Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000216177
Querying Taster for transcript #2: ENST00000381198
MT speed 0 s - this script 3.336533 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PNPLA5polymorphism_automatic0.992864331300739simple_aaeaffectedL140Fsingle base exchangers2071883show file
PNPLA5polymorphism_automatic0.999999999998666without_aaeaffectedsingle base exchangers2071883show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.00713566869926052 (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) chr22:44286950G>AN/A show variant in all transcripts   IGV
HGNC symbol PNPLA5
Ensembl transcript ID ENST00000216177
Genbank transcript ID NM_138814
UniProt peptide Q7Z6Z6
alteration type single base exchange
alteration region CDS
DNA changes c.418C>T
cDNA.548C>T
g.944C>T
AA changes L140F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 140
frameshift no
known variant Reference ID: rs2071883
databasehomozygous (A/A)heterozygousallele carriers
1000G1968101006
ExAC19851367715662
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5251
1.1081
(flanking)0.491
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 increased935wt: 0.6717 / mu: 0.7310 (marginal change - not scored)wt: TGGTCACTGACTTCGCCACCTGCGATGAGCTCATCCAGGTG
mu: TGGTCACTGACTTCGCCACCTGCGATGAGTTCATCCAGGTG		 acct|GCGA
Acc increased942wt: 0.78 / mu: 0.88wt: TGACTTCGCCACCTGCGATGAGCTCATCCAGGTGTGGGGCG
mu: TGACTTCGCCACCTGCGATGAGTTCATCCAGGTGTGGGGCG		 atga|GCTC
Donor marginally increased937wt: 0.9536 / mu: 0.9710 (marginal change - not scored)wt: ACCTGCGATGAGCTC
mu: ACCTGCGATGAGTTC		 CTGC|gatg
Donor marginally increased947wt: 0.9163 / mu: 0.9537 (marginal change - not scored)wt: AGCTCATCCAGGTGT
mu: AGTTCATCCAGGTGT		 CTCA|tcca
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      140FLVTDFATCDELIQALVCTLYFPF
mutated  not conserved    140FLVTDFATCDEFIQALVCTLYFP
Ptroglodytes  all identical  ENSPTRG00000014478  140FLVTDFATRDELIQALVCTSYFP
Mmulatta  all identical  ENSMMUG00000002020  140FLATDFATRDELIQALVCTLYFP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000018868  140FIVTDFATRDEFIQALICTLYLP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000044086  138LVSDFSSKEELIQALICSCFIP
Dmelanogaster  all conserved  FBgn0036449  129ISEFESREEVLQALLCACFIP
Celegans  all identical  C05D11.7  139IDEYRSNADLIDAIMCSCFIP
Xtropicalis  all identical  ENSXETG00000004865  138VLVSEFNSKEELIQALICSAFVP
protein features
start (aa)end (aa)featuredetails 
12181DOMAINPatatin.lost
319319CONFLICTK -> E (in Ref. 1; BAC86866).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1290 / 1290
position (AA) of stopcodon in wt / mu AA sequence 430 / 430
position of stopcodon in wt / mu cDNA 1420 / 1420
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 131 / 131
chromosome 22
strand -1
last intron/exon boundary 1330
theoretical NMD boundary in CDS 1149
length of CDS 1290
coding sequence (CDS) position 418
cDNA position
(for ins/del: last normal base / first normal base)		 548
gDNA position
(for ins/del: last normal base / first normal base)		 944
chromosomal position
(for ins/del: last normal base / first normal base)		 44286950
original gDNA sequence snippet ACTTCGCCACCTGCGATGAGCTCATCCAGGTGTGGGGCGGG
altered gDNA sequence snippet ACTTCGCCACCTGCGATGAGTTCATCCAGGTGTGGGGCGGG
original cDNA sequence snippet ACTTCGCCACCTGCGATGAGCTCATCCAGGCCTTGGTCTGC
altered cDNA sequence snippet ACTTCGCCACCTGCGATGAGTTCATCCAGGCCTTGGTCTGC
wildtype AA sequence MGFLEEEGRW NLSFSGAGYL GAHHVGATEC LRQRAPRLLQ GARRIYGSSS GALNAVSIVC
GKSVDFCCSH LLGMVGQLER LSLSILHPAY APIEHVKQQL QDALPPDAHV LASQRLGISL
TRWPDGRNFL VTDFATCDEL IQALVCTLYF PFYCGLIPPE FRGERYIDGA LSNNLPFADC
PSTITVSPFH GTVDICPQST SPNLHELNVF NFSFQISTEN FFLGLICLIP PSLEVVADNC
RQGYLDALRF LERRGLTKEP VLWTLVSKEP PAPADGNWDA GCDQRWKGGL SLNWKVPHVQ
VKDVPNFEQL SPELEAALKK ACTRDPSRWA RFWHSGPGQV LTYLLLPCTL PFEYIYFRSR
RLVVWLPDVP ADLWWMQGLL RNMALEVFSR TKAQLLGPIS PPATRVLETS PLQPQIAPHR
EELGPTHQA*
mutated AA sequence MGFLEEEGRW NLSFSGAGYL GAHHVGATEC LRQRAPRLLQ GARRIYGSSS GALNAVSIVC
GKSVDFCCSH LLGMVGQLER LSLSILHPAY APIEHVKQQL QDALPPDAHV LASQRLGISL
TRWPDGRNFL VTDFATCDEF IQALVCTLYF PFYCGLIPPE FRGERYIDGA LSNNLPFADC
PSTITVSPFH GTVDICPQST SPNLHELNVF NFSFQISTEN FFLGLICLIP PSLEVVADNC
RQGYLDALRF LERRGLTKEP VLWTLVSKEP PAPADGNWDA GCDQRWKGGL SLNWKVPHVQ
VKDVPNFEQL SPELEAALKK ACTRDPSRWA RFWHSGPGQV LTYLLLPCTL PFEYIYFRSR
RLVVWLPDVP ADLWWMQGLL RNMALEVFSR TKAQLLGPIS PPATRVLETS PLQPQIAPHR
EELGPTHQA*
speed 0.69 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: without_aae, prob: 1.33364631515823e-12 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr22:44286950G>AN/A show variant in all transcripts   IGV
HGNC symbol PNPLA5
Ensembl transcript ID ENST00000381198
Genbank transcript ID N/A
UniProt peptide Q7Z6Z6
alteration type single base exchange
alteration region intron
DNA changes g.944C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2071883
databasehomozygous (A/A)heterozygousallele carriers
1000G1968101006
ExAC19851367715662
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5251
1.1081
(flanking)0.491
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 increased935wt: 0.6717 / mu: 0.7310 (marginal change - not scored)wt: TGGTCACTGACTTCGCCACCTGCGATGAGCTCATCCAGGTG
mu: TGGTCACTGACTTCGCCACCTGCGATGAGTTCATCCAGGTG		 acct|GCGA
Acc increased942wt: 0.78 / mu: 0.88wt: TGACTTCGCCACCTGCGATGAGCTCATCCAGGTGTGGGGCG
mu: TGACTTCGCCACCTGCGATGAGTTCATCCAGGTGTGGGGCG		 atga|GCTC
Donor marginally increased937wt: 0.9536 / mu: 0.9710 (marginal change - not scored)wt: ACCTGCGATGAGCTC
mu: ACCTGCGATGAGTTC		 CTGC|gatg
Donor marginally increased947wt: 0.9163 / mu: 0.9537 (marginal change - not scored)wt: AGCTCATCCAGGTGT
mu: AGTTCATCCAGGTGT		 CTCA|tcca
distance from splice site 618
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
12181DOMAINPatatin.might get lost (downstream of altered splice site)
319319CONFLICTK -> E (in Ref. 1; BAC86866).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 134 / 134
chromosome 22
strand -1
last intron/exon boundary 991
theoretical NMD boundary in CDS 807
length of CDS 948
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 944
chromosomal position
(for ins/del: last normal base / first normal base)		 44286950
original gDNA sequence snippet ACTTCGCCACCTGCGATGAGCTCATCCAGGTGTGGGGCGGG
altered gDNA sequence snippet ACTTCGCCACCTGCGATGAGTTCATCCAGGTGTGGGGCGGG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGFLEEEGRW NLSFSGAGYL GAHHVGATEC LRQRAPRLLQ GARRIYGSSS GALNAVSIVC
GKSVDCPSTI TVSPFHGTVD ICPQSTSPNL HELNVFNFSF QISTENFFLG LICLIPPSLE
VVADNCRQGY LDALRFLERR GLTKEPVLWT LVSKEPPAPA DGNWDAGCDQ RWKGGLSLNW
KVPHVQVKDV PNFEQLSPEL EAALKKACTR DPSRWARFWH SGPGQVLTYL LLPCTLPFEY
IYFRSRRLVV WLPDVPADLW WMQGLLRNMA LEVFSRTKAQ LLGPISPPAT RVLETSPLQP
QIAPHREELG PTHQA*
mutated AA sequence N/A
speed 0.70 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