mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999996347895 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:56435885G>TN/A show variant in all transcripts IGV

HGNC symbol

RNF43

Ensembl transcript ID

ENST00000581868

Genbank transcript ID

N/A

UniProt peptide

Q68DV7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.871C>A
cDNA.1069C>A
g.59072C>A

AA changes

L291M Score: 15 explain score(s)

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

291

frameshift

known variant

Reference ID: rs2526374

database	homozygous (T/T)	heterozygous	allele carriers
1000G	415	1171	1586
ExAC	9443	13881	23324

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.116	0.012
	2.132	0.069
(flanking)	-0.79	0.065

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	59075	wt: 0.9892 / mu: 0.9934 (marginal change - not scored)	wt: GACTGAGCCACCTCC mu: GAATGAGCCACCTCC	CTGA\|gcca
Donor gained	59067	0.38	mu: AGGCTGGGGAATGAG	GCTG\|ggga
Donor gained	59068	0.40	mu: GGCTGGGGAATGAGC	CTGG\|ggaa

distance from splice site

300

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

291

mutated

all conserved

291

Ptroglodytes

all identical

ENSPTRG00000034322

418

Mmulatta

all identical

ENSMMUG00000007004

420

Fcatus

all identical

ENSFCAG00000012267

418

Mmusculus

all identical

ENSMUSG00000034177

418

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no alignment

Y47D3B.11

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
219	783	TOPO_DOM	Cytoplasmic (Potential).	lost
272	313	ZN_FING	RING-type; atypical.	lost
290	290	MUTAGEN	C->S: Dominant-negative mutant, loss of E3 ligase activity and activation of the Wnt signaling pathway; when associated with S-292.	might get lost (downstream of altered splice site)
292	292	MUTAGEN	H->S: Dominant-negative mutant, loss of E3 ligase activity and activation of the Wnt signaling pathway; when associated with S-290.	might get lost (downstream of altered splice site)
295	295	MUTAGEN	H->S: Dominant-negative mutant, loss of E3 ligase activity and activation of the Wnt signaling pathway; when associated with S-298.	might get lost (downstream of altered splice site)
298	298	MUTAGEN	C->S: Dominant-negative mutant, loss of E3 ligase activity and activation of the Wnt signaling pathway; when associated with S-295.	might get lost (downstream of altered splice site)
313	313	CONFLICT	M -> V (in Ref. 1; BAD51435 and 2; BAA91085).	might get lost (downstream of altered splice site)
401	401	CONFLICT	E -> K (in Ref. 2; BAH12429).	might get lost (downstream of altered splice site)
443	503	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
547	557	COMPBIAS	His-rich.	might get lost (downstream of altered splice site)
569	760	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
600	600	CONFLICT	R -> G (in Ref. 1; BAD51435 and 2; BAA91085).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2229 / 2229

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

743 / 743

position of stopcodon in wt / mu cDNA

2427 / 2427

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

871

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

1069

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

59072

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

56435885

original gDNA sequence snippet

CCTATGCACAAGGCTGGGGACTGAGCCACCTCCAATCCACC

altered gDNA sequence snippet

CCTATGCACAAGGCTGGGGAATGAGCCACCTCCAATCCACC

original cDNA sequence snippet

CCTATGCACAAGGCTGGGGACTGAGCCACCTCCAATCCACC

altered cDNA sequence snippet

CCTATGCACAAGGCTGGGGAATGAGCCACCTCCAATCCACC

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

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 MSHLQSTSQH
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*

speed

0.35 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