Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.205352110561329 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960296)
  • known disease mutation: rs18373 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7357648C>AN/A show variant in all transcripts   IGV
HGNC symbol CHRNB1
Ensembl transcript ID ENST00000306071
Genbank transcript ID NM_000747
UniProt peptide P11230
alteration type single base exchange
alteration region CDS
DNA changes c.853C>A
cDNA.920C>A
g.9269C>A
AA changes L285M Score: 15 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 285
frameshift no
known variant Reference ID: rs137852811
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18373 (pathogenic for Myasthenic syndrome, congenital, 2a, slow-channel) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960296)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960296)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960296)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.1931
2.3221
(flanking)4.2551
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 increased9266wt: 0.5598 / mu: 0.5986 (marginal change - not scored)wt: TGGGGCTCTCAATCTTTGCCCTGCTGACCCTTACTGTGTTC
mu: TGGGGCTCTCAATCTTTGCCCTGATGACCCTTACTGTGTTC		 gccc|TGCT
Acc gained92680.43mu: GGGCTCTCAATCTTTGCCCTGATGACCCTTACTGTGTTCCT cctg|ATGA
Donor gained92650.53mu: TTTGCCCTGATGACC TGCC|ctga
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      285GEKMGLSIFALLTLTVFLLLLADK
mutated  all conserved    285GEKMGLSIFALMTLTVFLLLLAD
Ptroglodytes  all identical  ENSPTRG00000008689  285GEKMGLSIFALLTLTVFLLLLAD
Mmulatta  not conserved  ENSMMUG00000017690  285GNGGRGSHPFVIGSASSFLKLLGS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000041189  285GEKMGLSIFALLTLTVFLLLLAD
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000004322  278GEKMTLSISVLIALTVFMLLLAD
Drerio  all conserved  ENSDARG00000022532  273GEKMTLSISVLIALTVFMLLLAD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
277295TRANSMEMHelical; (Potential).lost
311332TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
333469TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
390390MOD_RESPhosphotyrosine; by Tyr-kinases (By similarity).might get lost (downstream of altered splice site)
470488TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1506 / 1506
position (AA) of stopcodon in wt / mu AA sequence 502 / 502
position of stopcodon in wt / mu cDNA 1573 / 1573
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 68 / 68
chromosome 17
strand 1
last intron/exon boundary 1433
theoretical NMD boundary in CDS 1315
length of CDS 1506
coding sequence (CDS) position 853
cDNA position
(for ins/del: last normal base / first normal base)		 920
gDNA position
(for ins/del: last normal base / first normal base)		 9269
chromosomal position
(for ins/del: last normal base / first normal base)		 7357648
original gDNA sequence snippet GGCTCTCAATCTTTGCCCTGCTGACCCTTACTGTGTTCCTG
altered gDNA sequence snippet GGCTCTCAATCTTTGCCCTGATGACCCTTACTGTGTTCCTG
original cDNA sequence snippet GGCTCTCAATCTTTGCCCTGCTGACCCTTACTGTGTTCCTG
altered cDNA sequence snippet GGCTCTCAATCTTTGCCCTGATGACCCTTACTGTGTTCCTG
wildtype AA sequence MTPGALLMLL GALGAPLAPG VRGSEAEGRL REKLFSGYDS SVRPAREVGD RVRVSVGLIL
AQLISLNEKD EEMSTKVYLD LEWTDYRLSW DPAEHDGIDS LRITAESVWL PDVVLLNNND
GNFDVALDIS VVVSSDGSVR WQPPGIYRSS CSIQVTYFPF DWQNCTMVFS SYSYDSSEVS
LQTGLGPDGQ GHQEIHIHEG TFIENGQWEI IHKPSRLIQP PGDPRGGREG QRQEVIFYLI
IRRKPLFYLV NVIAPCILIT LLAIFVFYLP PDAGEKMGLS IFALLTLTVF LLLLADKVPE
TSLSVPIIIK YLMFTMVLVT FSVILSVVVL NLHHRSPHTH QMPLWVRQIF IHKLPLYLRL
KRPKPERDLM PEPPHCSSPG SGWGRGTDEY FIRKPPSDFL FPKPNRFQPE LSAPDLRRFI
DGPNRAVALL PELREVVSSI SYIARQLQEQ EDHDALKEDW QFVAMVVDRL FLWTFIIFTS
VGTLVIFLDA TYHLPPPDPF P*
mutated AA sequence MTPGALLMLL GALGAPLAPG VRGSEAEGRL REKLFSGYDS SVRPAREVGD RVRVSVGLIL
AQLISLNEKD EEMSTKVYLD LEWTDYRLSW DPAEHDGIDS LRITAESVWL PDVVLLNNND
GNFDVALDIS VVVSSDGSVR WQPPGIYRSS CSIQVTYFPF DWQNCTMVFS SYSYDSSEVS
LQTGLGPDGQ GHQEIHIHEG TFIENGQWEI IHKPSRLIQP PGDPRGGREG QRQEVIFYLI
IRRKPLFYLV NVIAPCILIT LLAIFVFYLP PDAGEKMGLS IFALMTLTVF LLLLADKVPE
TSLSVPIIIK YLMFTMVLVT FSVILSVVVL NLHHRSPHTH QMPLWVRQIF IHKLPLYLRL
KRPKPERDLM PEPPHCSSPG SGWGRGTDEY FIRKPPSDFL FPKPNRFQPE LSAPDLRRFI
DGPNRAVALL PELREVVSSI SYIARQLQEQ EDHDALKEDW QFVAMVVDRL FLWTFIIFTS
VGTLVIFLDA TYHLPPPDPF P*
speed 1.32 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