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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000263265
Querying Taster for transcript #2: ENST00000355496
MT speed 3.69 s - this script 7.587659 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PLEKHA4polymorphism_automatic0.000246802064477025simple_aaeaffectedI37Vsingle base exchangers506425show file
PLEKHA4polymorphism_automatic0.00194150810696903simple_aaeaffectedI37Vsingle base exchangers506425show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999753197935523 (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) chr19:49368843T>CN/A show variant in all transcripts   IGV
HGNC symbol PLEKHA4
Ensembl transcript ID ENST00000355496
Genbank transcript ID NM_001161354
UniProt peptide Q9H4M7
alteration type single base exchange
alteration region CDS
DNA changes c.109A>G
cDNA.660A>G
g.3042A>G
AA changes I37V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
37
frameshift no
known variant Reference ID: rs506425
databasehomozygous (C/C)heterozygousallele carriers
1000G6698541523
ExAC80141673924753
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6761
1.1351
(flanking)1.3331
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased3036wt: 0.39 / mu: 0.98wt: CAGTAAACAAGATCC
mu: CAGTAAACAAGGTCC
 GTAA|acaa
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      37SPKKPTRAVNKIHAFGKRGNALRR
mutated  all conserved    37SPKKPTRAVNKVHAFGKRGNALR
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  all conserved  ENSFCAG00000003344  37STKKPTRAVSKVHAFGKRGNALR
Mmusculus  all conserved  ENSMUSG00000040428  37STKKPTRAVHKVHAFGKRNNALR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000071460  34D-----KGQDKVQTFGKRCQAAK
Dmelanogaster  all identical  FBgn0085412  356APLDRKKSAGSIQAL--KSPITK
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000004571  9TRSVKRVHTFGKREYSIK
protein features
start (aa)end (aa)featuredetails 
54153DOMAINPH.might get lost (downstream of altered splice site)
5564STRANDmight get lost (downstream of altered splice site)
6669STRANDmight get lost (downstream of altered splice site)
7280STRANDmight get lost (downstream of altered splice site)
8389STRANDmight get lost (downstream of altered splice site)
97100STRANDmight get lost (downstream of altered splice site)
101103HELIXmight get lost (downstream of altered splice site)
105108STRANDmight get lost (downstream of altered splice site)
116124STRANDmight get lost (downstream of altered splice site)
131134STRANDmight get lost (downstream of altered splice site)
138152HELIXmight get lost (downstream of altered splice site)
162353COMPBIASPro-rich.might get lost (downstream of altered splice site)
590590CONFLICTS -> N (in Ref. 1; AAG01896).might get lost (downstream of altered splice site)
779779CONFLICTF -> L (in Ref. 1; AAG01896).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1752 / 1752
position (AA) of stopcodon in wt / mu AA sequence 584 / 584
position of stopcodon in wt / mu cDNA 2303 / 2303
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 552 / 552
chromosome 19
strand -1
last intron/exon boundary 2333
theoretical NMD boundary in CDS 1731
length of CDS 1752
coding sequence (CDS) position 109
cDNA position
(for ins/del: last normal base / first normal base)
660
gDNA position
(for ins/del: last normal base / first normal base)
3042
chromosomal position
(for ins/del: last normal base / first normal base)
49368843
original gDNA sequence snippet CCACCCGGGCAGTAAACAAGATCCACGCCTTTGGGAAGAGA
altered gDNA sequence snippet CCACCCGGGCAGTAAACAAGGTCCACGCCTTTGGGAAGAGA
original cDNA sequence snippet CCACCCGGGCAGTAAACAAGATCCACGCCTTTGGGAAGAGA
altered cDNA sequence snippet CCACCCGGGCAGTAAACAAGGTCCACGCCTTTGGGAAGAGA
wildtype AA sequence MEGSRPRSSL SLASSASTIS SLSSLSPKKP TRAVNKIHAF GKRGNALRRD PNLPVHIRGW
LHKQDSSGLR LWKRRWFVLS GHCLFYYKDS REESVLGSVL LPSYNIRPDG PGAPRGRRFT
FTAEHPGMRT YVLAADTLED LRGWLRALGR ASRAEGDDYG QPRSPARPQP GEGPGGPGGP
PEVSRGEEGR ISESPEVTRL SRGRGRPRLL TPSPTTDLHS GLQMRRARSP DLFTPLSRPP
SPLSLPRPRS APARRPPAPS GDTAPPARPH TPLSRIDVRP PLDWGPQRQT LSRPPTPRRG
PPSEAGGGKP PRSPQHWSQE PRTQPGPPLE STFHQSLETD TLLTKLCGQD RLLRRLQEEI
DQKQEEKEQL EAALELTRQQ LGQATREAGA PGRAWGRQRL LQDRLVSVRA TLCHLTQERE
RVWDTYSGLE QELGTLRETL EYLLHLGSPQ DRVSAQQQLW MVEDTLAGLG GPQKPPPHTE
PDSPSPVLQG EESSERESLP ESLELSSPRS PETDWGRPPG GDKDLASPHL GLGSPRVSRA
SSPEGRHLPS PQLGTKSKEH HPLLADFRRS PGAGSQPLPS PGY*
mutated AA sequence MEGSRPRSSL SLASSASTIS SLSSLSPKKP TRAVNKVHAF GKRGNALRRD PNLPVHIRGW
LHKQDSSGLR LWKRRWFVLS GHCLFYYKDS REESVLGSVL LPSYNIRPDG PGAPRGRRFT
FTAEHPGMRT YVLAADTLED LRGWLRALGR ASRAEGDDYG QPRSPARPQP GEGPGGPGGP
PEVSRGEEGR ISESPEVTRL SRGRGRPRLL TPSPTTDLHS GLQMRRARSP DLFTPLSRPP
SPLSLPRPRS APARRPPAPS GDTAPPARPH TPLSRIDVRP PLDWGPQRQT LSRPPTPRRG
PPSEAGGGKP PRSPQHWSQE PRTQPGPPLE STFHQSLETD TLLTKLCGQD RLLRRLQEEI
DQKQEEKEQL EAALELTRQQ LGQATREAGA PGRAWGRQRL LQDRLVSVRA TLCHLTQERE
RVWDTYSGLE QELGTLRETL EYLLHLGSPQ DRVSAQQQLW MVEDTLAGLG GPQKPPPHTE
PDSPSPVLQG EESSERESLP ESLELSSPRS PETDWGRPPG GDKDLASPHL GLGSPRVSRA
SSPEGRHLPS PQLGTKSKEH HPLLADFRRS PGAGSQPLPS PGY*
speed 2.09 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: 0.998058491893031 (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) chr19:49368843T>CN/A show variant in all transcripts   IGV
HGNC symbol PLEKHA4
Ensembl transcript ID ENST00000263265
Genbank transcript ID NM_020904
UniProt peptide Q9H4M7
alteration type single base exchange
alteration region CDS
DNA changes c.109A>G
cDNA.660A>G
g.3042A>G
AA changes I37V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
37
frameshift no
known variant Reference ID: rs506425
databasehomozygous (C/C)heterozygousallele carriers
1000G6698541523
ExAC80141673924753
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6761
1.1351
(flanking)1.3331
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased3036wt: 0.39 / mu: 0.98wt: CAGTAAACAAGATCC
mu: CAGTAAACAAGGTCC
 GTAA|acaa
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      37SPKKPTRAVNKIHAFGKRGNALRR
mutated  all conserved    37SPKKPTRAVNKVHAFGKRGNALR
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000003344  n/a
Mmusculus  all conserved  ENSMUSG00000040428  37STKKPTRAVHKVHAFGKRNNALR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000071460  34D-----KGQDKVQTFGKRCQAAK
Dmelanogaster  all identical  FBgn0085412  356APLDRKKSAGSIQAL--KSPITK
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000004571  9TRSVKRVHTFGKREYSIK
protein features
start (aa)end (aa)featuredetails 
54153DOMAINPH.might get lost (downstream of altered splice site)
5564STRANDmight get lost (downstream of altered splice site)
6669STRANDmight get lost (downstream of altered splice site)
7280STRANDmight get lost (downstream of altered splice site)
8389STRANDmight get lost (downstream of altered splice site)
97100STRANDmight get lost (downstream of altered splice site)
101103HELIXmight get lost (downstream of altered splice site)
105108STRANDmight get lost (downstream of altered splice site)
116124STRANDmight get lost (downstream of altered splice site)
131134STRANDmight get lost (downstream of altered splice site)
138152HELIXmight get lost (downstream of altered splice site)
162353COMPBIASPro-rich.might get lost (downstream of altered splice site)
590590CONFLICTS -> N (in Ref. 1; AAG01896).might get lost (downstream of altered splice site)
779779CONFLICTF -> L (in Ref. 1; AAG01896).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2340 / 2340
position (AA) of stopcodon in wt / mu AA sequence 780 / 780
position of stopcodon in wt / mu cDNA 2891 / 2891
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 552 / 552
chromosome 19
strand -1
last intron/exon boundary 2629
theoretical NMD boundary in CDS 2027
length of CDS 2340
coding sequence (CDS) position 109
cDNA position
(for ins/del: last normal base / first normal base)
660
gDNA position
(for ins/del: last normal base / first normal base)
3042
chromosomal position
(for ins/del: last normal base / first normal base)
49368843
original gDNA sequence snippet CCACCCGGGCAGTAAACAAGATCCACGCCTTTGGGAAGAGA
altered gDNA sequence snippet CCACCCGGGCAGTAAACAAGGTCCACGCCTTTGGGAAGAGA
original cDNA sequence snippet CCACCCGGGCAGTAAACAAGATCCACGCCTTTGGGAAGAGA
altered cDNA sequence snippet CCACCCGGGCAGTAAACAAGGTCCACGCCTTTGGGAAGAGA
wildtype AA sequence MEGSRPRSSL SLASSASTIS SLSSLSPKKP TRAVNKIHAF GKRGNALRRD PNLPVHIRGW
LHKQDSSGLR LWKRRWFVLS GHCLFYYKDS REESVLGSVL LPSYNIRPDG PGAPRGRRFT
FTAEHPGMRT YVLAADTLED LRGWLRALGR ASRAEGDDYG QPRSPARPQP GEGPGGPGGP
PEVSRGEEGR ISESPEVTRL SRGRGRPRLL TPSPTTDLHS GLQMRRARSP DLFTPLSRPP
SPLSLPRPRS APARRPPAPS GDTAPPARPH TPLSRIDVRP PLDWGPQRQT LSRPPTPRRG
PPSEAGGGKP PRSPQHWSQE PRTQAHSGSP TYLQLPPRPP GTRASMVLLP GPPLESTFHQ
SLETDTLLTK LCGQDRLLRR LQEEIDQKQE EKEQLEAALE LTRQQLGQAT REAGAPGRAW
GRQRLLQDRL VSVRATLCHL TQERERVWDT YSGLEQELGT LRETLEYLLH LGSPQDRVSA
QQQLWMVEDT LAGLGGPQKP PPHTEPDSPS PVLQGEESSE RESLPESLEL SSPRSPETDW
GRPPGGDKDL ASPHLGLGSP RVSRASSPEG RHLPSPQLGT KAPVARPRMS AQEQLERMRR
NQECGRPFPR PTSPRLLTLG RTLSPARRQP DVEQRPVVGH SGAQKWLRSS GSWSSPRNTT
PYLPTSEGHR ERVLSLSQAL ATEASQWHRM MTGGNLDSQG DPLPGVPLPP SDPTRQETPP
PRSPPVANSG STGFSRRGSG RGGGPTPWGP AWDAGIAPPV LPQDEGAWPL RVTLLQSSF*
mutated AA sequence MEGSRPRSSL SLASSASTIS SLSSLSPKKP TRAVNKVHAF GKRGNALRRD PNLPVHIRGW
LHKQDSSGLR LWKRRWFVLS GHCLFYYKDS REESVLGSVL LPSYNIRPDG PGAPRGRRFT
FTAEHPGMRT YVLAADTLED LRGWLRALGR ASRAEGDDYG QPRSPARPQP GEGPGGPGGP
PEVSRGEEGR ISESPEVTRL SRGRGRPRLL TPSPTTDLHS GLQMRRARSP DLFTPLSRPP
SPLSLPRPRS APARRPPAPS GDTAPPARPH TPLSRIDVRP PLDWGPQRQT LSRPPTPRRG
PPSEAGGGKP PRSPQHWSQE PRTQAHSGSP TYLQLPPRPP GTRASMVLLP GPPLESTFHQ
SLETDTLLTK LCGQDRLLRR LQEEIDQKQE EKEQLEAALE LTRQQLGQAT REAGAPGRAW
GRQRLLQDRL VSVRATLCHL TQERERVWDT YSGLEQELGT LRETLEYLLH LGSPQDRVSA
QQQLWMVEDT LAGLGGPQKP PPHTEPDSPS PVLQGEESSE RESLPESLEL SSPRSPETDW
GRPPGGDKDL ASPHLGLGSP RVSRASSPEG RHLPSPQLGT KAPVARPRMS AQEQLERMRR
NQECGRPFPR PTSPRLLTLG RTLSPARRQP DVEQRPVVGH SGAQKWLRSS GSWSSPRNTT
PYLPTSEGHR ERVLSLSQAL ATEASQWHRM MTGGNLDSQG DPLPGVPLPP SDPTRQETPP
PRSPPVANSG STGFSRRGSG RGGGPTPWGP AWDAGIAPPV LPQDEGAWPL RVTLLQSSF*
speed 1.60 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