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 marginally increased1144wt: 0.7827 / mu: 0.7846 (marginal change - not scored)wt: AACTGTTCGCTTATTTTCCGGTGGGAAGAGCTACTCCGAGG
mu: AACTGTTCGCTTATTTTCCTGTGGGAAGAGCTACTCCGAGG		 ccgg|TGGG
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
Donor increased1147wt: 0.72 / mu: 0.92wt: CGGTGGGAAGAGCTA
mu: CTGTGGGAAGAGCTA		 GTGG|gaag
Donor marginally increased1145wt: 0.9955 / mu: 0.9969 (marginal change - not scored)wt: TCCGGTGGGAAGAGC
mu: TCCTGTGGGAAGAGC		 CGGT|ggga
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 0.45 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