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: ENST00000376573
Querying Taster for transcript #2: ENST00000545335
Querying Taster for transcript #3: ENST00000323883
MT speed 0 s - this script 2.561789 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PIP4K2Apolymorphism_automatic0.999999660957612simple_aaeaffectedN192Ssingle base exchangers2230469show file
PIP4K2Apolymorphism_automatic0.999999748043269simple_aaeaffectedN251Ssingle base exchangers2230469show file
PIP4K2Apolymorphism_automatic0.999999748043269simple_aaeaffectedN111Ssingle base exchangers2230469show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 3.39042388254508e-07 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM068312)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:22839628T>CN/A show variant in all transcripts   IGV
HGNC symbol PIP4K2A
Ensembl transcript ID ENST00000545335
Genbank transcript ID N/A
UniProt peptide P48426
alteration type single base exchange
alteration region CDS
DNA changes c.575A>G
cDNA.781A>G
g.163857A>G
AA changes N192S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 192
frameshift no
known variant Reference ID: rs2230469
databasehomozygous (C/C)heterozygousallele carriers
1000G163737900
ExAC50702256527635

known disease mutation at this position, please check HGMD for details (HGMD ID CM068312)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5141
3.3681
(flanking)4.9241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased163856wt: 0.26 / mu: 0.89wt: ACAACAACAAGAAGG
mu: ACAACAGCAAGAAGG		 AACA|acaa
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      192NEGQKIYIDDNNKKVFLEKLKKDV
mutated  all conserved    192NEGQKIYIDDNSKKVFLEKLKKD
Ptroglodytes  all identical  ENSPTRG00000002355  203NEGQKIYIDDNNKKVFLEKLKKD
Mmulatta  all identical  ENSMMUG00000015034  203NEGQKIYIDDNNKKVFLEKLKKD
Fcatus  all identical  ENSFCAG00000005491  250NEGQKIYIDDNNKKAFLEKLKKD
Mmusculus  all identical  ENSMUSG00000026737  251NEGQKIYIDDNNKKIFLEKLKKD
Ggallus  all identical  ENSGALG00000007877  203NDGQKIHIDENNKRMFLEKLKKD
Trubripes  all identical  ENSTRUG00000002428  251NDGQKIYIDEENKKMFLEKLRKD
Drerio  all conserved  ENSDARG00000003776  250NDGQKIYIDDESKKIFLNKLQKD
Dmelanogaster  not conserved  FBgn0039924  249KQKVKLDIGKEAKDKLMDTLSND
Celegans  not conserved  Y48G9A.8  248EQNWKLNLPPEAGKLLIEMLTSD
Xtropicalis  all identical  ENSXETG00000030058  248NDGQKIYIDENNKKLFLEKLKKD
protein features
start (aa)end (aa)featuredetails 
33405DOMAINPIPK.lost
189197STRANDlost
202204STRANDmight get lost (downstream of altered splice site)
207212STRANDmight get lost (downstream of altered splice site)
215217STRANDmight get lost (downstream of altered splice site)
223226HELIXmight get lost (downstream of altered splice site)
228230STRANDmight get lost (downstream of altered splice site)
235240HELIXmight get lost (downstream of altered splice site)
249268HELIXmight get lost (downstream of altered splice site)
271273STRANDmight get lost (downstream of altered splice site)
275282STRANDmight get lost (downstream of altered splice site)
283291HELIXmight get lost (downstream of altered splice site)
304304MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
312312MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
316316MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
320320MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
333333CONFLICTD -> E (in Ref. 3; AAB35041).might get lost (downstream of altered splice site)
334336TURNmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
351358STRANDmight get lost (downstream of altered splice site)
362364STRANDmight get lost (downstream of altered splice site)
390404HELIXmight get lost (downstream of altered splice site)
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 1250 / 1250
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 207 / 207
chromosome 10
strand -1
last intron/exon boundary 1170
theoretical NMD boundary in CDS 913
length of CDS 1044
coding sequence (CDS) position 575
cDNA position
(for ins/del: last normal base / first normal base)		 781
gDNA position
(for ins/del: last normal base / first normal base)		 163857
chromosomal position
(for ins/del: last normal base / first normal base)		 22839628
original gDNA sequence snippet GATTTATATTGATGACAACAACAAGAAGGTCTTCCTGGAAA
altered gDNA sequence snippet GATTTATATTGATGACAACAGCAAGAAGGTCTTCCTGGAAA
original cDNA sequence snippet GATTTATATTGATGACAACAACAAGAAGGTCTTCCTGGAAA
altered cDNA sequence snippet GATTTATATTGATGACAACAGCAAGAAGGTCTTCCTGGAAA
wildtype AA sequence MLMPDDFKAY SKIKVDNHLF NKENMPSHFK FKEYCPMVFR NLRERFGIDD QDFQNSLTRS
APLPNDSQAR SGARFHTSYD KRYIIKTITS EDVAEMHNIL KKYHQYIVEC HGITLLPQFL
GMYRLNVDGV EIYVIVTRNV FSHRLSVYRK YDLKGSTVAR EASDKEKAKE LPTLKDNDFI
NEGQKIYIDD NNKKVFLEKL KKDVEFLAQL KLMDYSLLVG IHDVERAEQE EVECEENDGE
EEGESDGTHP VGTPPDSPGN TLNSSPPLAP GEFDPNIDVY GIKCHENSPR KEVYFMAIID
ILTHYDAKKK AAHAAKTVKH GAGAEISTVN PEQYSKRFLD FIGHILT*
mutated AA sequence MLMPDDFKAY SKIKVDNHLF NKENMPSHFK FKEYCPMVFR NLRERFGIDD QDFQNSLTRS
APLPNDSQAR SGARFHTSYD KRYIIKTITS EDVAEMHNIL KKYHQYIVEC HGITLLPQFL
GMYRLNVDGV EIYVIVTRNV FSHRLSVYRK YDLKGSTVAR EASDKEKAKE LPTLKDNDFI
NEGQKIYIDD NSKKVFLEKL KKDVEFLAQL KLMDYSLLVG IHDVERAEQE EVECEENDGE
EEGESDGTHP VGTPPDSPGN TLNSSPPLAP GEFDPNIDVY GIKCHENSPR KEVYFMAIID
ILTHYDAKKK AAHAAKTVKH GAGAEISTVN PEQYSKRFLD FIGHILT*
speed 0.31 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

polymorphism

 Model: simple_aae, prob: 2.51956731334177e-07 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM068312)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:22839628T>CN/A show variant in all transcripts   IGV
HGNC symbol PIP4K2A
Ensembl transcript ID ENST00000376573
Genbank transcript ID NM_005028
UniProt peptide P48426
alteration type single base exchange
alteration region CDS
DNA changes c.752A>G
cDNA.981A>G
g.163857A>G
AA changes N251S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 251
frameshift no
known variant Reference ID: rs2230469
databasehomozygous (C/C)heterozygousallele carriers
1000G163737900
ExAC50702256527635

known disease mutation at this position, please check HGMD for details (HGMD ID CM068312)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5141
3.3681
(flanking)4.9241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased163856wt: 0.26 / mu: 0.89wt: ACAACAACAAGAAGG
mu: ACAACAGCAAGAAGG		 AACA|acaa
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      251NEGQKIYIDDNNKKVFLEKLKKDV
mutated  all conserved    251EGQKIYIDDNSKKVFLEKLKKD
Ptroglodytes  all identical  ENSPTRG00000002355  203NEGQKIYIDDNNKKVFLEKLKKD
Mmulatta  all identical  ENSMMUG00000015034  203NEGQKIYIDDNNKKVFLEKLKKD
Fcatus  all identical  ENSFCAG00000005491  250NEGQKIYIDDNNKKAFLEKLKKD
Mmusculus  all identical  ENSMUSG00000026737  251EGQKIYIDDNNKKIFLEKLKKD
Ggallus  all identical  ENSGALG00000007877  203NDGQKIHIDENNKRMFLEKLKKD
Trubripes  all identical  ENSTRUG00000002428  251DGQKIYIDEENKKMFLEKLRKD
Drerio  all conserved  ENSDARG00000003776  250DGQKIYIDDESKKIFLNKLQKD
Dmelanogaster  not conserved  FBgn0039924  249KQKVKLDIGKEAKDKLM
Celegans  not conserved  Y48G9A.8  248KLNLPPEAGKLLIEMLTSD
Xtropicalis  all identical  ENSXETG00000030058  248ENNKKLFLEKLKKD
protein features
start (aa)end (aa)featuredetails 
33405DOMAINPIPK.lost
249268HELIXlost
271273STRANDmight get lost (downstream of altered splice site)
275282STRANDmight get lost (downstream of altered splice site)
283291HELIXmight get lost (downstream of altered splice site)
304304MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
312312MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
316316MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
320320MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
333333CONFLICTD -> E (in Ref. 3; AAB35041).might get lost (downstream of altered splice site)
334336TURNmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
351358STRANDmight get lost (downstream of altered splice site)
362364STRANDmight get lost (downstream of altered splice site)
390404HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1221 / 1221
position (AA) of stopcodon in wt / mu AA sequence 407 / 407
position of stopcodon in wt / mu cDNA 1450 / 1450
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 230 / 230
chromosome 10
strand -1
last intron/exon boundary 1370
theoretical NMD boundary in CDS 1090
length of CDS 1221
coding sequence (CDS) position 752
cDNA position
(for ins/del: last normal base / first normal base)		 981
gDNA position
(for ins/del: last normal base / first normal base)		 163857
chromosomal position
(for ins/del: last normal base / first normal base)		 22839628
original gDNA sequence snippet GATTTATATTGATGACAACAACAAGAAGGTCTTCCTGGAAA
altered gDNA sequence snippet GATTTATATTGATGACAACAGCAAGAAGGTCTTCCTGGAAA
original cDNA sequence snippet GATTTATATTGATGACAACAACAAGAAGGTCTTCCTGGAAA
altered cDNA sequence snippet GATTTATATTGATGACAACAGCAAGAAGGTCTTCCTGGAAA
wildtype AA sequence MATPGNLGSS VLASKTKTKK KHFVAQKVKL FRASDPLLSV LMWGVNHSIN ELSHVQIPVM
LMPDDFKAYS KIKVDNHLFN KENMPSHFKF KEYCPMVFRN LRERFGIDDQ DFQNSLTRSA
PLPNDSQARS GARFHTSYDK RYIIKTITSE DVAEMHNILK KYHQYIVECH GITLLPQFLG
MYRLNVDGVE IYVIVTRNVF SHRLSVYRKY DLKGSTVARE ASDKEKAKEL PTLKDNDFIN
EGQKIYIDDN NKKVFLEKLK KDVEFLAQLK LMDYSLLVGI HDVERAEQEE VECEENDGEE
EGESDGTHPV GTPPDSPGNT LNSSPPLAPG EFDPNIDVYG IKCHENSPRK EVYFMAIIDI
LTHYDAKKKA AHAAKTVKHG AGAEISTVNP EQYSKRFLDF IGHILT*
mutated AA sequence MATPGNLGSS VLASKTKTKK KHFVAQKVKL FRASDPLLSV LMWGVNHSIN ELSHVQIPVM
LMPDDFKAYS KIKVDNHLFN KENMPSHFKF KEYCPMVFRN LRERFGIDDQ DFQNSLTRSA
PLPNDSQARS GARFHTSYDK RYIIKTITSE DVAEMHNILK KYHQYIVECH GITLLPQFLG
MYRLNVDGVE IYVIVTRNVF SHRLSVYRKY DLKGSTVARE ASDKEKAKEL PTLKDNDFIN
EGQKIYIDDN SKKVFLEKLK KDVEFLAQLK LMDYSLLVGI HDVERAEQEE VECEENDGEE
EGESDGTHPV GTPPDSPGNT LNSSPPLAPG EFDPNIDVYG IKCHENSPRK EVYFMAIIDI
LTHYDAKKKA AHAAKTVKHG AGAEISTVNP EQYSKRFLDF IGHILT*
speed 0.29 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: 2.51956731334177e-07 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM068312)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:22839628T>CN/A show variant in all transcripts   IGV
HGNC symbol PIP4K2A
Ensembl transcript ID ENST00000323883
Genbank transcript ID N/A
UniProt peptide P48426
alteration type single base exchange
alteration region CDS
DNA changes c.332A>G
cDNA.387A>G
g.163857A>G
AA changes N111S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 111
frameshift no
known variant Reference ID: rs2230469
databasehomozygous (C/C)heterozygousallele carriers
1000G163737900
ExAC50702256527635

known disease mutation at this position, please check HGMD for details (HGMD ID CM068312)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5141
3.3681
(flanking)4.9241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased163856wt: 0.26 / mu: 0.89wt: ACAACAACAAGAAGG
mu: ACAACAGCAAGAAGG		 AACA|acaa
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      111NEGQKIYIDDNNKKVFLEKLKKDV
mutated  all conserved    111NEGQKIYIDDNSKKVFLEKLK
Ptroglodytes  all identical  ENSPTRG00000002355  216NEGQKIYIDDNNKKVFLEKLK
Mmulatta  all identical  ENSMMUG00000015034  216NEGQKIYIDDNNKKVFLEKLK
Fcatus  all identical  ENSFCAG00000005491  263NEGQKIYIDDNNKKAFLEKLK
Mmusculus  all identical  ENSMUSG00000026737  264NEGQKIYIDDNNKKIFLEKLK
Ggallus  all identical  ENSGALG00000007877  216NDGQKIHIDENNKRMFLEKLK
Trubripes  all identical  ENSTRUG00000002428  264NDGQKIYIDEENKKMFLEKLR
Drerio  all conserved  ENSDARG00000003776  263NDGQKIYIDDESKKIFLNKLQ
Dmelanogaster  not conserved  FBgn0039924  262KQKVKLDIGKEAKDKLMDTLS
Celegans  not conserved  Y48G9A.8  261EQNWKLNLPPEAGKLLIEMLT
Xtropicalis  all identical  ENSXETG00000030058  261NDGQKIYIDENNKKLFLEKLK
protein features
start (aa)end (aa)featuredetails 
33405DOMAINPIPK.lost
109117HELIXlost
131131MUTAGENG->L: Abolishes catalytic activity; when associated with F-138.might get lost (downstream of altered splice site)
134136STRANDmight get lost (downstream of altered splice site)
138138MUTAGENY->F: Abolishes catalytic activity; when associated with L-131.might get lost (downstream of altered splice site)
140147STRANDmight get lost (downstream of altered splice site)
143143CONFLICTI -> M (in Ref. 3; AAB35041).might get lost (downstream of altered splice site)
145145MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
149168HELIXmight get lost (downstream of altered splice site)
169171TURNmight get lost (downstream of altered splice site)
177178CONFLICTQF -> HL (in Ref. 3; AAB35041).might get lost (downstream of altered splice site)
178186STRANDmight get lost (downstream of altered splice site)
189197STRANDmight get lost (downstream of altered splice site)
202204STRANDmight get lost (downstream of altered splice site)
207212STRANDmight get lost (downstream of altered splice site)
215217STRANDmight get lost (downstream of altered splice site)
223226HELIXmight get lost (downstream of altered splice site)
228230STRANDmight get lost (downstream of altered splice site)
235240HELIXmight get lost (downstream of altered splice site)
249268HELIXmight get lost (downstream of altered splice site)
271273STRANDmight get lost (downstream of altered splice site)
275282STRANDmight get lost (downstream of altered splice site)
283291HELIXmight get lost (downstream of altered splice site)
304304MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
312312MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
316316MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
320320MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
333333CONFLICTD -> E (in Ref. 3; AAB35041).might get lost (downstream of altered splice site)
334336TURNmight get lost (downstream of altered splice site)
340342STRANDmight get lost (downstream of altered splice site)
351358STRANDmight get lost (downstream of altered splice site)
362364STRANDmight get lost (downstream of altered splice site)
390404HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 801 / 801
position (AA) of stopcodon in wt / mu AA sequence 267 / 267
position of stopcodon in wt / mu cDNA 856 / 856
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 56 / 56
chromosome 10
strand -1
last intron/exon boundary 776
theoretical NMD boundary in CDS 670
length of CDS 801
coding sequence (CDS) position 332
cDNA position
(for ins/del: last normal base / first normal base)		 387
gDNA position
(for ins/del: last normal base / first normal base)		 163857
chromosomal position
(for ins/del: last normal base / first normal base)		 22839628
original gDNA sequence snippet GATTTATATTGATGACAACAACAAGAAGGTCTTCCTGGAAA
altered gDNA sequence snippet GATTTATATTGATGACAACAGCAAGAAGGTCTTCCTGGAAA
original cDNA sequence snippet GATTTATATTGATGACAACAACAAGAAGGTCTTCCTGGAAA
altered cDNA sequence snippet GATTTATATTGATGACAACAGCAAGAAGGTCTTCCTGGAAA
wildtype AA sequence MHNILKKYHQ YIVECHGITL LPQFLGMYRL NVDGVEIYVI VTRNVFSHRL SVYRKYDLKM
ANLKATFTFP KPTGSTVARE ASDKEKAKEL PTLKDNDFIN EGQKIYIDDN NKKVFLEKLK
KDVEFLAQLK LMDYSLLVGI HDVERAEQEE VECEENDGEE EGESDGTHPV GTPPDSPGNT
LNSSPPLAPG EFDPNIDVYG IKCHENSPRK EVYFMAIIDI LTHYDAKKKA AHAAKTVKHG
AGAEISTVNP EQYSKRFLDF IGHILT*
mutated AA sequence MHNILKKYHQ YIVECHGITL LPQFLGMYRL NVDGVEIYVI VTRNVFSHRL SVYRKYDLKM
ANLKATFTFP KPTGSTVARE ASDKEKAKEL PTLKDNDFIN EGQKIYIDDN SKKVFLEKLK
KDVEFLAQLK LMDYSLLVGI HDVERAEQEE VECEENDGEE EGESDGTHPV GTPPDSPGNT
LNSSPPLAPG EFDPNIDVYG IKCHENSPRK EVYFMAIIDI LTHYDAKKKA AHAAKTVKHG
AGAEISTVNP EQYSKRFLDF IGHILT*
speed 0.20 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

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