Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.992634292865322 (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
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:56492800T>CN/A show variant in all transcripts   IGV
HGNC symbol RNF43
Ensembl transcript ID ENST00000500597
Genbank transcript ID N/A
UniProt peptide Q68DV7
alteration type single base exchange
alteration region CDS
DNA changes c.139A>G
cDNA.627A>G
g.2157A>G
AA changes I47V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 47
frameshift no
known variant Reference ID: rs3744093
databasehomozygous (C/C)heterozygousallele carriers
1000G41710381455
ExAC104901178722277
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8721
0.6170.997
(flanking)0.0810.995
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 increased2148wt: 0.9476 / mu: 0.9644 (marginal change - not scored)wt: CAGAACAGAAAGCTA
mu: CAGAACAGAAAGCTG		 GAAC|agaa
Donor marginally increased2160wt: 0.8707 / mu: 0.9096 (marginal change - not scored)wt: CTATTATCAGAGTGA
mu: CTGTTATCAGAGTGA		 ATTA|tcag
distance from splice site 114
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      47VESERSAEQKAIIRVIPLKMDPTG
mutated  all conserved    47VESERSAEQKAVIRVIPLKMDPT
Ptroglodytes  all identical  ENSPTRG00000034322  47VESERSAEQKAIIRVIPLKMDPT
Mmulatta  all identical  ENSMMUG00000007004  47VESERSAEQKAIIRVIPLKMDPT
Fcatus  all identical  ENSFCAG00000012267  47VESERSAEQKAIIRVIPLKMDPT
Mmusculus  all conserved  ENSMUSG00000034177  47VESERSAEQKAVIRVIPLKMDPT
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 
24197TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2229 / 2229
position (AA) of stopcodon in wt / mu AA sequence 743 / 743
position of stopcodon in wt / mu cDNA 2717 / 2717
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 489 / 489
chromosome 17
strand -1
last intron/exon boundary 2674
theoretical NMD boundary in CDS 2135
length of CDS 2229
coding sequence (CDS) position 139
cDNA position
(for ins/del: last normal base / first normal base)		 627
gDNA position
(for ins/del: last normal base / first normal base)		 2157
chromosomal position
(for ins/del: last normal base / first normal base)		 56492800
original gDNA sequence snippet GATCAGCAGAACAGAAAGCTATTATCAGAGTGATCCCCTTG
altered gDNA sequence snippet GATCAGCAGAACAGAAAGCTGTTATCAGAGTGATCCCCTTG
original cDNA sequence snippet GATCAGCAGAACAGAAAGCTATTATCAGAGTGATCCCCTTG
altered cDNA sequence snippet GATCAGCAGAACAGAAAGCTGTTATCAGAGTGATCCCCTTG
wildtype AA sequence MSGGHQLQLA ALWPWLLMAT LQAGFGRTGL VLAAAVESER SAEQKAIIRV IPLKMDPTGK
LNLTLEGVFA GVAEITPAEG KLMQARMAGE RGASAVLFDI TEDRAAAEQL QQPLGLTWPV
VLIWGNDAEK LMEFVYKNQK AHVRIELKEP PAWPDYDVWI LMTVVGTIFV IILASVLRIR
CRPRHSRPDP LQQRTAWAIS QLATRRYQAS CRQARGEWPD SGSSCSSAPV CAICLEEFSE
GQELRVISCL HEFHRNCVDP WLHQHRTCPL CMFNITEGDS FSQSLGPSRS YQEPGRRLHL
IRQHPGHAHY HLPAAYLLGP SRSAVARPPR PGPFLPSQEP GMGPRHHRFP RAAHPRAPGE
QQRLAGAQHP YAQGWGLSHL QSTSQHPAAC PVPLRRARPP DSSGSGESYC TERSGYLADG
PASDSSSGPC HGSSSDSVVN CTDISLQGVH GSSSTFCSSL SSDFDPLVYC SPKGDPQRVD
MQPSVTSRPR SLDSVVPTGE TQVSSHVHYH RHRHHHYKKR FQWHGRKPGP ETGVPQSRPP
IPRTQPQPEP PSPDQQVTRS NSAAPSGRLS NPQCPRALPE PAPGPVDASS ICPSTSSLFN
LQKSSLSARH PQRKRRGGPS EPTPGSRPQD ATVHPACQIF PHYTPSVAYP WSPEAHPLIC
GPPGLDKRLL PETPGPCYSN SQPVWLCLTP RQPLEPHPPG EGPSEWSSDT AEGRPCPYPH
CQVLSAQPGS EEELEELCEQ AV*
mutated AA sequence MSGGHQLQLA ALWPWLLMAT LQAGFGRTGL VLAAAVESER SAEQKAVIRV IPLKMDPTGK
LNLTLEGVFA GVAEITPAEG KLMQARMAGE RGASAVLFDI TEDRAAAEQL QQPLGLTWPV
VLIWGNDAEK LMEFVYKNQK AHVRIELKEP PAWPDYDVWI LMTVVGTIFV IILASVLRIR
CRPRHSRPDP LQQRTAWAIS QLATRRYQAS CRQARGEWPD SGSSCSSAPV CAICLEEFSE
GQELRVISCL HEFHRNCVDP WLHQHRTCPL CMFNITEGDS FSQSLGPSRS YQEPGRRLHL
IRQHPGHAHY HLPAAYLLGP SRSAVARPPR PGPFLPSQEP GMGPRHHRFP RAAHPRAPGE
QQRLAGAQHP YAQGWGLSHL QSTSQHPAAC PVPLRRARPP DSSGSGESYC TERSGYLADG
PASDSSSGPC HGSSSDSVVN CTDISLQGVH GSSSTFCSSL SSDFDPLVYC SPKGDPQRVD
MQPSVTSRPR SLDSVVPTGE TQVSSHVHYH RHRHHHYKKR FQWHGRKPGP ETGVPQSRPP
IPRTQPQPEP PSPDQQVTRS NSAAPSGRLS NPQCPRALPE PAPGPVDASS ICPSTSSLFN
LQKSSLSARH PQRKRRGGPS EPTPGSRPQD ATVHPACQIF PHYTPSVAYP WSPEAHPLIC
GPPGLDKRLL PETPGPCYSN SQPVWLCLTP RQPLEPHPPG EGPSEWSSDT AEGRPCPYPH
CQVLSAQPGS EEELEELCEQ AV*
speed 0.94 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