Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999676915      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970303)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618961C>TN/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.280G>A
cDNA.298G>A
g.10240G>A
AA changes V94M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 94
frameshift no
known variant Reference ID: rs137852799
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8721
5.8851
(flanking)2.0181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102360.95mu: GGCTCTGTCATGGCC CTCT|gtca
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      94KLGTWTYDGSVVAINPESDQPDLS
mutated  all conserved    94KLGTWTYDGSVMAINPESDQPDL
Ptroglodytes  all identical  ENSPTRG00000012658  201KLGTWTYDGSVVAINPESDQPDL
Mmulatta  all identical  ENSMMUG00000021796  200KLGTWTYDGSVVAINPESDQPDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  176KLGTWTYDGSVVAINPESDQPDL
Ggallus  all identical  ENSGALG00000009301  186KLGTWTYDGTMVVINPESDRPDL
Trubripes  all identical  ENSTRUG00000008738  197KLGTWTYDGLLVVINPDSDRPDL
Drerio  all identical  ENSDARG00000009021  176KLGTWTYDGNLVIINPDSDRPDL
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  213VFGSWTYNSEEVRLHWYNNIQAVQL
Xtropicalis  all identical  ENSXETG00000025418  176KFGTWTYDGTLVVINPDRDRPDL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
173173DISULFIDmight get lost (downstream of altered splice site)
186186CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
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 280
cDNA position
(for ins/del: last normal base / first normal base)		 298
gDNA position
(for ins/del: last normal base / first normal base)		 10240
chromosomal position
(for ins/del: last normal base / first normal base)		 175618961
original gDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGTAGGT
altered gDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGTAGGT
original cDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGAAAGC
altered cDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGAAAGC
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 GSVMAINPES 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*
speed 0.14 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