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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000254853
Querying Taster for transcript #2: ENST00000512825
Querying Taster for transcript #3: ENST00000424747
MT speed 5.08 s - this script 5.690388 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SLC52A1polymorphism_automatic0.999199578786213simple_aaeaffectedV296Msingle base exchangers2304445show file
SLC52A1polymorphism_automatic0.999199578786213simple_aaeaffectedV296Msingle base exchangers2304445show file
SLC52A1polymorphism_automatic0.999199578786213simple_aaeaffectedV296Msingle base exchangers2304445show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000800421213786819 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4936898C>TN/A show variant in all transcripts   IGV
HGNC symbol SLC52A1
Ensembl transcript ID ENST00000254853
Genbank transcript ID NM_017986
UniProt peptide Q9NWF4
alteration type single base exchange
alteration region CDS
DNA changes c.886G>A
cDNA.1559G>A
g.18407G>A
AA changes V296M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
296
frameshift no
known variant Reference ID: rs2304445
databasehomozygous (T/T)heterozygousallele carriers
1000G2989391237
ExAC48242029425118
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8961
0.5260.985
(flanking)-0.9040.969
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained184030.79mu: ACCAATGGCATGCTG CAAT|ggca
distance from splice site 125
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      296LMAFTSAVTNGVLPSVQSFSCLPY
mutated  all conserved    296LMAFTSAVTNGMLPSV
Ptroglodytes  all identical  ENSPTRG00000008621  296LMAFTSALTNGVLPSV
Mmulatta  all identical  ENSMMUG00000011344  296LLAITSALTNGVLPAV
Fcatus  all identical  ENSFCAG00000007727  175LLAVTNALTNGVL
Mmusculus  all identical  ENSMUSG00000022560  298VLPAVQSFSCLP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002732  286LLAVSNALTNGVLPSVQ
Drerio  all identical  ENSDARG00000092367  265LLGISNALTNGVLPSVQSFTCLP
Dmelanogaster  all conserved  FBgn0039882  341LIGAISLFSNGMFGSIQSYSS
Celegans  all conserved  Y47D7A.14  321TTALVNAQMNGIITSVQSYAALP
Xtropicalis  all conserved  ENSXETG00000013476  289LLGLSNALTNGILPSVQTYSC
protein features
start (aa)end (aa)featuredetails 
280300TRANSMEMHelical; (Potential).lost
315335TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342362TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
369389TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1347 / 1347
position (AA) of stopcodon in wt / mu AA sequence 449 / 449
position of stopcodon in wt / mu cDNA 2020 / 2020
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 674 / 674
chromosome 17
strand -1
last intron/exon boundary 1808
theoretical NMD boundary in CDS 1084
length of CDS 1347
coding sequence (CDS) position 886
cDNA position
(for ins/del: last normal base / first normal base)
1559
gDNA position
(for ins/del: last normal base / first normal base)
18407
chromosomal position
(for ins/del: last normal base / first normal base)
4936898
original gDNA sequence snippet CCAGTGCCGTGACCAATGGCGTGCTGCCTTCTGTGCAGAGC
altered gDNA sequence snippet CCAGTGCCGTGACCAATGGCATGCTGCCTTCTGTGCAGAGC
original cDNA sequence snippet CCAGTGCCGTGACCAATGGCGTGCTGCCTTCTGTGCAGAGC
altered cDNA sequence snippet CCAGTGCCGTGACCAATGGCATGCTGCCTTCTGTGCAGAGC
wildtype AA sequence MAAPTLGRLV LTHLLVALFG MGSWAAVNGI WVELPVVVKD LPEGWSLPSY LSVVVALGNL
GLLVVTLWRQ LAPGKGEQVP IQVVQVLSVV GTALLAPLWH HVAPVAGQLH SVAFLTLALV
LAMACCTSNV TFLPFLSHLP PPFLRSFFLG QGLSALLPCV LALVQGVGRL ECPPAPTNGT
SGPPLDFPER FPASTFFWAL TALLVTSAAA FRGLLLLLPS LPSVTTGGSG PELQLGSPGA
EEEEKEEEEA LPLQEPPSQA AGTIPGPDPE AHQLFSAHGA FLLGLMAFTS AVTNGVLPSV
QSFSCLPYGR LAYHLAVVLG SAANPLACFL AMGVLCRSLA GLVGLSLLGM LFGAYLMALA
ILSPCPPLVG TTAGVVLVVL SWVLCLCVFS YVKVAASSLL HGGGRPALLA AGVAIQVGSL
LGAGAMFPPT SIYHVFQSRK DCVDPCGP*
mutated AA sequence MAAPTLGRLV LTHLLVALFG MGSWAAVNGI WVELPVVVKD LPEGWSLPSY LSVVVALGNL
GLLVVTLWRQ LAPGKGEQVP IQVVQVLSVV GTALLAPLWH HVAPVAGQLH SVAFLTLALV
LAMACCTSNV TFLPFLSHLP PPFLRSFFLG QGLSALLPCV LALVQGVGRL ECPPAPTNGT
SGPPLDFPER FPASTFFWAL TALLVTSAAA FRGLLLLLPS LPSVTTGGSG PELQLGSPGA
EEEEKEEEEA LPLQEPPSQA AGTIPGPDPE AHQLFSAHGA FLLGLMAFTS AVTNGMLPSV
QSFSCLPYGR LAYHLAVVLG SAANPLACFL AMGVLCRSLA GLVGLSLLGM LFGAYLMALA
ILSPCPPLVG TTAGVVLVVL SWVLCLCVFS YVKVAASSLL HGGGRPALLA AGVAIQVGSL
LGAGAMFPPT SIYHVFQSRK DCVDPCGP*
speed 1.81 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

polymorphism

Model: simple_aae, prob: 0.000800421213786819 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4936898C>TN/A show variant in all transcripts   IGV
HGNC symbol SLC52A1
Ensembl transcript ID ENST00000512825
Genbank transcript ID N/A
UniProt peptide Q9NWF4
alteration type single base exchange
alteration region CDS
DNA changes c.886G>A
cDNA.2298G>A
g.18407G>A
AA changes V296M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
296
frameshift no
known variant Reference ID: rs2304445
databasehomozygous (T/T)heterozygousallele carriers
1000G2989391237
ExAC48242029425118
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8961
0.5260.985
(flanking)-0.9040.969
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained184030.79mu: ACCAATGGCATGCTG CAAT|ggca
distance from splice site 125
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      296LMAFTSAVTNGVLPSVQSFSCLPY
mutated  all conserved    296LMAFTSAVTNGMLPSV
Ptroglodytes  all identical  ENSPTRG00000008621  296LMAFTSALTNGVLPSV
Mmulatta  all identical  ENSMMUG00000011344  296LLAITSALTNGVLPAV
Fcatus  all identical  ENSFCAG00000007727  175LLAVTNALTNGVL
Mmusculus  all identical  ENSMUSG00000022560  298VLPAVQSFSCLP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002732  286LLAVSNALTNGVLPSVQ
Drerio  all identical  ENSDARG00000092367  268LLGISNALTNGVLPSVQSFTCLP
Dmelanogaster  all conserved  FBgn0039882  341LIGAISLFSNGMFGSIQSYSS
Celegans  all conserved  Y47D7A.14  321TTALVNAQMNGIITSVQSYAALP
Xtropicalis  all conserved  ENSXETG00000013476  289LLGLSNALTNGILPSVQTYSC
protein features
start (aa)end (aa)featuredetails 
280300TRANSMEMHelical; (Potential).lost
315335TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342362TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
369389TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1053 / 1053
position (AA) of stopcodon in wt / mu AA sequence 351 / 351
position of stopcodon in wt / mu cDNA 2465 / 2465
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 1413 / 1413
chromosome 17
strand -1
last intron/exon boundary 2423
theoretical NMD boundary in CDS 960
length of CDS 1053
coding sequence (CDS) position 886
cDNA position
(for ins/del: last normal base / first normal base)
2298
gDNA position
(for ins/del: last normal base / first normal base)
18407
chromosomal position
(for ins/del: last normal base / first normal base)
4936898
original gDNA sequence snippet CCAGTGCCGTGACCAATGGCGTGCTGCCTTCTGTGCAGAGC
altered gDNA sequence snippet CCAGTGCCGTGACCAATGGCATGCTGCCTTCTGTGCAGAGC
original cDNA sequence snippet CCAGTGCCGTGACCAATGGCGTGCTGCCTTCTGTGCAGAGC
altered cDNA sequence snippet CCAGTGCCGTGACCAATGGCATGCTGCCTTCTGTGCAGAGC
wildtype AA sequence MAAPTLGRLV LTHLLVALFG MGSWAAVNGI WVELPVVVKD LPEGWSLPSY LSVVVALGNL
GLLVVTLWRQ LAPGKGEQVP IQVVQVLSVV GTALLAPLWH HVAPVAGQLH SVAFLTLALV
LAMACCTSNV TFLPFLSHLP PPFLRSFFLG QGLSALLPCV LALVQGVGRL ECPPAPTNGT
SGPPLDFPER FPASTFFWAL TALLVTSAAA FRGLLLLLPS LPSVTTGGSG PELQLGSPGA
EEEEKEEEEA LPLQEPPSQA AGTIPGPDPE AHQLFSAHGA FLLGLMAFTS AVTNGVLPSV
QSFSCLPYGR LAYHLAVVLG SAANPLACFL AMGVLCRCCR GCCVCVCSHM *
mutated AA sequence MAAPTLGRLV LTHLLVALFG MGSWAAVNGI WVELPVVVKD LPEGWSLPSY LSVVVALGNL
GLLVVTLWRQ LAPGKGEQVP IQVVQVLSVV GTALLAPLWH HVAPVAGQLH SVAFLTLALV
LAMACCTSNV TFLPFLSHLP PPFLRSFFLG QGLSALLPCV LALVQGVGRL ECPPAPTNGT
SGPPLDFPER FPASTFFWAL TALLVTSAAA FRGLLLLLPS LPSVTTGGSG PELQLGSPGA
EEEEKEEEEA LPLQEPPSQA AGTIPGPDPE AHQLFSAHGA FLLGLMAFTS AVTNGMLPSV
QSFSCLPYGR LAYHLAVVLG SAANPLACFL AMGVLCRCCR GCCVCVCSHM *
speed 1.99 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

polymorphism

Model: simple_aae, prob: 0.000800421213786819 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4936898C>TN/A show variant in all transcripts   IGV
HGNC symbol SLC52A1
Ensembl transcript ID ENST00000424747
Genbank transcript ID NM_001104577
UniProt peptide Q9NWF4
alteration type single base exchange
alteration region CDS
DNA changes c.886G>A
cDNA.1599G>A
g.18407G>A
AA changes V296M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
296
frameshift no
known variant Reference ID: rs2304445
databasehomozygous (T/T)heterozygousallele carriers
1000G2989391237
ExAC48242029425118
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8961
0.5260.985
(flanking)-0.9040.969
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained184030.79mu: ACCAATGGCATGCTG CAAT|ggca
distance from splice site 125
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      296LMAFTSAVTNGVLPSVQSFSCLPY
mutated  all conserved    296LMAFTSAVTNGMLPSV
Ptroglodytes  all identical  ENSPTRG00000008621  296LMAFTSALTNGVLPSV
Mmulatta  all identical  ENSMMUG00000011344  296LLAITSALTNGVLPAV
Fcatus  all identical  ENSFCAG00000007727  175LLAVTNALTNGVL
Mmusculus  all identical  ENSMUSG00000022560  298VLPAVQSFSCLP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002732  286LLAVSNALTNGVLPSVQ
Drerio  all identical  ENSDARG00000092367  265LLGISNALTNGVLPSVQSFTCLP
Dmelanogaster  all conserved  FBgn0039882  341LIGAISLFSNGMFGSIQSYSS
Celegans  all conserved  Y47D7A.14  321TTALVNAQMNGIITSVQSYAALP
Xtropicalis  all conserved  ENSXETG00000013476  289LLGLSNALTNGILPSVQTYSC
protein features
start (aa)end (aa)featuredetails 
280300TRANSMEMHelical; (Potential).lost
315335TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342362TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
369389TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
407427TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1347 / 1347
position (AA) of stopcodon in wt / mu AA sequence 449 / 449
position of stopcodon in wt / mu cDNA 2060 / 2060
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 714 / 714
chromosome 17
strand -1
last intron/exon boundary 1848
theoretical NMD boundary in CDS 1084
length of CDS 1347
coding sequence (CDS) position 886
cDNA position
(for ins/del: last normal base / first normal base)
1599
gDNA position
(for ins/del: last normal base / first normal base)
18407
chromosomal position
(for ins/del: last normal base / first normal base)
4936898
original gDNA sequence snippet CCAGTGCCGTGACCAATGGCGTGCTGCCTTCTGTGCAGAGC
altered gDNA sequence snippet CCAGTGCCGTGACCAATGGCATGCTGCCTTCTGTGCAGAGC
original cDNA sequence snippet CCAGTGCCGTGACCAATGGCGTGCTGCCTTCTGTGCAGAGC
altered cDNA sequence snippet CCAGTGCCGTGACCAATGGCATGCTGCCTTCTGTGCAGAGC
wildtype AA sequence MAAPTLGRLV LTHLLVALFG MGSWAAVNGI WVELPVVVKD LPEGWSLPSY LSVVVALGNL
GLLVVTLWRQ LAPGKGEQVP IQVVQVLSVV GTALLAPLWH HVAPVAGQLH SVAFLTLALV
LAMACCTSNV TFLPFLSHLP PPFLRSFFLG QGLSALLPCV LALVQGVGRL ECPPAPTNGT
SGPPLDFPER FPASTFFWAL TALLVTSAAA FRGLLLLLPS LPSVTTGGSG PELQLGSPGA
EEEEKEEEEA LPLQEPPSQA AGTIPGPDPE AHQLFSAHGA FLLGLMAFTS AVTNGVLPSV
QSFSCLPYGR LAYHLAVVLG SAANPLACFL AMGVLCRSLA GLVGLSLLGM LFGAYLMALA
ILSPCPPLVG TTAGVVLVVL SWVLCLCVFS YVKVAASSLL HGGGRPALLA AGVAIQVGSL
LGAGAMFPPT SIYHVFQSRK DCVDPCGP*
mutated AA sequence MAAPTLGRLV LTHLLVALFG MGSWAAVNGI WVELPVVVKD LPEGWSLPSY LSVVVALGNL
GLLVVTLWRQ LAPGKGEQVP IQVVQVLSVV GTALLAPLWH HVAPVAGQLH SVAFLTLALV
LAMACCTSNV TFLPFLSHLP PPFLRSFFLG QGLSALLPCV LALVQGVGRL ECPPAPTNGT
SGPPLDFPER FPASTFFWAL TALLVTSAAA FRGLLLLLPS LPSVTTGGSG PELQLGSPGA
EEEEKEEEEA LPLQEPPSQA AGTIPGPDPE AHQLFSAHGA FLLGLMAFTS AVTNGMLPSV
QSFSCLPYGR LAYHLAVVLG SAANPLACFL AMGVLCRSLA GLVGLSLLGM LFGAYLMALA
ILSPCPPLVG TTAGVVLVVL SWVLCLCVFS YVKVAASSLL HGGGRPALLA AGVAIQVGSL
LGAGAMFPPT SIYHVFQSRK DCVDPCGP*
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

Problems