mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM063956)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:11986061T>CN/A show variant in all transcripts IGV

HGNC symbol

DKK3

Ensembl transcript ID

ENST00000450094

Genbank transcript ID

N/A

UniProt peptide

Q9UBP4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.919A>G
cDNA.920A>G
g.45256A>G

AA changes

R307G Score: 125 explain score(s)

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

307

frameshift

known variant

Reference ID: rs3206824

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1655	757	2412
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM063956)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.042	0.042
	-0.82	0
(flanking)	-0.691	0

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 increased	45255	wt: 0.45 / mu: 0.70	wt: GCGCTGAGGGAGCCT mu: GCGCTGGGGGAGCCT	GCTG\|aggg

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

not conserved

ENSPTRG00000003368

335

Mmulatta

not conserved

ENSMMUG00000022862

335

Fcatus

not conserved

ENSFCAG00000000925

269

Mmusculus

not conserved

ENSMUSG00000030772

335

Ggallus

all conserved

ENSGALG00000005551

335

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077630

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
338	343	COMPBIAS	Poly-Ala.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

969 / 969

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

323 / 323

position of stopcodon in wt / mu cDNA

970 / 970

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

2 / 2

chromosome

strand

-1

last intron/exon boundary

748

theoretical NMD boundary in CDS

696

length of CDS

969

coding sequence (CDS) position

919

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

920

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

45256

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

11986061

original gDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered gDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

original cDNA sequence snippet

TGACTGAAGAGATGGCGCTGAGGGAGCCTGCGGCTGCCGCC

altered cDNA sequence snippet

TGACTGAAGAGATGGCGCTGGGGGAGCCTGCGGCTGCCGCC

wildtype AA sequence

MQRLGATLLC LLLAAAVPTA PAPAPTATSA PVKPGPALSY PQEEATLNEM FREVEELMED
TQHKLRSAVE EMEAEEAAAK ASSEVNLANL PPSYHNETNT DTKVGNNTIH VHREIHKECI
IDEDCGPSMY CQFASFQYTC QPCRGQRMLC TRDSECCGDQ LCVWGHCTKM ATRGSNGTIC
DNQRDCQPGL CCAFQRGLLF PVCTPLPVEG ELCHDPASRL LDLITWELEP DGALDRCPCA
SGLLCQPHSH SLVYVCKPTF VGSRDQDGEI LLPREVPDEY EVGSFMEEVR QELEDLERSL
TEEMALREPA AAAAALLGGE EI*

mutated AA sequence

speed

0.52 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