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: ENST00000293780
Querying Taster for transcript #2: ENST00000381365
MT speed 0 s - this script 3.995341 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHRNEdisease_causing_automatic0.999989998169422simple_aaeaffected0L241Fsingle base exchangers28999110show file
C17orf107disease_causing_automatic1without_aaeaffected0single base exchangers28999110show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999989998169422 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024237)
  • known disease mutation: rs18352 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4804366G>AN/A show variant in all transcripts   IGV
HGNC symbol CHRNE
Ensembl transcript ID ENST00000293780
Genbank transcript ID NM_000080
UniProt peptide Q04844
alteration type single base exchange
alteration region CDS
DNA changes c.721C>T
cDNA.732C>T
g.2004C>T
AA changes L241F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 241
frameshift no
known variant Reference ID: rs28999110
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18352 (pathogenic for Myasthenic syndrome, congenital, 4a, slow-channel) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024237)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024237)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024237)
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
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3421
3.6811
(flanking)0.0440.993
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2014wt: 0.24 / mu: 0.41wt: CCGGAAGCCGCTCTTCTACGTCATTAACATCATCGTGCCCT
mu: CCGGAAGCCGTTCTTCTACGTCATTAACATCATCGTGCCCT		 acgt|CATT
Donor increased2007wt: 0.63 / mu: 0.73wt: CGCTCTTCTACGTCA
mu: CGTTCTTCTACGTCA		 CTCT|tcta
Acc gained20120.35mu: CGCCGGAAGCCGTTCTTCTACGTCATTAACATCATCGTGCC ctac|GTCA
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      241VIYSLIIRRKPLFYVINIIVPCVL
mutated  not conserved    241FFYVINIIVPCV
Ptroglodytes  all identical  ENSPTRG00000008612  241LFYVINIIVPCV
Mmulatta  all identical  ENSMMUG00000002409  241LFYVINIIVPCV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000014609  241LFYVINIIVPCV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000034307  246VYYNIIIQRKPLFYVINIILPCS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000014957  250IVFILIIQRKPLFYIINIIVPCV
protein features
start (aa)end (aa)featuredetails 
240264TRANSMEMHelical; (Potential).lost
265272TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
273291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292306TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
307328TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
329456TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
457480TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
481493TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1482 / 1482
position (AA) of stopcodon in wt / mu AA sequence 494 / 494
position of stopcodon in wt / mu cDNA 1493 / 1493
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 12 / 12
chromosome 17
strand -1
last intron/exon boundary 1338
theoretical NMD boundary in CDS 1276
length of CDS 1482
coding sequence (CDS) position 721
cDNA position
(for ins/del: last normal base / first normal base)		 732
gDNA position
(for ins/del: last normal base / first normal base)		 2004
chromosomal position
(for ins/del: last normal base / first normal base)		 4804366
original gDNA sequence snippet TCATCATCCGCCGGAAGCCGCTCTTCTACGTCATTAACATC
altered gDNA sequence snippet TCATCATCCGCCGGAAGCCGTTCTTCTACGTCATTAACATC
original cDNA sequence snippet TCATCATCCGCCGGAAGCCGCTCTTCTACGTCATTAACATC
altered cDNA sequence snippet TCATCATCCGCCGGAAGCCGTTCTTCTACGTCATTAACATC
wildtype AA sequence MARAPLGVLL LLGLLGRGVG KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL
ISLNEKEETL TTSVWIGIDW QDYRLNYSKD DFGGIETLRV PSELVWLPEI VLENNIDGQF
GVAYDANVLV YEGGSVTWLP PAIYRSVCAV EVTYFPFDWQ NCSLIFRSQT YNAEEVEFTF
AVDNDGKTIN KIDIDTEAYT ENGEWAIDFC PGVIRRHHGG ATDGPGETDV IYSLIIRRKP
LFYVINIIVP CVLISGLVLL AYFLPAQAGG QKCTVSINVL LAQTVFLFLI AQKIPETSLS
VPLLGRFLIF VMVVATLIVM NCVIVLNVSQ RTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV AESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*
mutated AA sequence MARAPLGVLL LLGLLGRGVG KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL
ISLNEKEETL TTSVWIGIDW QDYRLNYSKD DFGGIETLRV PSELVWLPEI VLENNIDGQF
GVAYDANVLV YEGGSVTWLP PAIYRSVCAV EVTYFPFDWQ NCSLIFRSQT YNAEEVEFTF
AVDNDGKTIN KIDIDTEAYT ENGEWAIDFC PGVIRRHHGG ATDGPGETDV IYSLIIRRKP
FFYVINIIVP CVLISGLVLL AYFLPAQAGG QKCTVSINVL LAQTVFLFLI AQKIPETSLS
VPLLGRFLIF VMVVATLIVM NCVIVLNVSQ RTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV AESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*
speed 0.98 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

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM024237)
  • known disease mutation: rs18352 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4804366G>AN/A show variant in all transcripts   IGV
HGNC symbol C17orf107
Ensembl transcript ID ENST00000381365
Genbank transcript ID NM_001145536
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.1338G>A
g.1654G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28999110
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18352 (pathogenic for Myasthenic syndrome, congenital, 4a, slow-channel) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024237)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024237)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024237)
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
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3421
3.6811
(flanking)0.0440.993
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 369)
effectgDNA positionscoredetection sequence  exon-intron border
Donor gained16500.46mu: CGTAGAAGAACGGCT TAGA|agaa
distance from splice site 835
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 signal is predicted to be ok
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 228 / 228
chromosome 17
strand 1
last intron/exon boundary 504
theoretical NMD boundary in CDS 226
length of CDS 573
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 1338
gDNA position
(for ins/del: last normal base / first normal base)		 1654
chromosomal position
(for ins/del: last normal base / first normal base)		 4804366
original gDNA sequence snippet GATGTTAATGACGTAGAAGAGCGGCTTCCGGCGGATGATGA
altered gDNA sequence snippet GATGTTAATGACGTAGAAGAACGGCTTCCGGCGGATGATGA
original cDNA sequence snippet GATGTTAATGACGTAGAAGAGCGGCTTCCGGCGGATGATGA
altered cDNA sequence snippet GATGTTAATGACGTAGAAGAACGGCTTCCGGCGGATGATGA
wildtype AA sequence MKGTPSSLDT LMWIYHFHSS TEVALQPPLL SSLELSVAAA HEYLEQRFRE LKSLEPPEPK
MQGMLPAPKP TLGLVLREAT ASLVSFGTTL LEISALWLQQ EARRLDGSAG PAPDGRDPGA
ALSRVAQAAG QGVRQAGAAV GASARLLVQG AWLCLCGRGL QGSASFLRQS QQQLGLGIPG
EPVSSGHGVS *
mutated AA sequence N/A
speed 1.01 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