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 CD031829)
known disease mutation at this position (HGMD CM960484)
known disease mutation: rs8787 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:47256335A>GN/A show variant in all transcripts IGV

HGNC symbol

DDB2

Ensembl transcript ID

ENST00000378601

Genbank transcript ID

N/A

UniProt peptide

Q92466

alteration type

single base exchange

alteration region

intron

DNA changes

g.19843A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434639
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8787 (pathogenic for Xeroderma pigmentosum, group E) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CD031829)

known disease mutation at this position, please check HGMD for details (HGMD ID CD031829)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960484)

known disease mutation at this position, please check HGMD for details (HGMD ID CD031829)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960484)
known disease mutation at this position, please check HGMD for details (HGMD ID CD031829)

known disease mutation at this position, please check HGMD for details (HGMD ID CD031829)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960484)
known disease mutation at this position, please check HGMD for details (HGMD ID CD031829)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960484)

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
H3K4me2, Histone, Histone 3 Lysine 4 Di-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)	4.026	1
	5.054	1
(flanking)	3.502	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 gained	19842	0.88	mu: AAAAAGGAAGTGACG	AAAG\|gaag
Donor gained	19837	0.60	mu: TGCACAAAAAGGAAG	CACA\|aaaa

distance from splice site

112

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
240	280	REPEAT	WD 3.	might get lost (downstream of altered splice site)
241	243	STRAND		might get lost (downstream of altered splice site)
245	250	STRAND		might get lost (downstream of altered splice site)
255	262	STRAND		might get lost (downstream of altered splice site)
256	274	MOTIF	DWD box.	might get lost (downstream of altered splice site)
258	258	MUTAGEN	L->A: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
262	262	MUTAGEN	S->A: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
264	264	MUTAGEN	D->A: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
269	269	MUTAGEN	I->A: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
269	271	STRAND		might get lost (downstream of altered splice site)
270	270	MUTAGEN	W->A: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
272	272	MUTAGEN	L->A: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
272	274	TURN		might get lost (downstream of altered splice site)
273	273	MUTAGEN	R->A: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
277	279	STRAND		might get lost (downstream of altered splice site)
278	278	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
282	286	STRAND		might get lost (downstream of altered splice site)
286	325	REPEAT	WD 4.	might get lost (downstream of altered splice site)
291	293	STRAND		might get lost (downstream of altered splice site)
300	310	STRAND		might get lost (downstream of altered splice site)
312	326	STRAND		might get lost (downstream of altered splice site)
335	337	STRAND		might get lost (downstream of altered splice site)
346	349	STRAND		might get lost (downstream of altered splice site)
350	350	MUTAGEN	L->P: Impairs interaction with DDB1.	might get lost (downstream of altered splice site)
351	354	STRAND		might get lost (downstream of altered splice site)
364	366	STRAND		might get lost (downstream of altered splice site)
372	375	STRAND		might get lost (downstream of altered splice site)
377	379	STRAND		might get lost (downstream of altered splice site)
382	386	STRAND		might get lost (downstream of altered splice site)
389	391	TURN		might get lost (downstream of altered splice site)
389	426	REPEAT	WD 5.	might get lost (downstream of altered splice site)
397	400	STRAND		might get lost (downstream of altered splice site)
407	410	STRAND		might get lost (downstream of altered splice site)
412	417	STRAND		might get lost (downstream of altered splice site)

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)

19843

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

47256335

original gDNA sequence snippet

ATCTCAGAATGCACAAAAAGAAAGTGACGCATGTGGCCCTG

altered gDNA sequence snippet

ATCTCAGAATGCACAAAAAGGAAGTGACGCATGTGGCCCTG

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

0.62 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