Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999996833362 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM994574)
  • known disease mutation: rs18382 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175614763C>TN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000409219
Genbank transcript ID N/A
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.913G>A
cDNA.931G>A
g.14438G>A
AA changes V305I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 305
frameshift no
known variant Reference ID: rs137852804
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18382 (pathogenic for Congenital myasthenic syndrome 1B, fast-channel) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM994574)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994574)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994574)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.9871
6.0391
(flanking)-0.4960.782
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased14441wt: 0.21 / mu: 0.33wt: TGTTCACCATGGTGTTCGTCATTGCCTCCATCATCATCACT
mu: TGTTCACCATGGTGTTCATCATTGCCTCCATCATCATCACT		 gtca|TTGC
distance from splice site 90
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      305IGKYMLFTMVFVIASIIITVIVIN
mutated  all conserved    305TMVFIIASIIITVIVI
Ptroglodytes  all identical  ENSPTRG00000012658  330IGKYMLFTMVFVIASIIITVIII
Mmulatta  all identical  ENSMMUG00000021796  329IGKYMLFTMVFVIASIIITVIVI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  305TMVFVIASIIITVIVI
Ggallus  all identical  ENSGALG00000009301  315TMVFVIASIIITVIVI
Trubripes  all identical  ENSTRUG00000008738  326FTMVFVIASIIITVIVI
Drerio  all identical  ENSDARG00000009021  305IGKYMLFTMIFVIASIIITVIV
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  339MGKYLLLAFVLNITAVVGTVVIV
Xtropicalis  all identical  ENSXETG00000025418  305IGKYMLFTMVFVIA
protein features
start (aa)end (aa)featuredetails 
288306TRANSMEMHelical.lost
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 1134 / 1134
position (AA) of stopcodon in wt / mu AA sequence 378 / 378
position of stopcodon in wt / mu cDNA 1152 / 1152
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 1021
theoretical NMD boundary in CDS 952
length of CDS 1134
coding sequence (CDS) position 913
cDNA position
(for ins/del: last normal base / first normal base)		 931
gDNA position
(for ins/del: last normal base / first normal base)		 14438
chromosomal position
(for ins/del: last normal base / first normal base)		 175614763
original gDNA sequence snippet TGCTGTTCACCATGGTGTTCGTCATTGCCTCCATCATCATC
altered gDNA sequence snippet TGCTGTTCACCATGGTGTTCATCATTGCCTCCATCATCATC
original cDNA sequence snippet TGCTGTTCACCATGGTGTTCGTCATTGCCTCCATCATCATC
altered cDNA sequence snippet TGCTGTTCACCATGGTGTTCATCATTGCCTCCATCATCATC
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 WVRKAAAEWK 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 EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFIIASII ITVIVINTHH RSPSTHVMPN WVRKAAAEWK YVAMVMDHIL LGVFMLVCII
GTLAVFAGRL IELNQQG*
speed 1.09 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