Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999699973 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM994573)
  • known disease mutation: rs18383 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618252A>CN/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.757T>G
cDNA.775T>G
g.10949T>G
AA changes F253V Score: 50 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 253
frameshift no
known variant Reference ID: rs137852805
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs18383 (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 CM994573)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994573)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994573)
regulatory features H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
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
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.9631
4.9631
(flanking)-0.110.973
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased10939wt: 0.9707 / mu: 0.9734 (marginal change - not scored)wt: CTGCTCTTCTCCTTCTTAACTGGCCTGGTATTCTACCTGCC
mu: CTGCTCTTCTCCTTCTTAACTGGCCTGGTAGTCTACCTGCC		 aact|GGCC
Acc marginally increased10944wt: 0.7326 / mu: 0.7952 (marginal change - not scored)wt: CTTCTCCTTCTTAACTGGCCTGGTATTCTACCTGCCCACAG
mu: CTTCTCCTTCTTAACTGGCCTGGTAGTCTACCTGCCCACAG		 gcct|GGTA
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      253CLLFSFLTGLVFYLPTDSGEKMTL
mutated  not conserved    253CLLFSFLTGLVVYLPTDSGEKMT
Ptroglodytes  all identical  ENSPTRG00000012658  278CLLFSFLTGLVFYLPTDSGEKMT
Mmulatta  all identical  ENSMMUG00000021796  277CLLFSFLTGLVFYLPTDSGEKMT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  253CLLFSFLTSLVFYLPTDSGEKMT
Ggallus  all identical  ENSGALG00000009301  263CLLFSFLTGFVFYLPTDSGEKMT
Trubripes  all identical  ENSTRUG00000008738  274CMLFSFLTGLVFYLPTDSGEKMT
Drerio  all identical  ENSDARG00000009021  253CMLFSFLTGLVFYL
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  292TVLMAFLSVMAFYLPVD
Xtropicalis  all identical  ENSXETG00000025418  253LTGLVFYLPTDSGEKMT
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
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 757
cDNA position
(for ins/del: last normal base / first normal base)		 775
gDNA position
(for ins/del: last normal base / first normal base)		 10949
chromosomal position
(for ins/del: last normal base / first normal base)		 175618252
original gDNA sequence snippet CCTTCTTAACTGGCCTGGTATTCTACCTGCCCACAGACTCA
altered gDNA sequence snippet CCTTCTTAACTGGCCTGGTAGTCTACCTGCCCACAGACTCA
original cDNA sequence snippet CCTTCTTAACTGGCCTGGTATTCTACCTGCCCACAGACTCA
altered cDNA sequence snippet CCTTCTTAACTGGCCTGGTAGTCTACCTGCCCACAGACTCA
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 LVVYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKAAAEWK YVAMVMDHIL LGVFMLVCII
GTLAVFAGRL IELNQQG*
speed 1.11 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