mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 3.21222635679473e-13 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:56492800T>CN/A show variant in all transcripts IGV

HGNC symbol

RNF43

Ensembl transcript ID

ENST00000581868

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.2157A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3744093

database	homozygous (C/C)	heterozygous	allele carriers
1000G	417	1038	1455
ExAC	10490	11787	22277

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.872	1
	0.617	0.997
(flanking)	0.081	0.995

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 marginally increased	2148	wt: 0.9476 / mu: 0.9644 (marginal change - not scored)	wt: CAGAACAGAAAGCTA mu: CAGAACAGAAAGCTG	GAAC\|agaa
Donor marginally increased	2160	wt: 0.8707 / mu: 0.9096 (marginal change - not scored)	wt: CTATTATCAGAGTGA mu: CTGTTATCAGAGTGA	ATTA\|tcag

distance from splice site

1578

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

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

199 / 199

chromosome

strand

-1

last intron/exon boundary

770

theoretical NMD boundary in CDS

521

length of CDS

2229

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)

2157

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

56492800

original gDNA sequence snippet

GATCAGCAGAACAGAAAGCTATTATCAGAGTGATCCCCTTG

altered gDNA sequence snippet

GATCAGCAGAACAGAAAGCTGTTATCAGAGTGATCCCCTTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAGERGASAV LFDITEDRAA AEQLQQPLGL TWPVVLIWGN DAEKLMEFVY KNQKAHVRIE
LKEPPAWPDY DVWILMTVVG TIFVIILASV LRIRCRPRHS RPDPLQQRTA WAISQLATRR
YQASCRQARG EWPDSGSSCS SAPVCAICLE EFSEGQELRV ISCLHEFHRN CVDPWLHQHR
TCPLCMFNIT EGDSFSQSLG PSRSYQEPGR RLHLIRQHPG HAHYHLPAAY LLGPSRSAVA
RPPRPGPFLP SQEPGMGPRH HRFPRAAHPR APGEQQRLAG AQHPYAQGWG LSHLQSTSQH
PAACPVPLRR ARPPDSSGSG ESYCTERSGY LADGPASDSS SGPCHGSSSD SVVNCTDISL
QGVHGSSSTF CSSLSSDFDP LVYCSPKGDP QRVDMQPSVT SRPRSLDSVV PTGETQVSSH
VHYHRHRHHH YKKRFQWHGR KPGPETGVPQ SRPPIPRTQP QPEPPSPDQQ VTRSNSAAPS
GRLSNPQCPR ALPEPAPGPV DASSICPSTS SLFNLQKSSL SARHPQRKRR GGPSEPTPGS
RPQDATVHPA CQIFPHYTPS VAYPWSPEAH PLICGPPGLD KRLLPETPGP CYSNSQPVWL
CLTPRQPLEP HPPGEGPSEW SSDTAEGRPC PYPHCQVLSA QPGEFSEGSG CGRERRLQLN
ISGQVKSANK GLMEAEKDTA EMTTKILNHR DSVSCWLECR NTPPLPGATP LVGRSQGGPR
EVLVWLRHQK GTWKAGCDGS CL*

mutated AA sequence

N/A

speed

0.75 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