Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.127985331701287 (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 ENST00000536404
Genbank transcript ID N/A
UniProt peptide P11230
alteration type single base exchange
alteration region CDS
DNA changes c.637C>A
cDNA.767C>A
g.9269C>A
AA changes L213M Score: 15 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 213
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      213GEKMGLSIFALLTLTVFLLLLADK
mutated  all conserved    213GEKMGLSIFALMTLTVFLLLLAD
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 
24244TOPO_DOMExtracellular (Potential).lost
245269TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
277295TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 1290 / 1290
position (AA) of stopcodon in wt / mu AA sequence 430 / 430
position of stopcodon in wt / mu cDNA 1420 / 1420
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 131 / 131
chromosome 17
strand 1
last intron/exon boundary 1280
theoretical NMD boundary in CDS 1099
length of CDS 1290
coding sequence (CDS) position 637
cDNA position
(for ins/del: last normal base / first normal base)		 767
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 MSTKVYLDLE WTDYRLSWDP AEHDGIDSLR ITAESVWLPD VVLLNNNDGN FDVALDISVV
VSSDGSVRWQ PPGIYRSSCS IQVTYFPFDW QNCTMVFSSY SYDSSEVSLQ TGLGPDGQGH
QEIHIHEGTF IENGQWEIIH KPSRLIQPPG DPRGGREGQR QEVIFYLIIR RKPLFYLVNV
IAPCILITLL AIFVFYLPPD AGEKMGLSIF ALLTLTVFLL LLADKVPETS LSVPIIIKYL
MFTMVLVTFS VILSVVVLNL HHRSPHTHQM PLWVRQIFIH KLPLYLRLKR PKPERDLMPE
PPHCSSPGSG WGRGTDEYFI RKPPSDFLFP KPNRFQPELS APDLRRFIDG PNRAVALLPE
LREVVSSISY IARQLQEQED HDALKEDWQF VAMVVDRLFL WTFIIFTSVG TLVIFLDATY
HLPPPDPFP*
mutated AA sequence MSTKVYLDLE WTDYRLSWDP AEHDGIDSLR ITAESVWLPD VVLLNNNDGN FDVALDISVV
VSSDGSVRWQ PPGIYRSSCS IQVTYFPFDW QNCTMVFSSY SYDSSEVSLQ TGLGPDGQGH
QEIHIHEGTF IENGQWEIIH KPSRLIQPPG DPRGGREGQR QEVIFYLIIR RKPLFYLVNV
IAPCILITLL AIFVFYLPPD AGEKMGLSIF ALMTLTVFLL LLADKVPETS LSVPIIIKYL
MFTMVLVTFS VILSVVVLNL HHRSPHTHQM PLWVRQIFIH KLPLYLRLKR PKPERDLMPE
PPHCSSPGSG WGRGTDEYFI RKPPSDFLFP KPNRFQPELS APDLRRFIDG PNRAVALLPE
LREVVSSISY IARQLQEQED HDALKEDWQF VAMVVDRLFL WTFIIFTSVG TLVIFLDATY
HLPPPDPFP*
speed 1.18 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