegans  all identical  K04D7.3  204SVMGFEGAFHGRSL
Xtropicalis  all identical  ENSXETG00000008691  220SILSFMGGFHGRTMGCLATTHSK
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1503 / 1503
position (AA) of stopcodon in wt / mu AA sequence 501 / 501
position of stopcodon in wt / mu cDNA 1691 / 1691
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 189 / 189
chromosome 16
strand 1
last intron/exon boundary 1570
theoretical NMD boundary in CDS 1331
length of CDS 1503
coding sequence (CDS) position 659
cDNA position
(for ins/del: last normal base / first normal base)		 847
gDNA position
(for ins/del: last normal base / first normal base)		 93684
chromosomal position
(for ins/del: last normal base / first normal base)		 8862105
original gDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGGGAC
altered gDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGGGAC
original cDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTTGCTTAGCGA
altered cDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTTGCTTAGCGA
wildtype AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGR TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK GVVLGGCGDK SIRFRPTLVF
RDHHAHLFLN IFSDILADFK *
mutated AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGK TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK GVVLGGCGDK SIRFRPTLVF
RDHHAHLFLN IFSDILADFK *
speed 0.85 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: 0.999999999593777 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980002)
  • known disease mutation: rs16216 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:8862105G>AN/A show variant in all transcripts   IGV
HGNC symbol ABAT
Ensembl transcript ID ENST00000567812
Genbank transcript ID N/A
UniProt peptide P80404
alteration type single base exchange
alteration region CDS
DNA changes c.704G>A
cDNA.966G>A
g.93684G>A
AA changes R235K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 235
frameshift no
known variant Reference ID: rs121434578
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16216 (pathogenic for Gamma-aminobutyric acid transaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2241
5.9321
(flanking)0.6141
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 increased93681wt: 0.7211 / mu: 0.7348 (marginal change - not scored)wt: CTTCATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGG
mu: CTTCATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGG		 atgg|GAGG
Donor marginally increased93679wt: 0.9578 / mu: 0.9984 (marginal change - not scored)wt: TTCCATGGGAGGACC
mu: TTCCATGGGAAGACC		 CCAT|ggga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      235SILSFMGAFHGRTMGCLATTHSKA
mutated  all conserved    235SILSFMGAFHGKTMGCL
Ptroglodytes  all identical  ENSPTRG00000007746  220SILSFMGAFHGRTMGCLATTHSK
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000001435  220SILSFMGAFHGRTLGCLATTHSK
Mmusculus  all identical  ENSMUSG00000057880  220SILSFMGAFHGRTMGCLATTHSK
Ggallus  all identical  ENSGALG00000007334  220AMLSFMGGFHGRTFGCLATTHSK
Trubripes  all identical  ENSTRUG00000010349  202SILSFMGAFHGRTMGCLATTHSK
Drerio  all identical  ENSDARG00000006031  220SILSFMGAFHGRTLGCLATTHSK
Dmelanogaster  all identical  FBgn0036927  208SILSFKGAFHGRTL
Celegans  all identical  K04D7.3  204SVMGFEGAFHGRSL
Xtropicalis  all identical  ENSXETG00000008691  220SILSFMGGFHGRTMGCLATTHSK
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1548 / 1548
position (AA) of stopcodon in wt / mu AA sequence 516 / 516
position of stopcodon in wt / mu cDNA 1810 / 1810
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 263 / 263
chromosome 16
strand 1
last intron/exon boundary 1689
theoretical NMD boundary in CDS 1376
length of CDS 1548
coding sequence (CDS) position 704
cDNA position
(for ins/del: last normal base / first normal base)		 966
gDNA position
(for ins/del: last normal base / first normal base)		 93684
chromosomal position
(for ins/del: last normal base / first normal base)		 8862105
original gDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGGGAC
altered gDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGGGAC
original cDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTTGCTTAGCGA
altered cDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTTGCTTAGCGA
wildtype AA sequence MWWQHAKGVP VPQGVMASML LAQRLACSFQ HSYRLLVPGS RHISQAAAKV DVEFDYDGPL
MKTEVPGPRS QELMKQLNII QNAEAVHFFC NYEESRGNYL VDVDGNRMLD LYSQISSVPI
GYSHPALLKL IQQPQNASMF VNRPALGILP PENFVEKLRQ SLLSVAPKGM SQLITMACGS
CSNENALKTI FMWYRSKERG QRGFSQEELE TCMINQAPGC PDYSILSFMG AFHGRTMGCL
ATTHSKAIHK IDIPSFDWPI APFPRLKYPL EEFVKENQQE EARCLEEVED LIVKYRKKKK
TVAGIIVEPI QSEGGDNHAS DDFFRKLRDI ARKHGCAFLV DEVQTGGGCT GKFWAHEHWG
LDDPADVMTF SKKMMTGGFF HKEEFRPNAP YRIFNTWLGD PSKNLLLAEV INIIKREDLL
NNAAHAGKAL LTGLLDLQAR YPQFISRVRG RGTFCSFDTP DDSIRNKLIL IARNKGVVLG
GCGDKSIRFR PTLVFRDHHA HLFLNIFSDI LADFK*
mutated AA sequence MWWQHAKGVP VPQGVMASML LAQRLACSFQ HSYRLLVPGS RHISQAAAKV DVEFDYDGPL
MKTEVPGPRS QELMKQLNII QNAEAVHFFC NYEESRGNYL VDVDGNRMLD LYSQISSVPI
GYSHPALLKL IQQPQNASMF VNRPALGILP PENFVEKLRQ SLLSVAPKGM SQLITMACGS
CSNENALKTI FMWYRSKERG QRGFSQEELE TCMINQAPGC PDYSILSFMG AFHGKTMGCL
ATTHSKAIHK IDIPSFDWPI APFPRLKYPL EEFVKENQQE EARCLEEVED LIVKYRKKKK
TVAGIIVEPI QSEGGDNHAS DDFFRKLRDI ARKHGCAFLV DEVQTGGGCT GKFWAHEHWG
LDDPADVMTF SKKMMTGGFF HKEEFRPNAP YRIFNTWLGD PSKNLLLAEV INIIKREDLL
NNAAHAGKAL LTGLLDLQAR YPQFISRVRG RGTFCSFDTP DDSIRNKLIL IARNKGVVLG
GCGDKSIRFR PTLVFRDHHA HLFLNIFSDI LADFK*
speed 0.86 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: 0.999999999593777 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980002)
  • known disease mutation: rs16216 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:8862105G>AN/A show variant in all transcripts   IGV
HGNC symbol ABAT
Ensembl transcript ID ENST00000425191
Genbank transcript ID N/A
UniProt peptide P80404
alteration type single base exchange
alteration region CDS
DNA changes c.659G>A
cDNA.919G>A
g.93684G>A
AA changes R220K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 220
frameshift no
known variant Reference ID: rs121434578
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16216 (pathogenic for Gamma-aminobutyric acid transaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2241
5.9321
(flanking)0.6141
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 increased93681wt: 0.7211 / mu: 0.7348 (marginal change - not scored)wt: CTTCATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGG
mu: CTTCATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGG		 atgg|GAGG
Donor marginally increased93679wt: 0.9578 / mu: 0.9984 (marginal change - not scored)wt: TTCCATGGGAGGACC
mu: TTCCATGGGAAGACC		 CCAT|ggga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      220SILSFMGAFHGRTMGCLATTHSKA
mutated  all conserved    220SILSFMGAFHGKTMGCLATTHSK
Ptroglodytes  all identical  ENSPTRG00000007746  220SILSFMGAFHGRTMGCLATTHSK
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000001435  220SILSFMGAFHGRTLGCLATTHSK
Mmusculus  all identical  ENSMUSG00000057880  220SILSFMGAFHGRTMGCLATTHSK
Ggallus  all identical  ENSGALG00000007334  220AMLSFMGGFHGRTFGCLATTHSK
Trubripes  all identical  ENSTRUG00000010349  202SILSFMGAFHGRTMGCLATTHSK
Drerio  all identical  ENSDARG00000006031  220SILSFMGAFHGRTLGCLATTHSK
Dmelanogaster  all identical  FBgn0036927  208SILSFKGAFHGRTL
Celegans  all identical  K04D7.3  204SVMGFEGAFHGRSL
Xtropicalis  all identical  ENSXETG00000008691  220SILSFMGGFHGRTMGCLATTHSK
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1503 / 1503
position (AA) of stopcodon in wt / mu AA sequence 501 / 501
position of stopcodon in wt / mu cDNA 1763 / 1763
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 261 / 261
chromosome 16
strand 1
last intron/exon boundary 1642
theoretical NMD boundary in CDS 1331
length of CDS 1503
coding sequence (CDS) position 659
cDNA position
(for ins/del: last normal base / first normal base)		 919
gDNA position
(for ins/del: last normal base / first normal base)		 93684
chromosomal position
(for ins/del: last normal base / first normal base)		 8862105
original gDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGGGAC
altered gDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGGGAC
original cDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTTGCTTAGCGA
altered cDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTTGCTTAGCGA
wildtype AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGR TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK GVVLGGCGDK SIRFRPTLVF
RDHHAHLFLN IFSDILADFK *
mutated AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGK TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK GVVLGGCGDK SIRFRPTLVF
RDHHAHLFLN IFSDILADFK *
speed 0.64 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: 0.999999999593777 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980002)
  • known disease mutation: rs16216 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:8862105G>AN/A show variant in all transcripts   IGV
HGNC symbol ABAT
Ensembl transcript ID ENST00000569156
Genbank transcript ID N/A
UniProt peptide P80404
alteration type single base exchange
alteration region CDS
DNA changes c.659G>A
cDNA.916G>A
g.93684G>A
AA changes R220K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 220
frameshift no
known variant Reference ID: rs121434578
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16216 (pathogenic for Gamma-aminobutyric acid transaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2241
5.9321
(flanking)0.6141
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 increased93681wt: 0.7211 / mu: 0.7348 (marginal change - not scored)wt: CTTCATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGG
mu: CTTCATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGG		 atgg|GAGG
Donor marginally increased93679wt: 0.9578 / mu: 0.9984 (marginal change - not scored)wt: TTCCATGGGAGGACC
mu: TTCCATGGGAAGACC		 CCAT|ggga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      220SILSFMGAFHGRTMGCLATTHSKA
mutated  all conserved    220SILSFMGAFHGKTMGCLATTHSK
Ptroglodytes  all identical  ENSPTRG00000007746  220SILSFMGAFHGRTMGCLATTHSK
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000001435  220SILSFMGAFHGRTLGCLATTHSK
Mmusculus  all identical  ENSMUSG00000057880  220SILSFMGAFHGRTMGCLATTHSK
Ggallus  all identical  ENSGALG00000007334  220AMLSFMGGFHGRTFGCLATTHSK
Trubripes  all identical  ENSTRUG00000010349  202SILSFMGAFHGRTMGCLATTHSK
Drerio  all identical  ENSDARG00000006031  220SILSFMGAFHGRTLGCLATTHSK
Dmelanogaster  all identical  FBgn0036927  208SILSFKGAFHGRTL
Celegans  all identical  K04D7.3  204SVMGFEGAFHGRSL
Xtropicalis  all identical  ENSXETG00000008691  220SILSFMGGFHGRTMGCLATTHSK
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1548 / 1548
position (AA) of stopcodon in wt / mu AA sequence 516 / 516
position of stopcodon in wt / mu cDNA 1805 / 1805
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 258 / 258
chromosome 16
strand 1
last intron/exon boundary 1639
theoretical NMD boundary in CDS 1331
length of CDS 1548
coding sequence (CDS) position 659
cDNA position
(for ins/del: last normal base / first normal base)		 916
gDNA position
(for ins/del: last normal base / first normal base)		 93684
chromosomal position
(for ins/del: last normal base / first normal base)		 8862105
original gDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGGGAC
altered gDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGGGAC
original cDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTTGCTTAGCGA
altered cDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTTGCTTAGCGA
wildtype AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGR TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK ALPACDFEKP RSSPTSCLFQ
VWCWVAVVTN PFVSVPRWSS GITTLTCSSI FSVTS*
mutated AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGK TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK ALPACDFEKP RSSPTSCLFQ
VWCWVAVVTN PFVSVPRWSS GITTLTCSSI FSVTS*
speed 1.02 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999593777 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980002)
  • known disease mutation: rs16216 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:8862105G>AN/A show variant in all transcripts   IGV
HGNC symbol ABAT
Ensembl transcript ID ENST00000396600
Genbank transcript ID NM_000663
UniProt peptide P80404
alteration type single base exchange
alteration region CDS
DNA changes c.659G>A
cDNA.1597G>A
g.93684G>A
AA changes R220K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 220
frameshift no
known variant Reference ID: rs121434578
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16216 (pathogenic for Gamma-aminobutyric acid transaminase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2241
5.9321
(flanking)0.6141
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 increased93681wt: 0.7211 / mu: 0.7348 (marginal change - not scored)wt: CTTCATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGG
mu: CTTCATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGG		 atgg|GAGG
Donor marginally increased93679wt: 0.9578 / mu: 0.9984 (marginal change - not scored)wt: TTCCATGGGAGGACC
mu: TTCCATGGGAAGACC		 CCAT|ggga
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      220SILSFMGAFHGRTMGCLATTHSKA
mutated  all conserved    220SILSFMGAFHGKTMGCLATTHSK
Ptroglodytes  all identical  ENSPTRG00000007746  220SILSFMGAFHGRTMGCLATTHSK
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000001435  220SILSFMGAFHGRTLGCLATTHSK
Mmusculus  all identical  ENSMUSG00000057880  220SILSFMGAFHGRTMGCLATTHSK
Ggallus  all identical  ENSGALG00000007334  220AMLSFMGGFHGRTFGCLATTHSK
Trubripes  all identical  ENSTRUG00000010349  202SILSFMGAFHGRTMGCLATTHSK
Drerio  all identical  ENSDARG00000006031  220SILSFMGAFHGRTLGCLATTHSK
Dmelanogaster  all identical  FBgn0036927  208SILSFKGAFHGRTL
Celegans  all identical  K04D7.3  204SVMGFEGAFHGRSL
Xtropicalis  all identical  ENSXETG00000008691  220SILSFMGGFHGRTMGCLATTHSK
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1503 / 1503
position (AA) of stopcodon in wt / mu AA sequence 501 / 501
position of stopcodon in wt / mu cDNA 2441 / 2441
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 939 / 939
chromosome 16
strand 1
last intron/exon boundary 2320
theoretical NMD boundary in CDS 1331
length of CDS 1503
coding sequence (CDS) position 659
cDNA position
(for ins/del: last normal base / first normal base)		 1597
gDNA position
(for ins/del: last normal base / first normal base)		 93684
chromosomal position
(for ins/del: last normal base / first normal base)		 8862105
original gDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTAAGGAGGGAC
altered gDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTAAGGAGGGAC
original cDNA sequence snippet CATGGGCGCGTTCCATGGGAGGACCATGGGTTGCTTAGCGA
altered cDNA sequence snippet CATGGGCGCGTTCCATGGGAAGACCATGGGTTGCTTAGCGA
wildtype AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGR TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK GVVLGGCGDK SIRFRPTLVF
RDHHAHLFLN IFSDILADFK *
mutated AA sequence MASMLLAQRL ACSFQHSYRL LVPGSRHISQ AAAKVDVEFD YDGPLMKTEV PGPRSQELMK
QLNIIQNAEA VHFFCNYEES RGNYLVDVDG NRMLDLYSQI SSVPIGYSHP ALLKLIQQPQ
NASMFVNRPA LGILPPENFV EKLRQSLLSV APKGMSQLIT MACGSCSNEN ALKTIFMWYR
SKERGQRGFS QEELETCMIN QAPGCPDYSI LSFMGAFHGK TMGCLATTHS KAIHKIDIPS
FDWPIAPFPR LKYPLEEFVK ENQQEEARCL EEVEDLIVKY RKKKKTVAGI IVEPIQSEGG
DNHASDDFFR KLRDIARKHG CAFLVDEVQT GGGCTGKFWA HEHWGLDDPA DVMTFSKKMM
TGGFFHKEEF RPNAPYRIFN TWLGDPSKNL LLAEVINIIK REDLLNNAAH AGKALLTGLL
DLQARYPQFI SRVRGRGTFC SFDTPDDSIR NKLILIARNK GVVLGGCGDK SIRFRPTLVF
RDHHAHLFLN IFSDILADFK *
speed 1.19 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
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Problems