mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999968788876569 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr17:39890715A>TN/A show variant in all transcripts IGV

HGNC symbol

JUP

Ensembl transcript ID

ENST00000540235

Genbank transcript ID

N/A

UniProt peptide

P14923

alteration type

single base exchange

alteration region

intron

DNA changes

g.52469T>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs4796603

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1570	716	2286
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
TAF7, Transcription Factor, TAF7 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.112	0.003
	0.79	0.003
(flanking)	-0.186	0.002

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	52468	wt: 0.20 / mu: 0.31	wt: TCTGGATCCCAGTTC mu: TCTGGAACCCAGTTC	TGGA\|tccc

distance from splice site

32916

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
300	308	HELIX		might get lost (downstream of altered splice site)
311	321	HELIX		might get lost (downstream of altered splice site)
325	338	HELIX		might get lost (downstream of altered splice site)
342	381	REPEAT	ARM 4.	might get lost (downstream of altered splice site)
344	350	HELIX		might get lost (downstream of altered splice site)
353	358	HELIX		might get lost (downstream of altered splice site)
359	362	HELIX		might get lost (downstream of altered splice site)
366	380	HELIX		might get lost (downstream of altered splice site)
383	420	REPEAT	ARM 5.	might get lost (downstream of altered splice site)
390	397	HELIX		might get lost (downstream of altered splice site)
398	401	TURN		might get lost (downstream of altered splice site)
405	418	HELIX		might get lost (downstream of altered splice site)
419	421	TURN		might get lost (downstream of altered splice site)
423	429	HELIX		might get lost (downstream of altered splice site)
423	464	REPEAT	ARM 6.	might get lost (downstream of altered splice site)
430	433	TURN		might get lost (downstream of altered splice site)
434	445	HELIX		might get lost (downstream of altered splice site)
449	462	HELIX		might get lost (downstream of altered splice site)
464	466	STRAND		might get lost (downstream of altered splice site)
469	477	HELIX		might get lost (downstream of altered splice site)
470	510	REPEAT	ARM 7.	might get lost (downstream of altered splice site)
478	480	TURN		might get lost (downstream of altered splice site)
481	487	HELIX		might get lost (downstream of altered splice site)
488	490	HELIX		might get lost (downstream of altered splice site)
495	508	HELIX		might get lost (downstream of altered splice site)
512	514	HELIX		might get lost (downstream of altered splice site)
512	551	REPEAT	ARM 8.	might get lost (downstream of altered splice site)
515	520	HELIX		might get lost (downstream of altered splice site)
523	543	HELIX		might get lost (downstream of altered splice site)
556	570	HELIX		might get lost (downstream of altered splice site)
574	582	HELIX		might get lost (downstream of altered splice site)
574	613	REPEAT	ARM 9.	might get lost (downstream of altered splice site)
586	592	HELIX		might get lost (downstream of altered splice site)
598	611	HELIX		might get lost (downstream of altered splice site)
615	623	HELIX		might get lost (downstream of altered splice site)
624	626	TURN		might get lost (downstream of altered splice site)
627	633	HELIX		might get lost (downstream of altered splice site)
639	651	HELIX		might get lost (downstream of altered splice site)
660	660	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
662	667	HELIX		might get lost (downstream of altered splice site)
665	665	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

1682

theoretical NMD boundary in CDS

1631

length of CDS

1776

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)

52469

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

39890715

original gDNA sequence snippet

GATCCCGAGCCACCTCTGGATCCCAGTTCCTCTCGGAAGCC

altered gDNA sequence snippet

GATCCCGAGCCACCTCTGGAACCCAGTTCCTCTCGGAAGCC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEVMNLMEQP IKVTEWQQTY TYDSGIHSGA NTCVPSVSSK GIMEEDEACG RQYTLKKTTT
YTQGVPPSQG DLEYQMSTTA RAKRVREAMC PGVSGEDSSL LLATQVEGQA TNLQRLAEPS
QLLKSAIVHL INYQDDAELA TRALPELTKL LNDEDPVVVT KAAMIVNQLS KKEASRRALM
GSPQLVAAVV RTMQNTSDLD TARCTTSILH NLSHHREGLL AIFKSGGIPA LVRMLSSPVE
SVLFYAITTL HNLLLYQEGA KMAVRLADGL QKMVPLLNKN NPKFLAITTD CLQLLAYGNQ
ESKILTATVD NANILLQIDN ARLAADDFRT KFETEQALRL SVEADINGLR RVLDELTLAR
ADLEMQIENL KEELAYLKKN HEEEMNALRG QVGGEINVEM DAAPGVDLSR ILNEMRDQYE
KMAEKNRKDA EDWFFSKTEE LNREVATNSE LVQSGKSEIS ELRRTMQALE IELQSQLSMK
ASLEGNLAET ENRYCVQLSQ IQGLIGSVEE QLAQLRCEME QQNQEYKILL DVKTRLEQEI
ATYRRLLEGE DAHLTQYKKE PVTTRQVRTI VEEVQDGKVI SSREQVHQTT R*

mutated AA sequence

N/A

speed

0.95 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