Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999695975440594      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs18358 (probable pathogenic)
  • known disease mutation at this position (HGMD CM970309)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4802804G>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.991C>T
cDNA.1002C>T
g.3566C>T
AA changes R331W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 331
frameshift no
known variant Reference ID: rs121909515
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs18358 (probable pathogenic for Congenital myasthenic syndrome 4C|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970309)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970309)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970309)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H2AZ, Histone, Histone 2A variant Z
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1821
1.3150.959
(flanking)0.3320.709
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased3564wt: 0.35 / mu: 0.66wt: CATCGTGCTCAACGTGTCCCAGCGGACGCCCACCACCCACG
mu: CATCGTGCTCAACGTGTCCCAGTGGACGCCCACCACCCACG		 ccca|GCGG
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      331MNCVIVLNVSQRTPTTHAMSPRLR
mutated  not conserved    331MNCVIVLNVSQWTPTTHAMSPRL
Ptroglodytes  no alignment  ENSPTRG00000008612  n/a
Mmulatta  all identical  ENSMMUG00000002409  331MNCVIVLNVSLRTPTTHSMSPRL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000014609  331MNCVIVLNVSLRTPTTHATSPRL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000034307  336CIIVLNYSLRSPSTHNMSQSI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000014957  340LSCVIVLNVSLRSPS
protein features
start (aa)end (aa)featuredetails 
329456TOPO_DOMCytoplasmic (Potential).lost
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 991
cDNA position
(for ins/del: last normal base / first normal base)		 1002
gDNA position
(for ins/del: last normal base / first normal base)		 3566
chromosomal position
(for ins/del: last normal base / first normal base)		 4802804
original gDNA sequence snippet TCGTGCTCAACGTGTCCCAGCGGACGCCCACCACCCACGCC
altered gDNA sequence snippet TCGTGCTCAACGTGTCCCAGTGGACGCCCACCACCCACGCC
original cDNA sequence snippet TCGTGCTCAACGTGTCCCAGCGGACGCCCACCACCCACGCC
altered cDNA sequence snippet TCGTGCTCAACGTGTCCCAGTGGACGCCCACCACCCACGCC
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 LAQTVFLFLI AQKIPETSLS
VPLLGRFLIF VMVVATLIVM NCVIVLNVSQ WTPTTHAMSP RLRHVLLELL PRLLGSPPPP
EAPRAASPPR RASSVGLLLR AEELILKKPR SELVFEGQRH RQGTWTAAFC QSLGAAAPEV
RCCVDAVNFV AESTRDQEAT GEEVSDWVRM GNALDNICFW AALVLFSVGS SLIFLGAYFN
RVPDLPYAPC IQP*
speed 1.07 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