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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: ENST00000367942
MT speed 0 s - this script 3.298468 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATF6polymorphism_automatic0.00499033949266803simple_aaeaffectedA145Psingle base exchangers2070150show file

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.995009660507332 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM068176)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:161761276G>CN/A show variant in all transcripts   IGV
HGNC symbol ATF6
Ensembl transcript ID ENST00000367942
Genbank transcript ID NM_007348
UniProt peptide P18850
alteration type single base exchange
alteration region CDS
DNA changes c.433G>C
cDNA.500G>C
g.25193G>C
AA changes A145P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 145
frameshift no
known variant Reference ID: rs2070150
databasehomozygous (C/C)heterozygousallele carriers
1000G127543670
ExAC22071137513582

known disease mutation at this position, please check HGMD for details (HGMD ID CM068176)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2060.973
0.1590.972
(flanking)0.9870.983
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased25193wt: 0.6657 / mu: 0.7223 (marginal change - not scored)wt: ACTCTAATAGTCTCTCTTCAGCGGAGCCACTGAAGGAAGAT
mu: ACTCTAATAGTCTCTCTTCACCGGAGCCACTGAAGGAAGAT		 tcag|CGGA
Acc marginally increased25194wt: 0.8144 / mu: 0.8310 (marginal change - not scored)wt: CTCTAATAGTCTCTCTTCAGCGGAGCCACTGAAGGAAGATA
mu: CTCTAATAGTCTCTCTTCACCGGAGCCACTGAAGGAAGATA		 cagc|GGAG
Acc marginally increased25191wt: 0.9045 / mu: 0.9143 (marginal change - not scored)wt: AAACTCTAATAGTCTCTCTTCAGCGGAGCCACTGAAGGAAG
mu: AAACTCTAATAGTCTCTCTTCACCGGAGCCACTGAAGGAAG		 cttc|AGCG
Acc marginally increased25196wt: 0.8012 / mu: 0.8174 (marginal change - not scored)wt: CTAATAGTCTCTCTTCAGCGGAGCCACTGAAGGAAGATAAG
mu: CTAATAGTCTCTCTTCACCGGAGCCACTGAAGGAAGATAAG		 gcgg|AGCC
Acc gained251950.99mu: TCTAATAGTCTCTCTTCACCGGAGCCACTGAAGGAAGATAA accg|GAGC
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      145LYGENSNSLSSAEPLKEDKPVTGP
mutated  not conserved    145LYGENSNSLSSPEPLKEDKPVTG
Ptroglodytes  all identical  ENSPTRG00000001596  145LYGENSNSPSSAEPLKEDKPVTG
Mmulatta  all identical  ENSMMUG00000004049  79LYGESSNSPSSAEPLKEDKPVTG
Fcatus  all identical  ENSFCAG00000014118  145LYGESSHSPSSAEPLKEDKPIIG
Mmusculus  not conserved  ENSMUSG00000026663  132LYGDSCNSPSSVEPLKEEKPVTG
Ggallus  not conserved  ENSGALG00000002658  88LYCKSSRSPASPEGDAEKKPIVG
Trubripes  no alignment  ENSTRUG00000006660  n/a
Drerio  not conserved  ENSDARG00000012656  148F---TEAPNEKKPSKR
Dmelanogaster  not conserved  FBgn0033010  115FQLDLTNSRNDL-PEPNSSPTRS
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000004747  108LYSDCSKSPKSPD
protein features
start (aa)end (aa)featuredetails 
1150REGIONTranscription activation.lost
1377TOPO_DOMCytoplasmic (Potential).lost
195195CONFLICTN -> I (in Ref. 4; AAH14969/AAH71997).might get lost (downstream of altered splice site)
198201CONFLICTVPAK -> IPPQ (in Ref. 4; AAH14969/ AAH71997).might get lost (downstream of altered splice site)
306369DOMAINbZIP.might get lost (downstream of altered splice site)
307307CONFLICTL -> I (in Ref. 5; no nucleotide entry).might get lost (downstream of altered splice site)
308339REGIONBasic motif (By similarity).might get lost (downstream of altered splice site)
325328COMPBIASPoly-Lys.might get lost (downstream of altered splice site)
348355REGIONLeucine-zipper (By similarity).might get lost (downstream of altered splice site)
354354CONFLICTT -> R (in Ref. 5; no nucleotide entry).might get lost (downstream of altered splice site)
366369CONFLICTNQRL -> LRNS (in Ref. 5; no nucleotide entry).might get lost (downstream of altered splice site)
378398TRANSMEMHelical; Signal-anchor for type II membrane protein; (Potential).might get lost (downstream of altered splice site)
391391MUTAGENN->F: Loss of proteolytic cleavage; when associated with L-394.might get lost (downstream of altered splice site)
394394MUTAGENP->L: Loss of proteolytic cleavage; when associated with F-391.might get lost (downstream of altered splice site)
399670TOPO_DOMLumenal (Potential).might get lost (downstream of altered splice site)
410410CONFLICTS -> G (in Ref. 1; AAB64434).might get lost (downstream of altered splice site)
415416MUTAGENRR->AA: Reduces proteolytic cleavage.might get lost (downstream of altered splice site)
419419MUTAGENL->V: Reduces proteolytic cleavage.might get lost (downstream of altered splice site)
419420SITECleavage; by PS1 (By similarity).might get lost (downstream of altered splice site)
463466COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
472472CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
474474MUTAGENT->I: Loss of glycosylation at Asn-472 and increase of Golgi translocation rate.might get lost (downstream of altered splice site)
513514CONFLICTAL -> VV (in Ref. 1; AAB64434).might get lost (downstream of altered splice site)
584584CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
586586MUTAGENT->I: Loss of glycosylation at Asn-584 and increase of Golgi translocation rate. Higher increase in Golgi translocation rate; when associated with Ile-645.might get lost (downstream of altered splice site)
643643CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
645645MUTAGENT->I: Loss of glycosylation at Asn-643 and increase of Golgi translocation rate. Higher increase in Golgi translocation rate; when associated with Ile-586.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2013 / 2013
position (AA) of stopcodon in wt / mu AA sequence 671 / 671
position of stopcodon in wt / mu cDNA 2080 / 2080
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 68 / 68
chromosome 1
strand 1
last intron/exon boundary 1872
theoretical NMD boundary in CDS 1754
length of CDS 2013
coding sequence (CDS) position 433
cDNA position
(for ins/del: last normal base / first normal base)		 500
gDNA position
(for ins/del: last normal base / first normal base)		 25193
chromosomal position
(for ins/del: last normal base / first normal base)		 161761276
original gDNA sequence snippet ACTCTAATAGTCTCTCTTCAGCGGAGCCACTGAAGGAAGAT
altered gDNA sequence snippet ACTCTAATAGTCTCTCTTCACCGGAGCCACTGAAGGAAGAT
original cDNA sequence snippet ACTCTAATAGTCTCTCTTCAGCGGAGCCACTGAAGGAAGAT
altered cDNA sequence snippet ACTCTAATAGTCTCTCTTCACCGGAGCCACTGAAGGAAGAT
wildtype AA sequence MGEPAGVAGT MESPFSPGLF HRLDEDWDSA LFAELGYFTD TDELQLEAAN ETYENNFDNL
DFDLDLMPWE SDIWDINNQI CTVKDIKAEP QPLSPASSSY SVSSPRSVDS YSSTQHVPEE
LDLSSSSQMS PLSLYGENSN SLSSAEPLKE DKPVTGPRNK TENGLTPKKK IQVNSKPSIQ
PKPLLLPAAP KTQTNSSVPA KTIIIQTVPT LMPLAKQQPI ISLQPAPTKG QTVLLSQPTV
VQLQAPGVLP SAQPVLAVAG GVTQLPNHVV NVVPAPSANS PVNGKLSVTK PVLQSTMRNV
GSDIAVLRRQ QRMIKNRESA CQSRKKKKEY MLGLEARLKA ALSENEQLKK ENGTLKRQLD
EVVSENQRLK VPSPKRRVVC VMIVLAFIIL NYGPMSMLEQ DSRRMNPSVS PANQRRHLLG
FSAKEAQDTS DGIIQKNSYR YDHSVSNDKA LMVLTEEPLL YIPPPPCQPL INTTESLRLN
HELRGWVHRH EVERTKSRRM TNNQQKTRIL QGALEQGSNS QLMAVQYTET TSSISRNSGS
ELQVYYASPR SYQDFFEAIR RRGDTFYVVS FRRDHLLLPA TTHNKTTRPK MSIVLPAINI
NENVINGQDY EVMMQIDCQV MDTRILHIKS SSVPPYLRDQ QRNQTNTFFG SPPAATEATH
VVSTIPESLQ *
mutated AA sequence MGEPAGVAGT MESPFSPGLF HRLDEDWDSA LFAELGYFTD TDELQLEAAN ETYENNFDNL
DFDLDLMPWE SDIWDINNQI CTVKDIKAEP QPLSPASSSY SVSSPRSVDS YSSTQHVPEE
LDLSSSSQMS PLSLYGENSN SLSSPEPLKE DKPVTGPRNK TENGLTPKKK IQVNSKPSIQ
PKPLLLPAAP KTQTNSSVPA KTIIIQTVPT LMPLAKQQPI ISLQPAPTKG QTVLLSQPTV
VQLQAPGVLP SAQPVLAVAG GVTQLPNHVV NVVPAPSANS PVNGKLSVTK PVLQSTMRNV
GSDIAVLRRQ QRMIKNRESA CQSRKKKKEY MLGLEARLKA ALSENEQLKK ENGTLKRQLD
EVVSENQRLK VPSPKRRVVC VMIVLAFIIL NYGPMSMLEQ DSRRMNPSVS PANQRRHLLG
FSAKEAQDTS DGIIQKNSYR YDHSVSNDKA LMVLTEEPLL YIPPPPCQPL INTTESLRLN
HELRGWVHRH EVERTKSRRM TNNQQKTRIL QGALEQGSNS QLMAVQYTET TSSISRNSGS
ELQVYYASPR SYQDFFEAIR RRGDTFYVVS FRRDHLLLPA TTHNKTTRPK MSIVLPAINI
NENVINGQDY EVMMQIDCQV MDTRILHIKS SSVPPYLRDQ QRNQTNTFFG SPPAATEATH
VVSTIPESLQ *
speed 1.23 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