Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999800531 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970304)
  • known disease mutation: rs18378 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175614855G>AN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000261007
Genbank transcript ID NM_001039523
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.896C>T
cDNA.963C>T
g.14346C>T
AA changes T299I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 299
frameshift no
known variant Reference ID: rs137852800
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18378 (pathogenic for Congenital myasthenic syndrome 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970304)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970304)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970304)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6610.64
6.1431
(flanking)5.0741
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased14354wt: 0.24 / mu: 0.32wt: TACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTG
mu: TACTGTCTTTGATTGTGTTCCTTCTGGTCATCGTGGAGCTG		 ttcc|TTCT
Acc marginally increased14353wt: 0.4964 / mu: 0.5223 (marginal change - not scored)wt: TTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCT
mu: TTACTGTCTTTGATTGTGTTCCTTCTGGTCATCGTGGAGCT		 gttc|CTTC
Acc increased14348wt: 0.67 / mu: 0.77wt: CTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTG
mu: CTGTCTTACTGTCTTTGATTGTGTTCCTTCTGGTCATCGTG		 actg|TGTT
Acc marginally increased14336wt: 0.2871 / mu: 0.3226 (marginal change - not scored)wt: CTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTT
mu: CTCTGAGCATCTCTGTCTTACTGTCTTTGATTGTGTTCCTT		 ttac|TGTC
Acc marginally increased14339wt: 0.3725 / mu: 0.3748 (marginal change - not scored)wt: TGAGCATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTG
mu: TGAGCATCTCTGTCTTACTGTCTTTGATTGTGTTCCTTCTG		 ctgt|CTTT
Acc increased14344wt: 0.41 / mu: 0.69wt: ATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCAT
mu: ATCTCTGTCTTACTGTCTTTGATTGTGTTCCTTCTGGTCAT		 tttg|ACTG
Acc increased14351wt: 0.45 / mu: 0.54wt: TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG
mu: TCTTACTGTCTTTGATTGTGTTCCTTCTGGTCATCGTGGAG		 gtgt|TCCT
Acc increased14357wt: 0.62 / mu: 0.76wt: TGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTGATC
mu: TGTCTTTGATTGTGTTCCTTCTGGTCATCGTGGAGCTGATC		 cttc|TGGT
Acc marginally increased14345wt: 0.7643 / mu: 0.7774 (marginal change - not scored)wt: TCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATC
mu: TCTCTGTCTTACTGTCTTTGATTGTGTTCCTTCTGGTCATC		 ttga|CTGT
Acc marginally increased14349wt: 0.9424 / mu: 0.9475 (marginal change - not scored)wt: TGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGG
mu: TGTCTTACTGTCTTTGATTGTGTTCCTTCTGGTCATCGTGG		 ctgt|GTTC
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      299MTLSISVLLSLTVFLLVIVELIPS
mutated  not conserved    299MTLSISVLLSLIVFLLVIVELIP
Ptroglodytes  all identical  ENSPTRG00000012658  299MTLSISVLLSLTVFLLVIVELIP
Mmulatta  all identical  ENSMMUG00000021796  298MTLSISVLLSLTVFLLVIVELIP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  274MTLSISVLLSLTVFLLVIVELIP
Ggallus  all identical  ENSGALG00000009301  284MTLSISVLLSLTVFLLVIVELIP
Trubripes  all identical  ENSTRUG00000008738  295MTLSISVLLSLTVFLLVIVELIP
Drerio  all identical  ENSDARG00000009021  274MTLSISVLLSLTVFLLVIVELIP
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  308VSLTISLLLALVVFLLLVSKILP
Xtropicalis  all identical  ENSXETG00000025418  274MTLSISVLLSLTVFLLVIVE
protein features
start (aa)end (aa)featuredetails 
288306TRANSMEMHelical.lost
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 1449 / 1449
position (AA) of stopcodon in wt / mu AA sequence 483 / 483
position of stopcodon in wt / mu cDNA 1516 / 1516
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 2
strand -1
last intron/exon boundary 1385
theoretical NMD boundary in CDS 1267
length of CDS 1449
coding sequence (CDS) position 896
cDNA position
(for ins/del: last normal base / first normal base)		 963
gDNA position
(for ins/del: last normal base / first normal base)		 14346
chromosomal position
(for ins/del: last normal base / first normal base)		 175614855
original gDNA sequence snippet CTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCG
altered gDNA sequence snippet CTCTGTCTTACTGTCTTTGATTGTGTTCCTTCTGGTCATCG
original cDNA sequence snippet CTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCG
altered cDNA sequence snippet CTCTGTCTTACTGTCTTTGATTGTGTTCCTTCTGGTCATCG
wildtype AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQGD MVDLPRPSCV TLGVPLFSHL QNEQWVDYNL KWNPDDYGGV
KKIHIPSEKI WRPDLVLYNN ADGDFAIVKF TKVLLQYTGH ITWTPPAIFK SYCEIIVTHF
PFDEQNCSMK LGTWTYDGSV VAINPESDQP DLSNFMESGE WVIKESRGWK HSVTYSCCPD
TPYLDITYHF VMQRLPLYFI VNVIIPCLLF SFLTGLVFYL PTDSGEKMTL SISVLLSLTV
FLLVIVELIP STSSAVPLIG KYMLFTMVFV IASIIITVIV INTHHRSPST HVMPNWVRKV
FIDTIPNIMF FSTMKRPSRE KQDKKIFTED IDISDISGKP GPPPMGFHSP LIKHPEVKSA
IEGIKYIAET MKSDQESNNA AAEWKYVAMV MDHILLGVFM LVCIIGTLAV FAGRLIELNQ
QG*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQGD MVDLPRPSCV TLGVPLFSHL QNEQWVDYNL KWNPDDYGGV
KKIHIPSEKI WRPDLVLYNN ADGDFAIVKF TKVLLQYTGH ITWTPPAIFK SYCEIIVTHF
PFDEQNCSMK LGTWTYDGSV VAINPESDQP DLSNFMESGE WVIKESRGWK HSVTYSCCPD
TPYLDITYHF VMQRLPLYFI VNVIIPCLLF SFLTGLVFYL PTDSGEKMTL SISVLLSLIV
FLLVIVELIP STSSAVPLIG KYMLFTMVFV IASIIITVIV INTHHRSPST HVMPNWVRKV
FIDTIPNIMF FSTMKRPSRE KQDKKIFTED IDISDISGKP GPPPMGFHSP LIKHPEVKSA
IEGIKYIAET MKSDQESNNA AAEWKYVAMV MDHILLGVFM LVCIIGTLAV FAGRLIELNQ
QG*
speed 0.87 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