Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.523570653919951 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:74725178G>AN/A show variant in all transcripts   IGV
HGNC symbol LBX2
Ensembl transcript ID ENST00000460508
Genbank transcript ID NM_001009812
UniProt peptide Q6XYB7
alteration type single base exchange
alteration region CDS
DNA changes c.461C>T
cDNA.2667C>T
g.7015C>T
AA changes S154F Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 154
frameshift no
known variant Reference ID: rs17009998
databasehomozygous (A/A)heterozygousallele carriers
1000G4517661217
ExAC48041627221076
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.560.629
1.1570.681
(flanking)-0.1090.687
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased7019wt: 0.26 / mu: 0.37wt: TCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCTTAGC
mu: TCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCTTAGC		 cccg|GAAG
Acc marginally increased7018wt: 0.2809 / mu: 0.3237 (marginal change - not scored)wt: CTCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCTTAG
mu: CTCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCTTAG		 cccc|GGAA
Acc marginally increased7020wt: 0.4759 / mu: 0.5471 (marginal change - not scored)wt: CGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCTTAGCA
mu: CGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCTTAGCA		 ccgg|AAGT
Donor marginally increased7017wt: 0.9905 / mu: 0.9929 (marginal change - not scored)wt: TGTCCCCGGAAGTCC
mu: TGTTCCCGGAAGTCC		 TCCC|cgga
distance from splice site 268
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      154MRADVASLRALSPEVLCSLALPEG
mutated  not conserved    154MRADVASLRALFPEVLCSLALPE
Ptroglodytes  all identical  ENSPTRG00000012092  158MRADVASLRALSPEVLCSLALPE
Mmulatta  all identical  ENSMMUG00000002125  158MRADVASLRALSPEVLCSLALPD
Fcatus  all identical  ENSFCAG00000007155  158MRADVASLRTLSPEVQCRLSLPD
Mmusculus  all identical  ENSMUSG00000034968  157MRADVASLCGLSPGVLCYPALPDST
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0011278  426LKKDFDSVKVFS
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 585 / 585
position (AA) of stopcodon in wt / mu AA sequence 195 / 195
position of stopcodon in wt / mu cDNA 2791 / 2791
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 2207 / 2207
chromosome 2
strand -1
last intron/exon boundary 2400
theoretical NMD boundary in CDS 143
length of CDS 585
coding sequence (CDS) position 461
cDNA position
(for ins/del: last normal base / first normal base)		 2667
gDNA position
(for ins/del: last normal base / first normal base)		 7015
chromosomal position
(for ins/del: last normal base / first normal base)		 74725178
original gDNA sequence snippet CGCCTCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCT
altered gDNA sequence snippet CGCCTCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCT
original cDNA sequence snippet CGCCTCGCTACGCGCGTTGTCCCCGGAAGTCCTGTGCAGCT
altered cDNA sequence snippet CGCCTCGCTACGCGCGTTGTTCCCGGAAGTCCTGTGCAGCT
wildtype AA sequence MGKRTSLEVS LGELGGEKCR GGRRSFPPLA ASRPARPGGW RWARRDLCKT ASRAENNSQA
CRPQRRAGPD ALGPGPFGRK RRKSRTAFTA QQVLELERRF VFQKYLAPSE RDGLATRLGL
ANAQVVTWFQ NRRAKLKRDV EEMRADVASL RALSPEVLCS LALPEGAPDP GLCLGPAGPD
SRPHLSDEEI QVDD*
mutated AA sequence MGKRTSLEVS LGELGGEKCR GGRRSFPPLA ASRPARPGGW RWARRDLCKT ASRAENNSQA
CRPQRRAGPD ALGPGPFGRK RRKSRTAFTA QQVLELERRF VFQKYLAPSE RDGLATRLGL
ANAQVVTWFQ NRRAKLKRDV EEMRADVASL RALFPEVLCS LALPEGAPDP GLCLGPAGPD
SRPHLSDEEI QVDD*
speed 0.15 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