Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999996281      (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 ENST00000409542
Genbank transcript ID N/A
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.559G>T
cDNA.577G>T
g.14330G>T
AA changes V187F Score: 50 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 187
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      187DSGEKMTLSISVLLSLTVFLLVIV
mutated  not conserved    187MTLSISFLLSLTVFLLVI
Ptroglodytes  all identical  ENSPTRG00000012658  294DSGEKMTLSISVLLSLTVFLL
Mmulatta  all identical  ENSMMUG00000021796  293DSGEKMTLSISVLLSLTVFLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  269DSGEKMTLSISVLLSLTVFLL
Ggallus  all identical  ENSGALG00000009301  279DSGEKMTLSISVLLSLTVFLL
Trubripes  all identical  ENSTRUG00000008738  290DSGEKMTLSISVLLSLTVFLLV
Drerio  all identical  ENSDARG00000009021  269DSGEKMTLSISVLLSLTVFLLV
Dmelanogaster  no homologue    
Celegans  all conserved  K11G12.2  303DSGEKVSLTISLLLALVVF
Xtropicalis  all identical  ENSXETG00000025418  269DSGEKMTLSISVLLSLTVFLL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
187187DISULFIDlost
237237DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
238238DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
256280TRANSMEMHelical.might get lost (downstream of altered splice site)
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 1128 / 1128
position (AA) of stopcodon in wt / mu AA sequence 376 / 376
position of stopcodon in wt / mu cDNA 1146 / 1146
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 19 / 19
chromosome 2
strand -1
last intron/exon boundary 1015
theoretical NMD boundary in CDS 946
length of CDS 1128
coding sequence (CDS) position 559
cDNA position
(for ins/del: last normal base / first normal base)		 577
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 TTNVRLKQNC SMKLGTWTYD GSVVAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISVLLS LTVFLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQNC SMKLGTWTYD GSVVAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISFLLS LTVFLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*
speed 0.89 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