Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999673154 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM062511)
  • known disease mutation: rs18387 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175612912G>CN/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.1068C>G
cDNA.1086C>G
g.16289C>G
AA changes C356W Score: 215 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 356
frameshift no
known variant Reference ID: rs137852808
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs18387 (pathogenic for Congenital myasthenic syndrome 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM062511)

known disease mutation at this position, please check HGMD for details (HGMD ID CM062511)
known disease mutation at this position, please check HGMD for details (HGMD ID CM062511)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.2450.981
-0.4310.88
(flanking)6.0461
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased16281wt: 0.34 / mu: 0.39wt: TACTCCTCGGAGTCTTCATGCTTGTTTGCATCATCGGAACC
mu: TACTCCTCGGAGTCTTCATGCTTGTTTGGATCATCGGAACC		 atgc|TTGT
Acc increased16288wt: 0.25 / mu: 0.77wt: CGGAGTCTTCATGCTTGTTTGCATCATCGGAACCCTAGCCG
mu: CGGAGTCTTCATGCTTGTTTGGATCATCGGAACCCTAGCCG		 tttg|CATC
Acc marginally increased16279wt: 0.7827 / mu: 0.8241 (marginal change - not scored)wt: CATACTCCTCGGAGTCTTCATGCTTGTTTGCATCATCGGAA
mu: CATACTCCTCGGAGTCTTCATGCTTGTTTGGATCATCGGAA		 tcat|GCTT
distance from splice site 72
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      356DHILLGVFMLVCIIGTLAVFAGRL
mutated  not conserved    356DHILLGVFMLVWIIGT
Ptroglodytes  all identical  ENSPTRG00000012658  463DHILLGVFMLVCIIGTLAVFAGR
Mmulatta  all identical  ENSMMUG00000021796  462DHILLGVFMLVCIIGTLAVFAGR
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  438DHILLGVFMLVCLIGTLAVFAGR
Ggallus  all identical  ENSGALG00000009301  448DHLLLVIFMLVCIIGTLAVFAGR
Trubripes  all identical  ENSTRUG00000008738  459DHILLCVFMAVCIIGT
Drerio  all identical  ENSDARG00000009021  438DHILLCVFMAVCIIGTLGVFAGR
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  537DRLILLIFFGVTLGGTLGI
Xtropicalis  all identical  ENSXETG00000025418  438DHILLAVFMTVCVIGTLAVFAGR
protein features
start (aa)end (aa)featuredetails 
342453TOPO_DOMCytoplasmic.lost
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 1068
cDNA position
(for ins/del: last normal base / first normal base)		 1086
gDNA position
(for ins/del: last normal base / first normal base)		 16289
chromosomal position
(for ins/del: last normal base / first normal base)		 175612912
original gDNA sequence snippet GGAGTCTTCATGCTTGTTTGCATCATCGGAACCCTAGCCGT
altered gDNA sequence snippet GGAGTCTTCATGCTTGTTTGGATCATCGGAACCCTAGCCGT
original cDNA sequence snippet GGAGTCTTCATGCTTGTTTGCATCATCGGAACCCTAGCCGT
altered cDNA sequence snippet GGAGTCTTCATGCTTGTTTGGATCATCGGAACCCTAGCCGT
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
MTLSISVLLS LTVFLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVWIIGT
LAVFAGRLIE LNQQG*
speed 0.96 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