Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999993264682 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:56435885G>TN/A show variant in all transcripts   IGV
HGNC symbol RNF43
Ensembl transcript ID ENST00000577716
Genbank transcript ID N/A
UniProt peptide Q68DV7
alteration type single base exchange
alteration region CDS
DNA changes c.1252C>A
cDNA.2000C>A
g.59072C>A
AA changes L418M Score: 15 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 418
frameshift no
known variant Reference ID: rs2526374
databasehomozygous (T/T)heterozygousallele carriers
1000G41511711586
ExAC94431388123324
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1160.012
2.1320.069
(flanking)-0.790.065
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased59075wt: 0.9892 / mu: 0.9934 (marginal change - not scored)wt: GACTGAGCCACCTCC
mu: GAATGAGCCACCTCC		 CTGA|gcca
Donor gained590670.38mu: AGGCTGGGGAATGAG GCTG|ggga
Donor gained590680.40mu: GGCTGGGGAATGAGC CTGG|ggaa
distance from splice site 300
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      418GAQHPYAQGWGLSHLQSTSQHPAA
mutated  all conserved    418GAQHPYAQGWGMSH
Ptroglodytes  all identical  ENSPTRG00000034322  418GAQHPYAQGWGLSH
Mmulatta  all identical  ENSMMUG00000007004  420GAQHPYAQGWGLSHLQSTSQHPA
Fcatus  all identical  ENSFCAG00000012267  418VAQHPYAQGWGLGR
Mmusculus  all identical  ENSMUSG00000034177  418VSPHPYAQGWGLNR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no alignment  Y47D3B.11  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
219783TOPO_DOMCytoplasmic (Potential).lost
443503COMPBIASSer-rich.might get lost (downstream of altered splice site)
547557COMPBIASHis-rich.might get lost (downstream of altered splice site)
569760COMPBIASPro-rich.might get lost (downstream of altered splice site)
600600CONFLICTR -> G (in Ref. 1; BAD51435 and 2; BAA91085).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2352 / 2352
position (AA) of stopcodon in wt / mu AA sequence 784 / 784
position of stopcodon in wt / mu cDNA 3100 / 3100
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 749 / 749
chromosome 17
strand -1
last intron/exon boundary 3057
theoretical NMD boundary in CDS 2258
length of CDS 2352
coding sequence (CDS) position 1252
cDNA position
(for ins/del: last normal base / first normal base)		 2000
gDNA position
(for ins/del: last normal base / first normal base)		 59072
chromosomal position
(for ins/del: last normal base / first normal base)		 56435885
original gDNA sequence snippet CCTATGCACAAGGCTGGGGACTGAGCCACCTCCAATCCACC
altered gDNA sequence snippet CCTATGCACAAGGCTGGGGAATGAGCCACCTCCAATCCACC
original cDNA sequence snippet CCTATGCACAAGGCTGGGGACTGAGCCACCTCCAATCCACC
altered cDNA sequence snippet CCTATGCACAAGGCTGGGGAATGAGCCACCTCCAATCCACC
wildtype AA sequence MSGGHQLQLA ALWPWLLMAT LQAGFGRTGL VLAAAVESER SAEQKAIIRV IPLKMDPTGK
LNLTLEGVFA GVAEITPAEG KLMQSHPLYL CNASDDDNLE PGFISIVKLE SPRRAPRPCL
SLASKARMAG ERGASAVLFD ITEDRAAAEQ LQQPLGLTWP VVLIWGNDAE KLMEFVYKNQ
KAHVRIELKE PPAWPDYDVW ILMTVVGTIF VIILASVLRI RCRPRHSRPD PLQQRTAWAI
SQLATRRYQA SCRQARGEWP DSGSSCSSAP VCAICLEEFS EGQELRVISC LHEFHRNCVD
PWLHQHRTCP LCMFNITEGD SFSQSLGPSR SYQEPGRRLH LIRQHPGHAH YHLPAAYLLG
PSRSAVARPP RPGPFLPSQE PGMGPRHHRF PRAAHPRAPG EQQRLAGAQH PYAQGWGLSH
LQSTSQHPAA CPVPLRRARP PDSSGSGESY CTERSGYLAD GPASDSSSGP CHGSSSDSVV
NCTDISLQGV HGSSSTFCSS LSSDFDPLVY CSPKGDPQRV DMQPSVTSRP RSLDSVVPTG
ETQVSSHVHY HRHRHHHYKK RFQWHGRKPG PETGVPQSRP PIPRTQPQPE PPSPDQQVTR
SNSAAPSGRL SNPQCPRALP EPAPGPVDAS SICPSTSSLF NLQKSSLSAR HPQRKRRGGP
SEPTPGSRPQ DATVHPACQI FPHYTPSVAY PWSPEAHPLI CGPPGLDKRL LPETPGPCYS
NSQPVWLCLT PRQPLEPHPP GEGPSEWSSD TAEGRPCPYP HCQVLSAQPG SEEELEELCE
QAV*
mutated AA sequence MSGGHQLQLA ALWPWLLMAT LQAGFGRTGL VLAAAVESER SAEQKAIIRV IPLKMDPTGK
LNLTLEGVFA GVAEITPAEG KLMQSHPLYL CNASDDDNLE PGFISIVKLE SPRRAPRPCL
SLASKARMAG ERGASAVLFD ITEDRAAAEQ LQQPLGLTWP VVLIWGNDAE KLMEFVYKNQ
KAHVRIELKE PPAWPDYDVW ILMTVVGTIF VIILASVLRI RCRPRHSRPD PLQQRTAWAI
SQLATRRYQA SCRQARGEWP DSGSSCSSAP VCAICLEEFS EGQELRVISC LHEFHRNCVD
PWLHQHRTCP LCMFNITEGD SFSQSLGPSR SYQEPGRRLH LIRQHPGHAH YHLPAAYLLG
PSRSAVARPP RPGPFLPSQE PGMGPRHHRF PRAAHPRAPG EQQRLAGAQH PYAQGWGMSH
LQSTSQHPAA CPVPLRRARP PDSSGSGESY CTERSGYLAD GPASDSSSGP CHGSSSDSVV
NCTDISLQGV HGSSSTFCSS LSSDFDPLVY CSPKGDPQRV DMQPSVTSRP RSLDSVVPTG
ETQVSSHVHY HRHRHHHYKK RFQWHGRKPG PETGVPQSRP PIPRTQPQPE PPSPDQQVTR
SNSAAPSGRL SNPQCPRALP EPAPGPVDAS SICPSTSSLF NLQKSSLSAR HPQRKRRGGP
SEPTPGSRPQ DATVHPACQI FPHYTPSVAY PWSPEAHPLI CGPPGLDKRL LPETPGPCYS
NSQPVWLCLT PRQPLEPHPP GEGPSEWSSD TAEGRPCPYP HCQVLSAQPG SEEELEELCE
QAV*
speed 1.16 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