mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.99999999998425 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM031666)
known disease mutation: rs8790 (pathogenic)
protein features (might be) affected
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

ENST00000256996

Genbank transcript ID

NM_000107

UniProt peptide

Q92466

alteration type

single base exchange

alteration region

CDS

DNA changes

c.919G>T
cDNA.1114G>T
g.20367G>T

AA changes

D307Y Score: 160 explain score(s)

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

307

frameshift

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

effect	gDNA position	score	wt 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

species

match

gene

alignment

Human

307

mutated

not conserved

307

Ptroglodytes

all identical

ENSPTRG00000003558

307

Mmulatta

all identical

ENSMMUG00000022964

307

Fcatus

all identical

ENSFCAG00000002526

307

Mmusculus

all identical

ENSMUSG00000002109

307

Ggallus

all identical

ENSGALG00000008218

327

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041140

314

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003980

317

protein features

start (aa)	end (aa)	feature	details
286	325	REPEAT	WD 4.	lost
300	310	STRAND		lost
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

919

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

1114

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 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 DLRQVRGKAS FLYSLPHRHP VNAACFSPDG
ARLLTTYQKS EIRVYSASQW DCPLGLIPHP HRHFQHLTPI KAAWHPRYNL IVVGRYPDPN
FKSCTPYELR TIDVFDGNSG KMMCQLYDPE SSGISSLNEF NPMGDTLASA MGYHILIWSQ
EEARTRK*

speed

0.55 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