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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 0 s - this script 2.466143 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHRNEdisease_causing_automatic0.99999972104981simple_aaeaffected0L289Fsingle base exchangers121909511show file
C17orf107disease_causing_automatic1without_aaeaffected0single base exchangers121909511show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999972104981 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960300)
  • known disease mutation: rs18344 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4804140G>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.865C>T
cDNA.876C>T
g.2230C>T
AA changes L289F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 289
frameshift no
known variant Reference ID: rs121909511
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18344 (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 CM960300)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960300)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960300)
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
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3810.997
5.3041
(flanking)1.2721
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 increased2233wt: 0.9816 / mu: 0.9840 (marginal change - not scored)wt: AGACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCAGAG
mu: AGACCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCCAGAG		 ctca|TTGC
Acc marginally increased2229wt: 0.7083 / mu: 0.7481 (marginal change - not scored)wt: GCCCAGACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCC
mu: GCCCAGACCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCC		 gttc|CTCA
Acc increased2241wt: 0.46 / mu: 0.59wt: TTCTTGTTCCTCATTGCCCAGAAAATCCCAGAGACTTCTCT
mu: TTCTTGTTCTTCATTGCCCAGAAAATCCCAGAGACTTCTCT		 ccag|AAAA
Acc marginally increased2236wt: 0.9652 / mu: 0.9815 (marginal change - not scored)wt: CCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCAGAGACT
mu: CCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCCAGAGACT		 attg|CCCA
Acc marginally increased2234wt: 0.9119 / mu: 0.9500 (marginal change - not scored)wt: GACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCAGAGA
mu: GACCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCCAGAGA		 tcat|TGCC
Acc marginally increased2232wt: 0.9799 / mu: 0.9891 (marginal change - not scored)wt: CAGACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCAGA
mu: CAGACCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCCAGA		 cctc|ATTG
Acc increased2240wt: 0.62 / mu: 0.85wt: CTTCTTGTTCCTCATTGCCCAGAAAATCCCAGAGACTTCTC
mu: CTTCTTGTTCTTCATTGCCCAGAAAATCCCAGAGACTTCTC		 ccca|GAAA
Acc marginally increased2239wt: 0.9695 / mu: 0.9749 (marginal change - not scored)wt: TCTTCTTGTTCCTCATTGCCCAGAAAATCCCAGAGACTTCT
mu: TCTTCTTGTTCTTCATTGCCCAGAAAATCCCAGAGACTTCT		 gccc|AGAA
Acc increased2235wt: 0.48 / mu: 0.66wt: ACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCAGAGAC
mu: ACCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCCAGAGAC		 catt|GCCC
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      289NVLLAQTVFLFLIAQKIPETSLSV
mutated  not conserved    289NVLLAQTVFLFFIAQKIPETSLS
Ptroglodytes  all identical  ENSPTRG00000008612  289NVLLAQTVFLFLIAQKIPETSLS
Mmulatta  all identical  ENSMMUG00000002409  289NVLLAQTVFLFLIAQKIPETSLS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000014609  289NVLLAQTVFLFLIAQKIPETSLS
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000034307  294SVLLAQTVFLILISQKIPETSLS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000014957  298SVLLAQTVFLFLIAQMIPETSLS
protein features
start (aa)end (aa)featuredetails 
273291TRANSMEMHelical; (Potential).lost
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 865
cDNA position
(for ins/del: last normal base / first normal base)		 876
gDNA position
(for ins/del: last normal base / first normal base)		 2230
chromosomal position
(for ins/del: last normal base / first normal base)		 4804140
original gDNA sequence snippet CCCAGACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCA
altered gDNA sequence snippet CCCAGACCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCCA
original cDNA sequence snippet CCCAGACCGTCTTCTTGTTCCTCATTGCCCAGAAAATCCCA
altered cDNA sequence snippet CCCAGACCGTCTTCTTGTTCTTCATTGCCCAGAAAATCCCA
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
LFYVINIIVP CVLISGLVLL AYFLPAQAGG QKCTVSINVL LAQTVFLFFI AQKIPETSLS
VPLLGRFLIF VMVVATLIVM NCVIVLNVSQ RTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV AESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*
speed 0.22 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 CM960300)
  • known disease mutation: rs18344 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4804140G>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.1112G>A
g.1428G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121909511
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18344 (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 CM960300)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960300)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960300)
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
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3810.997
5.3041
(flanking)1.2721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 292) splice site change occurs after stopcodon (at aa 293)
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased1419wt: 0.23 / mu: 0.27wt: AGAAGTCTCTGGGATTTTCTGGGCAATGAGGAACAAGAAGA
mu: AGAAGTCTCTGGGATTTTCTGGGCAATGAAGAACAAGAAGA		 tctg|GGCA
Donor marginally increased1429wt: 0.9348 / mu: 0.9677 (marginal change - not scored)wt: ATGAGGAACAAGAAG
mu: ATGAAGAACAAGAAG		 GAGG|aaca
Donor marginally increased1425wt: 0.2113 / mu: 0.2408 (marginal change - not scored)wt: GGCAATGAGGAACAA
mu: GGCAATGAAGAACAA		 CAAT|gagg
Donor marginally increased1432wt: 0.9693 / mu: 0.9753 (marginal change - not scored)wt: AGGAACAAGAAGACG
mu: AAGAACAAGAAGACG		 GAAC|aaga
Donor increased1423wt: 0.34 / mu: 0.99wt: TGGGCAATGAGGAAC
mu: TGGGCAATGAAGAAC		 GGCA|atga
Donor marginally increased1420wt: 0.9461 / mu: 0.9839 (marginal change - not scored)wt: TTCTGGGCAATGAGG
mu: TTCTGGGCAATGAAG		 CTGG|gcaa
distance from splice site 609
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)		 1112
gDNA position
(for ins/del: last normal base / first normal base)		 1428
chromosomal position
(for ins/del: last normal base / first normal base)		 4804140
original gDNA sequence snippet TGGGATTTTCTGGGCAATGAGGAACAAGAAGACGGTCTGGG
altered gDNA sequence snippet TGGGATTTTCTGGGCAATGAAGAACAAGAAGACGGTCTGGG
original cDNA sequence snippet TGGGATTTTCTGGGCAATGAGGAACAAGAAGACGGTCTGGG
altered cDNA sequence snippet TGGGATTTTCTGGGCAATGAAGAACAAGAAGACGGTCTGGG
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 0.22 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

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