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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 3.36 s - this script 8.099251 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHRNEdisease_causing_automatic0.999997365293796simple_aaeaffected0R167Lsingle base exchangers121909514show file
C17orf107disease_causing_automatic1without_aaeaffected0single base exchangers121909514show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999997365293796 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970307)
  • known disease mutation: rs18345 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4805227C>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.500G>T
cDNA.511G>T
g.1143G>T
AA changes R167L Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS
167
frameshift no
known variant Reference ID: rs121909514
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18345 (pathogenic for Myasthenic syndrome, congenital, 4a, slow-channel|Congenital myasthenic syndrome 4C) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970307)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970307)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970307)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1451
3.5411
(flanking)1.9441
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost1143sequence motif lost- wt: TCCG|gtgg
 mu: TCCT.gtgg
Acc increased1141wt: 0.32 / mu: 0.60wt: CAGAACTGTTCGCTTATTTTCCGGTGGGAAGAGCTACTCCG
mu: CAGAACTGTTCGCTTATTTTCCTGTGGGAAGAGCTACTCCG
 tttc|CGGT
Acc marginally increased1147wt: 0.9348 / mu: 0.9859 (marginal change - not scored)wt: TGTTCGCTTATTTTCCGGTGGGAAGAGCTACTCCGAGGCCC
mu: TGTTCGCTTATTTTCCTGTGGGAAGAGCTACTCCGAGGCCC
 gtgg|GAAG
Acc marginally increased1144wt: 0.7827 / mu: 0.7846 (marginal change - not scored)wt: AACTGTTCGCTTATTTTCCGGTGGGAAGAGCTACTCCGAGG
mu: AACTGTTCGCTTATTTTCCTGTGGGAAGAGCTACTCCGAGG
 ccgg|TGGG
Donor marginally increased1145wt: 0.9955 / mu: 0.9969 (marginal change - not scored)wt: TCCGGTGGGAAGAGC
mu: TCCTGTGGGAAGAGC
 CGGT|ggga
Donor increased1147wt: 0.72 / mu: 0.92wt: CGGTGGGAAGAGCTA
mu: CTGTGGGAAGAGCTA
 GTGG|gaag
Acc gained11450.99mu: ACTGTTCGCTTATTTTCCTGTGGGAAGAGCTACTCCGAGGC ctgt|GGGA
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      167PFDWQNCSLIFRSQTYNAEEVEFT
mutated  not conserved    167PFDWQNCSLIFLSQTYNAEEVEF
Ptroglodytes  all identical  ENSPTRG00000008612  167PFDWQNCSLIFRSQTYNAEEVEF
Mmulatta  all identical  ENSMMUG00000002409  167PFDWQNCSLIFRSQTYNAEEVEF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000014609  167PFDWQNCSLIFRSQTYNAEEVEF
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000034307  172PFDWQNCTLVFRSQTYSANEIDI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000014957  175PFDWQNCSLVFRSKTYSANDIDL
protein features
start (aa)end (aa)featuredetails 
21239TOPO_DOMExtracellular (Potential).lost
240264TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 500
cDNA position
(for ins/del: last normal base / first normal base)
511
gDNA position
(for ins/del: last normal base / first normal base)
1143
chromosomal position
(for ins/del: last normal base / first normal base)
4805227
original gDNA sequence snippet GAACTGTTCGCTTATTTTCCGGTGGGAAGAGCTACTCCGAG
altered gDNA sequence snippet GAACTGTTCGCTTATTTTCCTGTGGGAAGAGCTACTCCGAG
original cDNA sequence snippet GAACTGTTCGCTTATTTTCCGCTCTCAGACGTACAATGCCG
altered cDNA sequence snippet GAACTGTTCGCTTATTTTCCTCTCTCAGACGTACAATGCCG
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 NCSLIFLSQT 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*
speed 1.75 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 CM970307)
  • known disease mutation: rs18345 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4805227C>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.2199C>A
g.2515C>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs121909514
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18345 (pathogenic for Myasthenic syndrome, congenital, 4a, slow-channel|Congenital myasthenic syndrome 4C) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970307)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970307)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970307)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1451
3.5411
(flanking)1.9441
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 657)
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased2514wt: 0.38 / mu: 0.68wt: CCTCGGAGTAGCTCTTCCCACCGGAAAATAAGCGAACAGTT
mu: CCTCGGAGTAGCTCTTCCCACAGGAAAATAAGCGAACAGTT
 ccac|CGGA
Donor marginally increased2515wt: 0.9914 / mu: 0.9979 (marginal change - not scored)wt: CCCACCGGAAAATAA
mu: CCCACAGGAAAATAA
 CACC|ggaa
Donor marginally increased2516wt: 0.9629 / mu: 0.9801 (marginal change - not scored)wt: CCACCGGAAAATAAG
mu: CCACAGGAAAATAAG
 ACCG|gaaa
distance from splice site 1001
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)
2199
gDNA position
(for ins/del: last normal base / first normal base)
2515
chromosomal position
(for ins/del: last normal base / first normal base)
4805227
original gDNA sequence snippet CTCGGAGTAGCTCTTCCCACCGGAAAATAAGCGAACAGTTC
altered gDNA sequence snippet CTCGGAGTAGCTCTTCCCACAGGAAAATAAGCGAACAGTTC
original cDNA sequence snippet CTCGGAGTAGCTCTTCCCACCGGAAAATAAGCGAACAGTTC
altered cDNA sequence snippet CTCGGAGTAGCTCTTCCCACAGGAAAATAAGCGAACAGTTC
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 1.61 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