Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000541237
Querying Taster for transcript #2: ENST00000340934
MT speed 2.2 s - this script 6.064913 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AIDApolymorphism_automatic0.000872727326852951simple_aaeaffectedI2Tsingle base exchangers3811465show file
BROXpolymorphism_automatic0.999999999998375without_aaeaffectedsingle base exchangers3811465show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999127272673147 (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) chr1:222886119A>GN/A show variant in all transcripts   IGV
HGNC symbol AIDA
Ensembl transcript ID ENST00000541237
Genbank transcript ID N/A
UniProt peptide Q96BJ3
alteration type single base exchange
alteration region CDS
DNA changes c.5T>C
cDNA.408T>C
g.434T>C
AA changes I2T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
2
frameshift no
known variant Reference ID: rs3811465
databasehomozygous (G/G)heterozygousallele carriers
1000G14758422317
ExAC334418385182
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
PhyloPPhastCons
(flanking)0.2660.994
0.9650.998
(flanking)1.2281
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased435wt: 0.75 / mu: 0.87wt: ATGATAGCTACCGAG
mu: ATGACAGCTACCGAG
 GATA|gcta
Donor increased426wt: 0.66 / mu: 0.80wt: CCGGCGGCCATGATA
mu: CCGGCGGCCATGACA
 GGCG|gcca
distance from splice site 34
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      2 MIATEAVVRAAQGL
mutated  not conserved    2 MTATEAVVRAAQGLARHLQKEA
Ptroglodytes  no alignment  ENSPTRG00000002010  n/a
Mmulatta  no alignment  ENSMMUG00000015025  n/a
Fcatus  no alignment  ENSFCAG00000002260  n/a
Mmusculus  no alignment  ENSMUSG00000042901  n/a
Ggallus  no alignment  ENSGALG00000009426  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000014532  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000015034  n/a
protein features
start (aa)end (aa)featuredetails 
2762COILEDPotential.might get lost (downstream of altered splice site)
130130CONFLICTE -> G (in Ref. 1; BAB14281).might get lost (downstream of altered splice site)
144144MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
154221REGIONAxin-binding (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 849 / 849
position (AA) of stopcodon in wt / mu AA sequence 283 / 283
position of stopcodon in wt / mu cDNA 1252 / 1252
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 404 / 404
chromosome 1
strand -1
last intron/exon boundary 1156
theoretical NMD boundary in CDS 702
length of CDS 849
coding sequence (CDS) position 5
cDNA position
(for ins/del: last normal base / first normal base)
408
gDNA position
(for ins/del: last normal base / first normal base)
434
chromosomal position
(for ins/del: last normal base / first normal base)
222886119
original gDNA sequence snippet ACGTGACCCGGCGGCCATGATAGCTACCGAGGCGGTAGTGC
altered gDNA sequence snippet ACGTGACCCGGCGGCCATGACAGCTACCGAGGCGGTAGTGC
original cDNA sequence snippet ACGTGACCCGGCGGCCATGATAGCTACCGAGGCGGTAGTGC
altered cDNA sequence snippet ACGTGACCCGGCGGCCATGACAGCTACCGAGGCGGTAGTGC
wildtype AA sequence MIATEAVVRA AQGLARHLQK EAQAQHNNSE FTEEQKKTIG KIATCLELRS AALQSTQSQE
EFKLEDLKKL EPILKNILTY NKEFPFDVQP VPLRRILAPG EEENLEFEED EEEGGAGAGS
PDSFPARVPG TLLPRLPSEP GMTLLTIRIE KIGLKDAGQC IDPYITVSVK DLNGIDLTPV
QDTPVASRKE DTYVHFNVDI ELQKHVEKLT KGAAIFFEFK HYKPKKRFTS TKCFAFMEMD
EIKPGPIVIE LYKKPTDFKR KKLQLLTKKP LYLHLHQTLH KE*
mutated AA sequence MTATEAVVRA AQGLARHLQK EAQAQHNNSE FTEEQKKTIG KIATCLELRS AALQSTQSQE
EFKLEDLKKL EPILKNILTY NKEFPFDVQP VPLRRILAPG EEENLEFEED EEEGGAGAGS
PDSFPARVPG TLLPRLPSEP GMTLLTIRIE KIGLKDAGQC IDPYITVSVK DLNGIDLTPV
QDTPVASRKE DTYVHFNVDI ELQKHVEKLT KGAAIFFEFK HYKPKKRFTS TKCFAFMEMD
EIKPGPIVIE LYKKPTDFKR KKLQLLTKKP LYLHLHQTLH KE*
speed 1.00 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
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

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
databasehomozygous (G/G)heterozygousallele carriers
1000G14758422317
ExAC334418385182
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
PhyloPPhastCons
(flanking)0.2660.994
0.9650.998
(flanking)1.2281
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) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor gained2240.98mu: GTAGCTGTCATGGCC AGCT|gtca
distance from splice site 166
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
2123HELIXmight get lost (downstream of altered splice site)
2746HELIXmight get lost (downstream of altered splice site)
5468HELIXmight get lost (downstream of altered splice site)
6971HELIXmight get lost (downstream of altered splice site)
7581STRANDmight get lost (downstream of altered splice site)
8386TURNmight get lost (downstream of altered splice site)
9092STRANDmight get lost (downstream of altered splice site)
90408DOMAINBRO1.might get lost (downstream of altered splice site)
9597STRANDmight get lost (downstream of altered splice site)
102105STRANDmight get lost (downstream of altered splice site)
107130HELIXmight get lost (downstream of altered splice site)
137160HELIXmight get lost (downstream of altered splice site)
162164HELIXmight get lost (downstream of altered splice site)
173176STRANDmight get lost (downstream of altered splice site)
177201HELIXmight get lost (downstream of altered splice site)
206227HELIXmight get lost (downstream of altered splice site)
232263HELIXmight get lost (downstream of altered splice site)
267292HELIXmight get lost (downstream of altered splice site)
283283MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
298301STRANDmight get lost (downstream of altered splice site)
303305HELIXmight get lost (downstream of altered splice site)
307329HELIXmight get lost (downstream of altered splice site)
335335CONFLICTI -> T (in Ref. 1; BAF56045 and 2; BAB71331).might get lost (downstream of altered splice site)
347349STRANDmight get lost (downstream of altered splice site)
367371HELIXmight get lost (downstream of altered splice site)
375377HELIXmight get lost (downstream of altered splice site)
408408LIPIDS-farnesyl cysteine.might get lost (downstream of altered splice site)
408408MOD_RESCysteine methyl ester (Probable).might get lost (downstream of altered splice site)
409411PROPEPRemoved 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 1
strand 1
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 1.20 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
back to results table

Problems