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MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000265069
MT speed 1.34 s - this script 5.545295 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ZFRpolymorphism_automatic0.000429983249407018simple_aaeaffectedI520Tsingle base exchangers1051489show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999570016750593 (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) chr5:32400266A>GN/A show variant in all transcripts   IGV
HGNC symbol ZFR
Ensembl transcript ID ENST00000265069
Genbank transcript ID NM_016107
UniProt peptide Q96KR1
alteration type single base exchange
alteration region CDS
DNA changes c.1559T>C
cDNA.1662T>C
g.44602T>C
AA changes I520T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
520
frameshift no
known variant Reference ID: rs1051489
databasehomozygous (G/G)heterozygousallele carriers
1000G1528621014
ExAC61552045726612
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4790.962
1.6030.946
(flanking)-0.3580.751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased44594wt: 0.43 / mu: 0.72wt: AAAGCAGAAGACATA
mu: AAAGCAGAAGACACA
 AGCA|gaag
Donor marginally increased44606wt: 0.8759 / mu: 0.8890 (marginal change - not scored)wt: ATAAAAGGAACCGAA
mu: ACAAAAGGAACCGAA
 AAAA|ggaa
Donor marginally increased44601wt: 0.9794 / mu: 0.9886 (marginal change - not scored)wt: AAGACATAAAAGGAA
mu: AAGACACAAAAGGAA
 GACA|taaa
Donor increased44597wt: 0.56 / mu: 0.74wt: GCAGAAGACATAAAA
mu: GCAGAAGACACAAAA
 AGAA|gaca
Donor increased44599wt: 0.60 / mu: 0.67wt: AGAAGACATAAAAGG
mu: AGAAGACACAAAAGG
 AAGA|cata
Donor gained446020.40mu: AGACACAAAAGGAAC ACAC|aaaa
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      520KLQSTGNKAEDIKGTECVKSTPVT
mutated  not conserved    520KLQSTGNKAEDTKGTECVKSTPV
Ptroglodytes  all identical  ENSPTRG00000016771  481KLQSTGNKAEDIKGT
Mmulatta  all identical  ENSMMUG00000001317  512KLQSTGNKTEDIKGTECVKSTPV
Fcatus  all conserved  ENSFCAG00000000354  473KLQSTGNKTEDLKGTECVKSTPV
Mmusculus  all conserved  ENSMUSG00000022201  520KLQSTGNKTEDLKGIDCVKNTPA
Ggallus  all conserved  ENSGALG00000003235  522KLQTTGSKLEEMKSTESVKTTP-
Trubripes  not conserved  ENSTRUG00000016620  530TRTEVKMDSSKA
Drerio  not conserved  ENSDARG00000027109  516KLQTTASKSDESKA-DAAKTAQS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000015598  479KLQSTGNKVDDSKMSDSAKTTPS
protein features
start (aa)end (aa)featuredetails 
643643CONFLICTE -> L (in Ref. 4; AAD40385).might get lost (downstream of altered splice site)
659659CONFLICTM -> I (in Ref. 1; CAC40818).might get lost (downstream of altered splice site)
7901038DOMAINDZF.might get lost (downstream of altered splice site)
794794CONFLICTL -> F (in Ref. 4; AAD40385).might get lost (downstream of altered splice site)
834834CONFLICTV -> F (in Ref. 4; AAD40385).might get lost (downstream of altered splice site)
910910MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
913913CONFLICTQ -> QE (in Ref. 1; CAC40818).might get lost (downstream of altered splice site)
10161016CONFLICTF -> K (in Ref. 1; CAC40818).might get lost (downstream of altered splice site)
10541054MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3225 / 3225
position (AA) of stopcodon in wt / mu AA sequence 1075 / 1075
position of stopcodon in wt / mu cDNA 3328 / 3328
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 104 / 104
chromosome 5
strand -1
last intron/exon boundary 3149
theoretical NMD boundary in CDS 2995
length of CDS 3225
coding sequence (CDS) position 1559
cDNA position
(for ins/del: last normal base / first normal base)
1662
gDNA position
(for ins/del: last normal base / first normal base)
44602
chromosomal position
(for ins/del: last normal base / first normal base)
32400266
original gDNA sequence snippet AGGAAATAAAGCAGAAGACATAAAAGGAACCGAATGTGTTA
altered gDNA sequence snippet AGGAAATAAAGCAGAAGACACAAAAGGAACCGAATGTGTTA
original cDNA sequence snippet AGGAAATAAAGCAGAAGACATAAAAGGAACCGAATGTGTTA
altered cDNA sequence snippet AGGAAATAAAGCAGAAGACACAAAAGGAACCGAATGTGTTA
wildtype AA sequence MIPICPVVSF TYVPSRLGED AKMATGNYFG FTHSGAAAAA AAAQYSQQPA SGVAYSHPTT
VASYTVHQAP VAAHTVTAAY APAAATVAVA RPAPVAVAAA ATAAAYGGYP TAHTATDYGY
TQRQQEAPPP PPPATTQNYQ DSYSYVRSTA PAVAYDSKQY YQQPTATAAA VAAAAQPQPS
VAETYYQTAP KAGYSQGATQ YTQAQQTRQV TAIKPATPSP ATTTFSIYPV SSTVQPVAAA
ATVVPSYTQS ATYSTTAVTY SGTSYSGYEA AVYSAASSYY QQQQQQQKQA AAAAAAAAAT
AAWTGTTFTK KAPFQNKQLK PKQPPKPPQI HYCDVCKISC AGPQTYKEHL EGQKHKKKEA
ALKASQNTSS SNSSTRGTQN QLRCELCDVS CTGADAYAAH IRGAKHQKVV KLHTKLGKPI
PSTEPNVVSQ ATSSTAVSAS KPTASPSSIA ANNCTVNTSS VATSSMKGLT TTGNSSLNST
SNTKVSAVPT NMAAKKTSTP KINFVGGNKL QSTGNKAEDI KGTECVKSTP VTSAVQIPEV
KQDTVSEPVT PASLAALQSD VQPVGHDYVE EVRNDEGKVI RFHCKLCECS FNDPNAKEMH
LKGRRHRLQY KKKVNPDLQV EVKPSIRARK IQEEKMRKQM QKEEYWRRRE EEERWRMEMR
RYEEDMYWRR MEEEQHHWDD RRRMPDGGYP HGPPGPLGLL GVRPGMPPQP QGPAPLRRPD
SSDDRYVMTK HATIYPTEEE LQAVQKIVSI TERALKLVSD SLSEHEKNKN KEGDDKKEGG
KDRALKGVLR VGVLAKGLLL RGDRNVNLVL LCSEKPSKTL LSRIAENLPK QLAVISPEKY
DIKCAVSEAA IILNSCVEPK MQVTITLTSP IIREENMREG DVTSGMVKDP PDVLDRQKCL
DALAALRHAK WFQARANGLQ SCVIIIRILR DLCQRVPTWS DFPSWAMELL VEKAISSASS
PQSPGDALRR VFECISSGII LKGSPGLLDP CEKDPFDTLA TMTDQQREDI TSSAQFALRL
LAFRQIHKVL GMDPLPQMSQ RFNIHNNRKR RRDSDGVDGF EAEGKKDKKD YDNF*
mutated AA sequence MIPICPVVSF TYVPSRLGED AKMATGNYFG FTHSGAAAAA AAAQYSQQPA SGVAYSHPTT
VASYTVHQAP VAAHTVTAAY APAAATVAVA RPAPVAVAAA ATAAAYGGYP TAHTATDYGY
TQRQQEAPPP PPPATTQNYQ DSYSYVRSTA PAVAYDSKQY YQQPTATAAA VAAAAQPQPS
VAETYYQTAP KAGYSQGATQ YTQAQQTRQV TAIKPATPSP ATTTFSIYPV SSTVQPVAAA
ATVVPSYTQS ATYSTTAVTY SGTSYSGYEA AVYSAASSYY QQQQQQQKQA AAAAAAAAAT
AAWTGTTFTK KAPFQNKQLK PKQPPKPPQI HYCDVCKISC AGPQTYKEHL EGQKHKKKEA
ALKASQNTSS SNSSTRGTQN QLRCELCDVS CTGADAYAAH IRGAKHQKVV KLHTKLGKPI
PSTEPNVVSQ ATSSTAVSAS KPTASPSSIA ANNCTVNTSS VATSSMKGLT TTGNSSLNST
SNTKVSAVPT NMAAKKTSTP KINFVGGNKL QSTGNKAEDT KGTECVKSTP VTSAVQIPEV
KQDTVSEPVT PASLAALQSD VQPVGHDYVE EVRNDEGKVI RFHCKLCECS FNDPNAKEMH
LKGRRHRLQY KKKVNPDLQV EVKPSIRARK IQEEKMRKQM QKEEYWRRRE EEERWRMEMR
RYEEDMYWRR MEEEQHHWDD RRRMPDGGYP HGPPGPLGLL GVRPGMPPQP QGPAPLRRPD
SSDDRYVMTK HATIYPTEEE LQAVQKIVSI TERALKLVSD SLSEHEKNKN KEGDDKKEGG
KDRALKGVLR VGVLAKGLLL RGDRNVNLVL LCSEKPSKTL LSRIAENLPK QLAVISPEKY
DIKCAVSEAA IILNSCVEPK MQVTITLTSP IIREENMREG DVTSGMVKDP PDVLDRQKCL
DALAALRHAK WFQARANGLQ SCVIIIRILR DLCQRVPTWS DFPSWAMELL VEKAISSASS
PQSPGDALRR VFECISSGII LKGSPGLLDP CEKDPFDTLA TMTDQQREDI TSSAQFALRL
LAFRQIHKVL GMDPLPQMSQ RFNIHNNRKR RRDSDGVDGF EAEGKKDKKD YDNF*
speed 1.34 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
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Problems