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: ENST00000378313
Querying Taster for transcript #2: ENST00000339153
MT speed 1.28 s - this script 3.311973 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
C19orf54polymorphism_automatic4.43606928089979e-05simple_aaeaffectedR70Psingle base exchangers2254343show file
C19orf54polymorphism_automatic1without_aaeaffectedsingle base exchangers2254343show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999955639307191 (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) chr19:41255500C>GN/A show variant in all transcripts   IGV
HGNC symbol C19orf54
Ensembl transcript ID ENST00000378313
Genbank transcript ID NM_198476
UniProt peptide Q5BKX5
alteration type single base exchange
alteration region CDS
DNA changes c.209G>C
cDNA.329G>C
g.909G>C
AA changes R70P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 70
frameshift no
known variant Reference ID: rs2254343
databasehomozygous (G/G)heterozygousallele carriers
1000G14698522321
ExAC563139989629
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4240.998
1.4481
(flanking)2.7131
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 increased920wt: 0.9562 / mu: 0.9731 (marginal change - not scored)wt: CTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAGCTC
mu: CTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAGCTC		 ttcg|GCCT
Acc marginally increased912wt: 0.2142 / mu: 0.2476 (marginal change - not scored)wt: CACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGA
mu: CACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGA		 gtca|TGTC
Acc marginally increased913wt: 0.9239 / mu: 0.9767 (marginal change - not scored)wt: ACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAG
mu: ACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAG		 tcat|GTCT
Acc increased915wt: 0.63 / mu: 0.85wt: AGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCC
mu: AGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCC		 atgt|CTTC
Acc marginally increased919wt: 0.9261 / mu: 0.9608 (marginal change - not scored)wt: CCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAGCT
mu: CCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAGCT		 cttc|GGCC
Acc increased917wt: 0.21 / mu: 0.42wt: GGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAG
mu: GGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAG		 gtct|TCGG
Acc gained9140.31mu: CAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGC catg|TCTT
Acc gained9110.45mu: CCACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAG cctc|ATGT
distance from splice site 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      70PPPPAATGPAPRHVFGLEKSQLLK
mutated  not conserved    70PPAATGPAPPHVFGLEKSQLL
Ptroglodytes  not conserved  ENSPTRG00000011006  70PPAATGPAPPHVFGLEKSQLL
Mmulatta  no alignment  ENSMMUG00000017708  n/a
Fcatus  not conserved  ENSFCAG00000018807  69PPAVGGPAPPHVFGLEKSQLL
Mmusculus  not conserved  ENSMUSG00000078786  67PPPAPPPPPPPPPLPSAVEPVLPHVYGLKNSQLL
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000009683  27PPPPPVLG-APGLSASESKKKLY
Drerio  not conserved  ENSDARG00000039513  29PPPPQPPSLARSES---SKKKLY
Dmelanogaster  no alignment  FBgn0053108  n/a
Celegans  no alignment  K07A1.3  n/a
Xtropicalis  not conserved  ENSXETG00000030884  33PPPPQIHLLPPT----VAKCKFF
protein features
start (aa)end (aa)featuredetails 
7070CONFLICTR -> P (in Ref. 3; BC020262).lost
316316MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1056 / 1056
position (AA) of stopcodon in wt / mu AA sequence 352 / 352
position of stopcodon in wt / mu cDNA 1176 / 1176
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 121 / 121
chromosome 19
strand -1
last intron/exon boundary 839
theoretical NMD boundary in CDS 668
length of CDS 1056
coding sequence (CDS) position 209
cDNA position
(for ins/del: last normal base / first normal base)		 329
gDNA position
(for ins/del: last normal base / first normal base)		 909
chromosomal position
(for ins/del: last normal base / first normal base)		 41255500
original gDNA sequence snippet TGCCACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGA
altered gDNA sequence snippet TGCCACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGA
original cDNA sequence snippet TGCCACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGA
altered cDNA sequence snippet TGCCACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGA
wildtype AA sequence MTSPCSPPLK PPISPPKTPV PQASSIPSPP LPPSPLDFSA LPSPPWSQQT PVPPPLPLPP
PPAATGPAPR HVFGLEKSQL LKEAFDKAGP VPKGREDVKR LLKLHKDRFR GDLRWILFCA
DLPSLIQEGP QCGLVALWMA GTLLSPPSGV PLERLIRVAT ERGYTAQGEM FSVADMGRLA
QEVLGCQAKL LSGGLGGPNR DLVLQHLVTG HPLLIPYDED FNHEPCQRKG HKAHWAVSAG
VLLGVRAVPS LGYTEDPELP GLFHPVLGTP CQPPSLPEEG SPGAVYLLSK QGKSWHYQLW
DYDQVRESNL QLTDFSPSRA TDGRVYVVPV GGVRAGLCGQ ALLLTPQDCS H*
mutated AA sequence MTSPCSPPLK PPISPPKTPV PQASSIPSPP LPPSPLDFSA LPSPPWSQQT PVPPPLPLPP
PPAATGPAPP HVFGLEKSQL LKEAFDKAGP VPKGREDVKR LLKLHKDRFR GDLRWILFCA
DLPSLIQEGP QCGLVALWMA GTLLSPPSGV PLERLIRVAT ERGYTAQGEM FSVADMGRLA
QEVLGCQAKL LSGGLGGPNR DLVLQHLVTG HPLLIPYDED FNHEPCQRKG HKAHWAVSAG
VLLGVRAVPS LGYTEDPELP GLFHPVLGTP CQPPSLPEEG SPGAVYLLSK QGKSWHYQLW
DYDQVRESNL QLTDFSPSRA TDGRVYVVPV GGVRAGLCGQ ALLLTPQDCS H*
speed 0.90 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: 1.25470307920951e-16 (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) chr19:41255500C>GN/A show variant in all transcripts   IGV
HGNC symbol C19orf54
Ensembl transcript ID ENST00000339153
Genbank transcript ID N/A
UniProt peptide Q5BKX5
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.232G>C
g.909G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2254343
databasehomozygous (G/G)heterozygousallele carriers
1000G14698522321
ExAC563139989629
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4240.998
1.4481
(flanking)2.7131
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -59) | splice site change before start ATG (at aa -58) | splice site change before start ATG (at aa -57) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased920wt: 0.9562 / mu: 0.9731 (marginal change - not scored)wt: CTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAGCTC
mu: CTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAGCTC		 ttcg|GCCT
Acc marginally increased912wt: 0.2142 / mu: 0.2476 (marginal change - not scored)wt: CACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGA
mu: CACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGA		 gtca|TGTC
Acc marginally increased913wt: 0.9239 / mu: 0.9767 (marginal change - not scored)wt: ACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAG
mu: ACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAG		 tcat|GTCT
Acc increased915wt: 0.63 / mu: 0.85wt: AGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCC
mu: AGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCC		 atgt|CTTC
Acc marginally increased919wt: 0.9261 / mu: 0.9608 (marginal change - not scored)wt: CCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAGCT
mu: CCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAGCT		 cttc|GGCC
Acc increased917wt: 0.21 / mu: 0.42wt: GGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGAAGAGCCAG
mu: GGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGCCAG		 gtct|TCGG
Acc gained9140.31mu: CAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAGAGC catg|TCTT
Acc gained9110.45mu: CCACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGAAG cctc|ATGT
distance from splice site 13
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
469COMPBIASPro-rich.might get lost (downstream of altered splice site)
7070CONFLICTR -> P (in Ref. 3; BC020262).might get lost (downstream of altered splice site)
316316MOD_RESPhosphoserine.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 416 / 416
chromosome 19
strand -1
last intron/exon boundary 812
theoretical NMD boundary in CDS 346
length of CDS 420
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 232
gDNA position
(for ins/del: last normal base / first normal base)		 909
chromosomal position
(for ins/del: last normal base / first normal base)		 41255500
original gDNA sequence snippet TGCCACAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGA
altered gDNA sequence snippet TGCCACAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGA
original cDNA sequence snippet ACTCAAAGGGCCTGCTCCCCGTCATGTCTTCGGCCTGGAGA
altered cDNA sequence snippet ACTCAAAGGGCCTGCTCCCCCTCATGTCTTCGGCCTGGAGA
wildtype AA sequence MRAGGLVDGR YSPVAPQWRP PGETHTGGHG KRLHGPGRDV LSTSYDEDFN HEPCQRKGHK
AHWAVSAGVL LGVRAVPSLG YTEDPELPGL FHPVLGTPCQ PPSLPEEGSP GAVYLLSKQG
KSWHYQLWDY DQGPPLSSH*
mutated AA sequence N/A
speed 0.38 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