mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999864489154 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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

ENST00000256996

Genbank transcript ID

NM_000107

UniProt peptide

Q92466

alteration type

single base exchange

alteration region

CDS

DNA changes

c.730A>G
cDNA.925A>G
g.19843A>G

AA changes

K244E Score: 56 explain score(s)

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

244

frameshift

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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

244

mutated

all conserved

244

Ptroglodytes

all identical

ENSPTRG00000003558

244

Mmulatta

all identical

ENSMMUG00000022964

244

Fcatus

all identical

ENSFCAG00000002526

244

Mmusculus

all identical

ENSMUSG00000002109

244

Ggallus

all identical

ENSGALG00000008218

264

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041140

253

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003980

253

protein features

start (aa)	end (aa)	feature	details
240	280	REPEAT	WD 3.	lost
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

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

strand

last intron/exon boundary

1430

theoretical NMD boundary in CDS

1184

length of CDS

1284

coding sequence (CDS) position

730

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

925

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

ATCTCAGAATGCACAAAAAGAAAGTGACGCATGTGGCCCTG

altered cDNA sequence snippet

ATCTCAGAATGCACAAAAAGGAAGTGACGCATGTGGCCCTG

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
HKKEVTHVAL NPCCDWFLAT ASVDQTVKIW DLRQVRGKAS FLYSLPHRHP VNAACFSPDG
ARLLTTDQKS EIRVYSASQW DCPLGLIPHP HRHFQHLTPI KAAWHPRYNL IVVGRYPDPN
FKSCTPYELR TIDVFDGNSG KMMCQLYDPE SSGISSLNEF NPMGDTLASA MGYHILIWSQ
EEARTRK*

speed

1.28 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