Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999147 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM962694)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:160113872A>GN/A show variant in all transcripts   IGV
HGNC symbol SOD2
Ensembl transcript ID ENST00000452684
Genbank transcript ID N/A
UniProt peptide P04179
alteration type single base exchange
alteration region CDS
DNA changes c.47T>C
cDNA.124T>C
g.69690T>C
AA changes V16A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 16
frameshift no
known variant Reference ID: rs4880
databasehomozygous (G/G)heterozygousallele carriers
1000G48810811569
ExAC13790518718977

known disease mutation at this position, please check HGMD for details (HGMD ID CM962694)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Cmyc, Transcription Factor, Cmyc TF binding
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.6350.046
1.1370.055
(flanking)1.7830.036
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      16AVCGTSRQLAPVLGYLGSRQKHSL
mutated  not conserved    16AVCGTSRQLAPALGYLGSRQKHS
Ptroglodytes  not conserved  ENSPTRG00000018757  16AVCGTSRQLAPALGYLGSRQKHS
Mmulatta  no alignment  ENSMMUG00000005885  n/a
Fcatus  not conserved  ENSFCAG00000002843  8SSRTLVPALGALGSRQKHS
Mmusculus  all identical  ENSMUSG00000006818  16AACSTGRRLGPVAGAAGSRHKHS
Ggallus  not conserved  ENSGALG00000011661  16ASAGRSRAALVAPLGCLVARQKHT
Trubripes  no alignment  ENSTRUG00000005242  n/a
Drerio  all conserved  ENSDARG00000042644  18PLLGAVTSRQKHA
Dmelanogaster  no alignment  FBgn0010213  n/a
Celegans  all identical  C08A9.1  16TARTASKLVQPVAGVLAVRSKHT
Xtropicalis  not conserved  ENSXETG00000021180  16SVCGRGRLRCAPALTYFTSREKHT
protein features
start (aa)end (aa)featuredetails 
124TRANSITMitochondrion.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 423 / 423
position (AA) of stopcodon in wt / mu AA sequence 141 / 141
position of stopcodon in wt / mu cDNA 500 / 500
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 78 / 78
chromosome 6
strand -1
last intron/exon boundary 101
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 423
coding sequence (CDS) position 47
cDNA position
(for ins/del: last normal base / first normal base)		 124
gDNA position
(for ins/del: last normal base / first normal base)		 69690
chromosomal position
(for ins/del: last normal base / first normal base)		 160113872
original gDNA sequence snippet CAGCAGGCAGCTGGCTCCGGTTTTGGGGTATCTGGGCTCCA
altered gDNA sequence snippet CAGCAGGCAGCTGGCTCCGGCTTTGGGGTATCTGGGCTCCA
original cDNA sequence snippet CAGCAGGCAGCTGGCTCCGGTTTTGGGGTATCTGGGCTCCA
altered cDNA sequence snippet CAGCAGGCAGCTGGCTCCGGCTTTGGGGTATCTGGGCTCCA
wildtype AA sequence MLSRAVCGTS RQLAPVLGYL GSRQKHSLPD LPYDYGALEP HINAQIMQLH HSKHHAAYVN
NLNVTEEKYQ EALAKGRFQA ERREAVPGRG DPREPGPIRT GLSVEENSLR ICTGSEFSRH
DSLSFKHMVY LIVEGVPRWV *
mutated AA sequence MLSRAVCGTS RQLAPALGYL GSRQKHSLPD LPYDYGALEP HINAQIMQLH HSKHHAAYVN
NLNVTEEKYQ EALAKGRFQA ERREAVPGRG DPREPGPIRT GLSVEENSLR ICTGSEFSRH
DSLSFKHMVY LIVEGVPRWV *
speed 0.77 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