Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999974251918 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960485)
  • known disease mutation: rs8788 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:47256423G>AN/A show variant in all transcripts   IGV
HGNC symbol DDB2
Ensembl transcript ID ENST00000256996
Genbank transcript ID NM_000107
UniProt peptide Q92466
alteration type single base exchange
alteration region CDS
DNA changes c.818G>A
cDNA.1013G>A
g.19931G>A
AA changes R273H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 273
frameshift no
known variant Reference ID: rs121434640
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs8788 (pathogenic for Xeroderma pigmentosum, group E) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960485)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960485)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960485)
regulatory features CBP, Transcription Factor, CBP Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8741
4.5311
(flanking)1.331
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 increased19936wt: 0.4054 / mu: 0.4390 (marginal change - not scored)wt: GCCAGGTTAGAGGGA
mu: ACCAGGTTAGAGGGA		 CAGG|ttag
Donor marginally increased19934wt: 0.8419 / mu: 0.9148 (marginal change - not scored)wt: GCGCCAGGTTAGAGG
mu: GCACCAGGTTAGAGG		 GCCA|ggtt
distance from splice site 63
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      273SVDQTVKIWDLRQVRGKASFLYSL
mutated  not conserved    273SVDQTVKIWDLHQVRGKASFLYS
Ptroglodytes  all identical  ENSPTRG00000003558  273SVDQTVKIWDLRQVRGKASFLYS
Mmulatta  all identical  ENSMMUG00000022964  273SVDQTVKIWDLRQVRGKASFLYS
Fcatus  all identical  ENSFCAG00000002526  273SVDQTVKIWDLRQVKGKSSCLHS
Mmusculus  all identical  ENSMUSG00000002109  273SIDQTVKIWDLRQIKGKDSFLYS
Ggallus  all identical  ENSGALG00000008218  293SVDQTVKIWDLRNI
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000041140  282SVDATVKLWDLRNIKDKNSYIAE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003980  282SVDQTVKLWDLRNIKDKSSYLYT
protein features
start (aa)end (aa)featuredetails 
240280REPEATWD 3.lost
256274MOTIFDWD box.lost
272274TURNlost
273273MUTAGENR->A: Impairs interaction with DDB1.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1284 / 1284
position (AA) of stopcodon in wt / mu AA sequence 428 / 428
position of stopcodon in wt / mu cDNA 1479 / 1479
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 196 / 196
chromosome 11
strand 1
last intron/exon boundary 1430
theoretical NMD boundary in CDS 1184
length of CDS 1284
coding sequence (CDS) position 818
cDNA position
(for ins/del: last normal base / first normal base)		 1013
gDNA position
(for ins/del: last normal base / first normal base)		 19931
chromosomal position
(for ins/del: last normal base / first normal base)		 47256423
original gDNA sequence snippet AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA
altered gDNA sequence snippet AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA
original cDNA sequence snippet AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA
altered cDNA sequence snippet AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA
wildtype AA sequence MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP
QILPPCRSIV RTLHQHKLGR ASWPSVQQGL QQSFLHTLDS YRILQKAAPF DRRATSLAWH
PTHPSTVAVG SKGGDIMLWN FGIKDKPTFI KGIGAGGSIT GLKFNPLNTN QFYASSMEGT
TRLQDFKGNI LRVFASSDTI NIWFCSLDVS ASSRMVVTGD NVGNVILLNM DGKELWNLRM
HKKKVTHVAL NPCCDWFLAT ASVDQTVKIW DLRQVRGKAS FLYSLPHRHP VNAACFSPDG
ARLLTTDQKS EIRVYSASQW DCPLGLIPHP HRHFQHLTPI KAAWHPRYNL IVVGRYPDPN
FKSCTPYELR TIDVFDGNSG KMMCQLYDPE SSGISSLNEF NPMGDTLASA MGYHILIWSQ
EEARTRK*
mutated AA sequence MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP
QILPPCRSIV RTLHQHKLGR ASWPSVQQGL QQSFLHTLDS YRILQKAAPF DRRATSLAWH
PTHPSTVAVG SKGGDIMLWN FGIKDKPTFI KGIGAGGSIT GLKFNPLNTN QFYASSMEGT
TRLQDFKGNI LRVFASSDTI NIWFCSLDVS ASSRMVVTGD NVGNVILLNM DGKELWNLRM
HKKKVTHVAL NPCCDWFLAT ASVDQTVKIW DLHQVRGKAS FLYSLPHRHP VNAACFSPDG
ARLLTTDQKS EIRVYSASQW DCPLGLIPHP HRHFQHLTPI KAAWHPRYNL IVVGRYPDPN
FKSCTPYELR TIDVFDGNSG KMMCQLYDPE SSGISSLNEF NPMGDTLASA MGYHILIWSQ
EEARTRK*
speed 1.30 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