mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM960485)
known disease mutation: rs8788 (pathogenic)

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

ENST00000378601

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.19931G>A

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

Reference ID: rs121434640

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

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

	PhyloP	PhastCons
(flanking)	2.874	1
	4.531	1
(flanking)	1.33	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	19936	wt: 0.4054 / mu: 0.4390 (marginal change - not scored)	wt: GCCAGGTTAGAGGGA mu: ACCAGGTTAGAGGGA	CAGG\|ttag
Donor marginally increased	19934	wt: 0.8419 / mu: 0.9148 (marginal change - not scored)	wt: GCGCCAGGTTAGAGG mu: GCACCAGGTTAGAGG	GCCA\|ggtt

distance from splice site

200

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

position (AA) of stopcodon in wt / mu AA sequence

N/A

position of stopcodon in wt / mu cDNA

N/A

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

strand

last intron/exon boundary

1252

theoretical NMD boundary in CDS

1006

length of CDS

735

coding sequence (CDS) position

N/A

cDNA position
(for ins/del: last normal base / first normal base)

N/A

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

N/A

altered cDNA sequence snippet

N/A

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 DGKELVSVPM
EPGS*

mutated AA sequence

N/A

speed

0.73 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