Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999468507 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040988)
  • known disease mutation: rs18384 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175614850A>GN/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.580T>C
cDNA.598T>C
g.14351T>C
AA changes F194L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 194
frameshift no
known variant Reference ID: rs137852806
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18384 (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 CM040988)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040988)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040988)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0741
5.0741
(flanking)3.4351
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 increased14345wt: 0.7643 / mu: 0.7979 (marginal change - not scored)wt: TCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATC
mu: TCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATC		 ttga|CTGT
Acc marginally increased14348wt: 0.6721 / mu: 0.7106 (marginal change - not scored)wt: CTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTG
mu: CTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTG		 actg|TGTT
Acc marginally increased14347wt: 0.6568 / mu: 0.6819 (marginal change - not scored)wt: TCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGT
mu: TCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGT		 gact|GTGT
Acc marginally increased14358wt: 0.8010 / mu: 0.8535 (marginal change - not scored)wt: GTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTGATCC
mu: GTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAGCTGATCC		 ttct|GGTC
Acc marginally increased14343wt: 0.9704 / mu: 0.9754 (marginal change - not scored)wt: CATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCA
mu: CATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCA		 cttt|GACT
Acc increased14344wt: 0.41 / mu: 0.48wt: ATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCAT
mu: ATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCAT		 tttg|ACTG
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      194LSISVLLSLTVFLLVIVELIPSTS
mutated  not conserved    194LSISVLLSLTVLLLVIVELIPST
Ptroglodytes  all identical  ENSPTRG00000012658  301LSISVLLSLTVFLL
Mmulatta  all identical  ENSMMUG00000021796  300LSISVLLSLTVFLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  276LSISVLLSLTVFLL
Ggallus  all identical  ENSGALG00000009301  286LSISVLLSLTVFLL
Trubripes  all identical  ENSTRUG00000008738  297LSISVLLSLTVFLLV
Drerio  all identical  ENSDARG00000009021  276LSISVLLSLTVFLLV
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  310LTISLLLALVVFLLLVSKILPPT
Xtropicalis  all identical  ENSXETG00000025418  276LSISVLLSLTVFLL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
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 580
cDNA position
(for ins/del: last normal base / first normal base)		 598
gDNA position
(for ins/del: last normal base / first normal base)		 14351
chromosomal position
(for ins/del: last normal base / first normal base)		 175614850
original gDNA sequence snippet TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG
altered gDNA sequence snippet TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG
original cDNA sequence snippet TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG
altered cDNA sequence snippet TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG
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 LTVLLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*
speed 0.95 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