Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999965645      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs18381 (probable pathogenic)
  • known disease mutation at this position (HGMD CM973279)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175614871C>AN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000348749
Genbank transcript ID NM_000079
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.805G>T
cDNA.883G>T
g.14330G>T
AA changes V269F Score: 50 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 269
frameshift no
known variant Reference ID: rs137852803
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs18381 (probable pathogenic for Congenital myasthenic syndrome 1A|Inborn genetic diseases) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM973279)

known disease mutation at this position, please check HGMD for details (HGMD ID CM973279)
known disease mutation at this position, please check HGMD for details (HGMD ID CM973279)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0741
6.1431
(flanking)-0.090.985
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased14336wt: 0.29 / mu: 0.75wt: CTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTT
mu: CTCTGAGCATCTCTTTCTTACTGTCTTTGACTGTGTTCCTT		 ttac|TGTC
Acc marginally increased14341wt: 0.9279 / mu: 0.9728 (marginal change - not scored)wt: AGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGT
mu: AGCATCTCTTTCTTACTGTCTTTGACTGTGTTCCTTCTGGT		 gtct|TTGA
Acc increased14339wt: 0.37 / mu: 0.81wt: TGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTG
mu: TGAGCATCTCTTTCTTACTGTCTTTGACTGTGTTCCTTCTG		 ctgt|CTTT
Acc increased14338wt: 0.59 / mu: 0.89wt: CTGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCT
mu: CTGAGCATCTCTTTCTTACTGTCTTTGACTGTGTTCCTTCT		 actg|TCTT
Acc increased14333wt: 0.30 / mu: 0.41wt: TGACTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTC
mu: TGACTCTGAGCATCTCTTTCTTACTGTCTTTGACTGTGTTC		 gtct|TACT
Acc increased14337wt: 0.61 / mu: 0.91wt: TCTGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTC
mu: TCTGAGCATCTCTTTCTTACTGTCTTTGACTGTGTTCCTTC		 tact|GTCT
Acc gained143340.69mu: GACTCTGAGCATCTCTTTCTTACTGTCTTTGACTGTGTTCC tctt|ACTG
Acc gained143350.38mu: ACTCTGAGCATCTCTTTCTTACTGTCTTTGACTGTGTTCCT ctta|CTGT
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      269DSGEKMTLSISVLLSLTVFLLVIV
mutated  not conserved    269DSGEKMTLSISFLLSLTVFLLVI
Ptroglodytes  all identical  ENSPTRG00000012658  294DSGEKMTLSISVLLSLTV
Mmulatta  all identical  ENSMMUG00000021796  293DSGEKMTLSISVLLSLTVF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  269DSGEKMTLSISVLLSLTVFLLVI
Ggallus  all identical  ENSGALG00000009301  279DSGEKMTLSISVLLSLTVFLLVI
Trubripes  all identical  ENSTRUG00000008738  290DSGEKMTLSISVLLSLTVFLLVI
Drerio  all identical  ENSDARG00000009021  269DSGEKMTLSISVLLSLTVFLLVI
Dmelanogaster  no homologue    
Celegans  all conserved  K11G12.2  303SGEKVSLTISLLLALVVFLLLV
Xtropicalis  all identical  ENSXETG00000025418  269DSGEKMTLSISVLLSLTVFLLVI
protein features
start (aa)end (aa)featuredetails 
256280TRANSMEMHelical.lost
288306TRANSMEMHelical.might get lost (downstream of altered splice site)
322341TRANSMEMHelical.might get lost (downstream of altered splice site)
342453TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
415415CONFLICTP -> F (in Ref. 4; AAD14247).might get lost (downstream of altered splice site)
454472TRANSMEMHelical.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1374 / 1374
position (AA) of stopcodon in wt / mu AA sequence 458 / 458
position of stopcodon in wt / mu cDNA 1452 / 1452
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 79 / 79
chromosome 2
strand -1
last intron/exon boundary 1321
theoretical NMD boundary in CDS 1192
length of CDS 1374
coding sequence (CDS) position 805
cDNA position
(for ins/del: last normal base / first normal base)		 883
gDNA position
(for ins/del: last normal base / first normal base)		 14330
chromosomal position
(for ins/del: last normal base / first normal base)		 175614871
original gDNA sequence snippet AGATGACTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTG
altered gDNA sequence snippet AGATGACTCTGAGCATCTCTTTCTTACTGTCTTTGACTGTG
original cDNA sequence snippet AGATGACTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTG
altered cDNA sequence snippet AGATGACTCTGAGCATCTCTTTCTTACTGTCTTTGACTGTG
wildtype AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISFL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*
speed 0.72 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