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 CM031666)
known disease mutation: rs8790 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:47256859G>TN/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

3'UTR

DNA changes

cDNA.936G>T
g.20367G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434642
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8790 (pathogenic for Xeroderma pigmentosum, group E) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031666)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031666)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031666)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.847	0.064
	6.262	1
(flanking)	5.171	1

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

splice sites

splice site change occurs after stopcodon (at aa 246) splice site change occurs after stopcodon (at aa 248)

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	20365	wt: 0.20 / mu: 0.44	wt: TGGAGCCCGGCTCCTGACCACGGACCAGAAGAGCGAGATCC mu: TGGAGCCCGGCTCCTGACCACGTACCAGAAGAGCGAGATCC	ccac\|GGAC
Donor increased	20360	wt: 0.31 / mu: 0.92	wt: CTCCTGACCACGGAC mu: CTCCTGACCACGTAC	CCTG\|acca
Acc gained	20371	0.53	mu: CCGGCTCCTGACCACGTACCAGAAGAGCGAGATCCGAGTTT	acca\|GAAG

distance from splice site

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

signal is predicted to be ok

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)

936

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

20367

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

47256859

original gDNA sequence snippet

GAGCCCGGCTCCTGACCACGGACCAGAAGAGCGAGATCCGA

altered gDNA sequence snippet

GAGCCCGGCTCCTGACCACGTACCAGAAGAGCGAGATCCGA

original cDNA sequence snippet

GAGCCCGGCTCCTGACCACGGACCAGAAGAGCGAGATCCGA

altered cDNA sequence snippet

GAGCCCGGCTCCTGACCACGTACCAGAAGAGCGAGATCCGA

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

1.04 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