mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 1.62542594401097e-12 (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)

chr1:222886119A>GN/A show variant in all transcripts IGV

HGNC symbol

BROX

Ensembl transcript ID

ENST00000340934

Genbank transcript ID

NM_144695

UniProt peptide

Q5VW32

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.225A>G
g.225A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3811465

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1475	842	2317
ExAC	3344	1838	5182

regulatory features

H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK12ac, Histone, Histone 2B Lysine 12 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H2AZ, Histone, Histone 2A variant Z
SIX5, Transcription Factor, SIX5 Transcription Factor Binding
ATF3, Transcription Factor, ATF3 Transcription Factor Binding
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
USF1, Transcription Factor, USF1 Transcription Factor Binding
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K56ac, Histone, Histone 3 Lysine 56 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.266	0.994
	0.965	0.998
(flanking)	1.228	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -60) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	224	0.98	mu: GTAGCTGTCATGGCC	AGCT\|gtca

distance from splice site

166

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
21	23	HELIX		might get lost (downstream of altered splice site)
27	46	HELIX		might get lost (downstream of altered splice site)
54	68	HELIX		might get lost (downstream of altered splice site)
69	71	HELIX		might get lost (downstream of altered splice site)
75	81	STRAND		might get lost (downstream of altered splice site)
83	86	TURN		might get lost (downstream of altered splice site)
90	92	STRAND		might get lost (downstream of altered splice site)
90	408	DOMAIN	BRO1.	might get lost (downstream of altered splice site)
95	97	STRAND		might get lost (downstream of altered splice site)
102	105	STRAND		might get lost (downstream of altered splice site)
107	130	HELIX		might get lost (downstream of altered splice site)
137	160	HELIX		might get lost (downstream of altered splice site)
162	164	HELIX		might get lost (downstream of altered splice site)
173	176	STRAND		might get lost (downstream of altered splice site)
177	201	HELIX		might get lost (downstream of altered splice site)
206	227	HELIX		might get lost (downstream of altered splice site)
232	263	HELIX		might get lost (downstream of altered splice site)
267	292	HELIX		might get lost (downstream of altered splice site)
283	283	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
298	301	STRAND		might get lost (downstream of altered splice site)
303	305	HELIX		might get lost (downstream of altered splice site)
307	329	HELIX		might get lost (downstream of altered splice site)
335	335	CONFLICT	I -> T (in Ref. 1; BAF56045 and 2; BAB71331).	might get lost (downstream of altered splice site)
347	349	STRAND		might get lost (downstream of altered splice site)
367	371	HELIX		might get lost (downstream of altered splice site)
375	377	HELIX		might get lost (downstream of altered splice site)
408	408	LIPID	S-farnesyl cysteine.	might get lost (downstream of altered splice site)
408	408	MOD_RES	Cysteine methyl ester (Probable).	might get lost (downstream of altered splice site)
409	411	PROPEP	Removed in mature form (Probable). /FTId=PRO_0000396736.	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

407 / 407

chromosome

strand

last intron/exon boundary

1556

theoretical NMD boundary in CDS

1099

length of CDS

1236

coding sequence (CDS) position

N/A

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

225

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

225

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

222886119

original gDNA sequence snippet

GCACTACCGCCTCGGTAGCTATCATGGCCGCCGGGTCACGT

altered gDNA sequence snippet

GCACTACCGCCTCGGTAGCTGTCATGGCCGCCGGGTCACGT

original cDNA sequence snippet

GCACTACCGCCTCGGTAGCTATCATGGCCGCCGGGTCACGT

altered cDNA sequence snippet

GCACTACCGCCTCGGTAGCTGTCATGGCCGCCGGGTCACGT

wildtype AA sequence

MTHWFHRNPL KATAPVSFNY YGVVTGPSAS KICNDLRSSR ARLLELFTDL SCNPEMMKNA
ADSYFSLLQG FINSLDESTQ ESKLRYIQNF KWTDTLQGQV PSAQQDAVFE LISMGFNVAL
WYTKYASRLA GKENITEDEA KEVHRSLKIA AGIFKHLKES HLPKLITPAE KGRDLESRLI
EAYVIQCQAE AQEVTIARAI ELKHAPGLIA ALAYETANFY QKADHTLSSL EPAYSAKWRK
YLHLKMCFYT AYAYCYHGET LLASDKCGEA IRSLQEAEKL YAKAEALCKE YGETKGPGPT
VKPSGHLFFR KLGNLVKNTL EKCQRENGFI YFQKIPTEAP QLELKANYGL VEPIPFEFPP
TSVQWTPETL AAFDLTKRPK DDSTKPKPEE EVKPVKEPDI KPQKDTGCYI S*

mutated AA sequence

N/A

speed

0.78 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