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: ENST00000458307
Querying Taster for transcript #2: ENST00000273588
Querying Taster for transcript #3: ENST00000395338
Querying Taster for transcript #4: ENST00000538581
Querying Taster for transcript #5: ENST00000546031
MT speed 0 s - this script 4.365503 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AMTdisease_causing0.999999999970897simple_aaeD276Hsingle base exchangers121964984show file
AMTdisease_causing0.999999999970897simple_aaeD276Hsingle base exchangers121964984show file
AMTdisease_causing0.999999999993574simple_aaeD220Hsingle base exchangers121964984show file
AMTdisease_causing0.999999999993574simple_aaeD179Hsingle base exchangers121964984show file
AMTdisease_causing0.999999999999877simple_aaeD232Hsingle base exchangers121964984show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999970897      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs11978 (probable pathogenic)
  • known disease mutation at this position (HGMD CM983428)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49456455C>GN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000273588
Genbank transcript ID NM_000481
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.826G>C
cDNA.1129G>C
g.3732G>C
AA changes D276H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 276
frameshift no
known variant Reference ID: rs121964984
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs11978 (probable pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4961
5.4411
(flanking)0.0310.991
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 increased3727wt: 0.7803 / mu: 0.8233 (marginal change - not scored)wt: GGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACA
mu: GGCAGGCCTCTGCCTGTATGGGAATCACATTGATGAACACA		 atgg|GAAT
Donor marginally increased3725wt: 0.9342 / mu: 0.9539 (marginal change - not scored)wt: CTGTATGGGAATGAC
mu: CTGTATGGGAATCAC		 GTAT|ggga
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      276RLEAGLCLYGNDIDEHTTPVEGSL
mutated  not conserved    276RLEAGLCLYGNHIDEHTTPVEGS
Ptroglodytes  all identical  ENSPTRG00000014924  276RLEAGLCLYGNDIDEHTTPVEGS
Mmulatta  all identical  ENSMMUG00000005452  276RLEAGLCLYGNDIDEHTTPVEGS
Fcatus  all identical  ENSFCAG00000009856  276RLEAGLCLYGSDIDEHTTPVEGS
Mmusculus  all identical  ENSMUSG00000032607  276RLEAGLCLYGNDIDEHTTPVEGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  286GLCLYGNDIDETTTPVEAT
Drerio  all identical  ENSDARG00000010862  283YGNDIDETTTPVEAT
Dmelanogaster  all identical  FBgn0032287  274RLEAGLCLYGSDIDSKTTPVEAA
Celegans  all identical  F25B4.1  272RLEAGLCLYGSDIEENTTPIEAG
Xtropicalis  all identical  ENSXETG00000005937  276RLEAGLCLYGNDIDETTSPVEAS
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1212 / 1212
position (AA) of stopcodon in wt / mu AA sequence 404 / 404
position of stopcodon in wt / mu cDNA 1515 / 1515
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 304 / 304
chromosome 3
strand -1
last intron/exon boundary 1337
theoretical NMD boundary in CDS 983
length of CDS 1212
coding sequence (CDS) position 826
cDNA position
(for ins/del: last normal base / first normal base)		 1129
gDNA position
(for ins/del: last normal base / first normal base)		 3732
chromosomal position
(for ins/del: last normal base / first normal base)		 49456455
original gDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered gDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
original cDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered cDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
wildtype AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEV RRKQQMAVVS KMPFVPTNYY TLK*
mutated AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNHIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEV RRKQQMAVVS KMPFVPTNYY TLK*
speed 0.68 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: 0.999999999970897      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs11978 (probable pathogenic)
  • known disease mutation at this position (HGMD CM983428)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49456455C>GN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000395338
Genbank transcript ID NM_001164712
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.826G>C
cDNA.1054G>C
g.3732G>C
AA changes D276H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 276
frameshift no
known variant Reference ID: rs121964984
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs11978 (probable pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4961
5.4411
(flanking)0.0310.991
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 increased3727wt: 0.7803 / mu: 0.8233 (marginal change - not scored)wt: GGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACA
mu: GGCAGGCCTCTGCCTGTATGGGAATCACATTGATGAACACA		 atgg|GAAT
Donor marginally increased3725wt: 0.9342 / mu: 0.9539 (marginal change - not scored)wt: CTGTATGGGAATGAC
mu: CTGTATGGGAATCAC		 GTAT|ggga
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      276RLEAGLCLYGNDIDEHTTPVEGSL
mutated  not conserved    276RLEAGLCLYGNHIDEHTTPVEGS
Ptroglodytes  all identical  ENSPTRG00000014924  276RLEAGLCLYGNDIDEHTTPVEGS
Mmulatta  all identical  ENSMMUG00000005452  276RLEAGLCLYGNDIDEHTTPVEGS
Fcatus  all identical  ENSFCAG00000009856  276RLEAGLCLYGSDIDEHTTPVEGS
Mmusculus  all identical  ENSMUSG00000032607  276RLEAGLCLYGNDIDEHTTPVEGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  286GLCLYGNDIDETTTPVEAT
Drerio  all identical  ENSDARG00000010862  283YGNDIDETTTPVEAT
Dmelanogaster  all identical  FBgn0032287  274RLEAGLCLYGSDIDSKTTPVEAA
Celegans  all identical  F25B4.1  272RLEAGLCLYGSDIEENTTPIEAG
Xtropicalis  all identical  ENSXETG00000005937  276RLEAGLCLYGNDIDETTSPVEAS
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1161 / 1161
position (AA) of stopcodon in wt / mu AA sequence 387 / 387
position of stopcodon in wt / mu cDNA 1389 / 1389
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 229 / 229
chromosome 3
strand -1
last intron/exon boundary 1366
theoretical NMD boundary in CDS 1087
length of CDS 1161
coding sequence (CDS) position 826
cDNA position
(for ins/del: last normal base / first normal base)		 1054
gDNA position
(for ins/del: last normal base / first normal base)		 3732
chromosomal position
(for ins/del: last normal base / first normal base)		 49456455
original gDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered gDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
original cDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered cDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
wildtype AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEL PSGPCF*
mutated AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNHIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEL PSGPCF*
speed 0.75 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: 0.999999999993574      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs11978 (probable pathogenic)
  • known disease mutation at this position (HGMD CM983428)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49456455C>GN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000538581
Genbank transcript ID NM_001164711
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.658G>C
cDNA.886G>C
g.3732G>C
AA changes D220H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 220
frameshift no
known variant Reference ID: rs121964984
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs11978 (probable pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4961
5.4411
(flanking)0.0310.991
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 increased3727wt: 0.7803 / mu: 0.8233 (marginal change - not scored)wt: GGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACA
mu: GGCAGGCCTCTGCCTGTATGGGAATCACATTGATGAACACA		 atgg|GAAT
Donor marginally increased3725wt: 0.9342 / mu: 0.9539 (marginal change - not scored)wt: CTGTATGGGAATGAC
mu: CTGTATGGGAATCAC		 GTAT|ggga
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      220RLEAGLCLYGNDIDEHTTPVEGSL
mutated  not conserved    220RLEAGLCLYGNHIDEHTTPVEGS
Ptroglodytes  all identical  ENSPTRG00000014924  276LEAGLCLYGNDIDEHTTPVEGS
Mmulatta  all identical  ENSMMUG00000005452  276LEAGLCLYGNDIDEHTTPVEGS
Fcatus  all identical  ENSFCAG00000009856  276LEAGLCLYGSDIDEHTTPVEGS
Mmusculus  all identical  ENSMUSG00000032607  276LEAGLCLYGNDIDEHTTPVEGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  286LEAGLCLYGNDIDETTTPVEAT
Drerio  all identical  ENSDARG00000010862  283LEAGLCLYGNDIDETTTPVEAT
Dmelanogaster  all identical  FBgn0032287  274RLEAGLCLYGSDIDSKTTPVEAA
Celegans  all identical  F25B4.1  272RLEAGLCLYGSDIEENTTPIEAG
Xtropicalis  all identical  ENSXETG00000005937  276LEAGLCLYGNDIDETTSPVEAS
protein features
start (aa)end (aa)featuredetails 
215222STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1044 / 1044
position (AA) of stopcodon in wt / mu AA sequence 348 / 348
position of stopcodon in wt / mu cDNA 1272 / 1272
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 229 / 229
chromosome 3
strand -1
last intron/exon boundary 1094
theoretical NMD boundary in CDS 815
length of CDS 1044
coding sequence (CDS) position 658
cDNA position
(for ins/del: last normal base / first normal base)		 886
gDNA position
(for ins/del: last normal base / first normal base)		 3732
chromosomal position
(for ins/del: last normal base / first normal base)		 49456455
original gDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered gDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
original cDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered cDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
wildtype AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ TKILGSDRVK LMESLVVGDI AELRPNQGTL
SLFTNEAGGI LDDLIVTNTS EGHLYVVSNA GCWEKDLALM QDKVRELQNQ GRDVGLEVLD
NALLALQGPT AAQVLQAGVA DDLRKLPFMT SAVMEVFGVS GCRVTRCGYT GEDGVEISVP
VAGAVHLATA ILKNPEVKLA GLAARDSLRL EAGLCLYGND IDEHTTPVEG SLSWTLGKRR
RAAMDFPGAK VIVPQLKGRV QRRRVGLMCE GAPMRAHSPI LNMEGTKIGT VTSGCPSPSL
KKNVAMGYVP CEYSRPGTML LVEVRRKQQM AVVSKMPFVP TNYYTLK*
mutated AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ TKILGSDRVK LMESLVVGDI AELRPNQGTL
SLFTNEAGGI LDDLIVTNTS EGHLYVVSNA GCWEKDLALM QDKVRELQNQ GRDVGLEVLD
NALLALQGPT AAQVLQAGVA DDLRKLPFMT SAVMEVFGVS GCRVTRCGYT GEDGVEISVP
VAGAVHLATA ILKNPEVKLA GLAARDSLRL EAGLCLYGNH IDEHTTPVEG SLSWTLGKRR
RAAMDFPGAK VIVPQLKGRV QRRRVGLMCE GAPMRAHSPI LNMEGTKIGT VTSGCPSPSL
KKNVAMGYVP CEYSRPGTML LVEVRRKQQM AVVSKMPFVP TNYYTLK*
speed 0.78 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: 0.999999999993574      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs11978 (probable pathogenic)
  • known disease mutation at this position (HGMD CM983428)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49456455C>GN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000546031
Genbank transcript ID N/A
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.535G>C
cDNA.727G>C
g.3732G>C
AA changes D179H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 179
frameshift no
known variant Reference ID: rs121964984
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs11978 (probable pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4961
5.4411
(flanking)0.0310.991
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 increased3727wt: 0.7803 / mu: 0.8233 (marginal change - not scored)wt: GGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACA
mu: GGCAGGCCTCTGCCTGTATGGGAATCACATTGATGAACACA		 atgg|GAAT
Donor marginally increased3725wt: 0.9342 / mu: 0.9539 (marginal change - not scored)wt: CTGTATGGGAATGAC
mu: CTGTATGGGAATCAC		 GTAT|ggga
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      179RLEAGLCLYGNDIDEHTTPVEGSL
mutated  not conserved    179RLEAGLCLYGNHIDEHTTPVEGS
Ptroglodytes  all identical  ENSPTRG00000014924  276RLEAGLCLYGNDIDEHTTPVEGS
Mmulatta  all identical  ENSMMUG00000005452  276RLEAGLCLYGNDIDEHTTPVEGS
Fcatus  all identical  ENSFCAG00000009856  276RLEAGLCLYGSDIDEHTTPVEGS
Mmusculus  all identical  ENSMUSG00000032607  276RLEAGLCLYGNDIDEHTTPVEGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  286RLEAGLCLYGNDIDETTTPVEAT
Drerio  all identical  ENSDARG00000010862  283RLEAGLCLYGNDIDETTTPVEAT
Dmelanogaster  all identical  FBgn0032287  274YGSDIDSKTTPVEAA
Celegans  all identical  F25B4.1  272SDIEENTTPIEAG
Xtropicalis  all identical  ENSXETG00000005937  276RLEAGLCLYGNDIDETTSPVEAS
protein features
start (aa)end (aa)featuredetails 
178184STRANDlost
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 1113 / 1113
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 193 / 193
chromosome 3
strand -1
last intron/exon boundary 935
theoretical NMD boundary in CDS 692
length of CDS 921
coding sequence (CDS) position 535
cDNA position
(for ins/del: last normal base / first normal base)		 727
gDNA position
(for ins/del: last normal base / first normal base)		 3732
chromosomal position
(for ins/del: last normal base / first normal base)		 49456455
original gDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered gDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
original cDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered cDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
wildtype AA sequence MESLVVGDIA ELRPNQGTLS LFTNEAGGIL DDLIVTNTSE GHLYVVSNAG CWEKDLALMQ
DKVRELQNQG RDVGLEVLDN ALLALQGPTA AQVLQAGVAD DLRKLPFMTS AVMEVFGVSG
CRVTRCGYTG EDGVEISVPV AGAVHLATAI LKNPEVKLAG LAARDSLRLE AGLCLYGNDI
DEHTTPVEGS LSWTLGKRRR AAMDFPGAKV IVPQLKGRVQ RRRVGLMCEG APMRAHSPIL
NMEGTKIGTV TSGCPSPSLK KNVAMGYVPC EYSRPGTMLL VEVRRKQQMA VVSKMPFVPT
NYYTLK*
mutated AA sequence MESLVVGDIA ELRPNQGTLS LFTNEAGGIL DDLIVTNTSE GHLYVVSNAG CWEKDLALMQ
DKVRELQNQG RDVGLEVLDN ALLALQGPTA AQVLQAGVAD DLRKLPFMTS AVMEVFGVSG
CRVTRCGYTG EDGVEISVPV AGAVHLATAI LKNPEVKLAG LAARDSLRLE AGLCLYGNHI
DEHTTPVEGS LSWTLGKRRR AAMDFPGAKV IVPQLKGRVQ RRRVGLMCEG APMRAHSPIL
NMEGTKIGTV TSGCPSPSLK KNVAMGYVPC EYSRPGTMLL VEVRRKQQMA VVSKMPFVPT
NYYTLK*
speed 0.66 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: 0.999999999999877      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs11978 (probable pathogenic)
  • known disease mutation at this position (HGMD CM983428)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49456455C>GN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000458307
Genbank transcript ID NM_001164710
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.694G>C
cDNA.713G>C
g.3732G>C
AA changes D232H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 232
frameshift no
known variant Reference ID: rs121964984
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs11978 (probable pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4961
5.4411
(flanking)0.0310.991
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 increased3727wt: 0.7803 / mu: 0.8233 (marginal change - not scored)wt: GGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACA
mu: GGCAGGCCTCTGCCTGTATGGGAATCACATTGATGAACACA		 atgg|GAAT
Donor marginally increased3725wt: 0.9342 / mu: 0.9539 (marginal change - not scored)wt: CTGTATGGGAATGAC
mu: CTGTATGGGAATCAC		 GTAT|ggga
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      232RLEAGLCLYGNDIDEHTTPVEGSL
mutated  not conserved    232RLEAGLCLYGNHIDEHTTPV
Ptroglodytes  all identical  ENSPTRG00000014924  276RLEAGLCLYGNDIDEHTTPVEGS
Mmulatta  all identical  ENSMMUG00000005452  276RLEAGLCLYGNDIDEHTTPVEGS
Fcatus  all identical  ENSFCAG00000009856  276RLEAGLCLYGSDIDEHTTPVEGS
Mmusculus  all identical  ENSMUSG00000032607  276RLEAGLCLYGNDIDEHTTPVEGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  286GLCLYGNDIDETTTPVEAT
Drerio  all identical  ENSDARG00000010862  283RLEAGLCLYGNDIDETTTPVEAT
Dmelanogaster  all identical  FBgn0032287  274RLEAGLCLYGSDIDSKTTPVEAA
Celegans  all identical  F25B4.1  272RLEAGLCLYGSDIEENTTPIEAG
Xtropicalis  all identical  ENSXETG00000005937  276RLEAGLCLYGNDIDETTSPVEAS
protein features
start (aa)end (aa)featuredetails 
225235STRANDlost
232232BINDINGSubstrate.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1080 / 1080
position (AA) of stopcodon in wt / mu AA sequence 360 / 360
position of stopcodon in wt / mu cDNA 1099 / 1099
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 20 / 20
chromosome 3
strand -1
last intron/exon boundary 921
theoretical NMD boundary in CDS 851
length of CDS 1080
coding sequence (CDS) position 694
cDNA position
(for ins/del: last normal base / first normal base)		 713
gDNA position
(for ins/del: last normal base / first normal base)		 3732
chromosomal position
(for ins/del: last normal base / first normal base)		 49456455
original gDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered gDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
original cDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered cDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
wildtype AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEAGLCLYG NDIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRRVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*
mutated AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEAGLCLYG NHIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRRVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*
speed 0.89 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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