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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: ENST00000396073
MT speed 0 s - this script 3.332533 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ENAMpolymorphism_automatic1.94955163124177e-13simple_aaeaffectedI648Tsingle base exchangers7671281show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999805 (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) chr4:71509086T>CN/A show variant in all transcripts   IGV
HGNC symbol ENAM
Ensembl transcript ID ENST00000396073
Genbank transcript ID NM_031889
UniProt peptide Q9NRM1
alteration type single base exchange
alteration region CDS
DNA changes c.1943T>C
cDNA.2224T>C
g.14626T>C
AA changes I648T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 648
frameshift no
known variant Reference ID: rs7671281
databasehomozygous (C/C)heterozygousallele carriers
1000G202506708
ExAC127177379008
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7620.001
-0.1330
(flanking)-0.1940
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased14623wt: 0.30 / mu: 0.39wt: GAAGGAGATAGTCCC
mu: GAAGGAGACAGTCCC		 AGGA|gata
Donor increased14621wt: 0.28 / mu: 0.64wt: CAGAAGGAGATAGTC
mu: CAGAAGGAGACAGTC		 GAAG|gaga
Donor increased14620wt: 0.59 / mu: 0.67wt: CCAGAAGGAGATAGT
mu: CCAGAAGGAGACAGT		 AGAA|ggag
Donor increased14617wt: 0.29 / mu: 0.37wt: AGACCAGAAGGAGAT
mu: AGACCAGAAGGAGAC		 ACCA|gaag
Donor increased14618wt: 0.48 / mu: 0.61wt: GACCAGAAGGAGATA
mu: GACCAGAAGGAGACA		 CCAG|aagg
distance from splice site 1355
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      648LYPINTPDQKEIVPYNEEDPVDPT
mutated  not conserved    648LYPINTPDQKETVPYNEEDPVDP
Ptroglodytes  not conserved  ENSPTRG00000016133  648LYPINTPDQKETVPYNEEDPVDP
Mmulatta  not conserved  ENSMMUG00000022102  644LYPINTPDHKETVPYNEEDPIDP
Fcatus  no alignment  ENSFCAG00000009208  n/a
Mmusculus  not conserved  ENSMUSG00000029286  787QYTMTSLDQKETEQYNEEDPIDP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000032124  633RN--NLLGQKEIYLYPDTELYHQ
protein features
start (aa)end (aa)featuredetails 
906906MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
911911MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
934934CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
948948CONFLICTD -> G (in Ref. 2; AAG43242).might get lost (downstream of altered splice site)
10401040CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3429 / 3429
position (AA) of stopcodon in wt / mu AA sequence 1143 / 1143
position of stopcodon in wt / mu cDNA 3710 / 3710
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 282 / 282
chromosome 4
strand 1
last intron/exon boundary 870
theoretical NMD boundary in CDS 538
length of CDS 3429
coding sequence (CDS) position 1943
cDNA position
(for ins/del: last normal base / first normal base)		 2224
gDNA position
(for ins/del: last normal base / first normal base)		 14626
chromosomal position
(for ins/del: last normal base / first normal base)		 71509086
original gDNA sequence snippet TACCCCAGACCAGAAGGAGATAGTCCCTTATAATGAAGAGG
altered gDNA sequence snippet TACCCCAGACCAGAAGGAGACAGTCCCTTATAATGAAGAGG
original cDNA sequence snippet TACCCCAGACCAGAAGGAGATAGTCCCTTATAATGAAGAGG
altered cDNA sequence snippet TACCCCAGACCAGAAGGAGACAGTCCCTTATAATGAAGAGG
wildtype AA sequence MLVLRCRLGT SFPKLDNLVP KGKMKILLVF LGLLGNSVAM PMHMPRMPGF SSKSEEMMRY
NQFNFMNGPH MAHLGPFFGN GLPQQFPQYQ MPMWPQPPPN TWHPRKSSAP KRHNKTDQTQ
ETQKPNQTQS KKPPQKRPLK QPSHNQPQPE EEAQPPQAFP PFGNGLFPYQ QPPWQIPQRL
PPPGYGRPPI SNEEGGNPYF GYFGYHGFGG RPPYYSEEMF EQDFEKPKEE DPPKAESPGT
EPTANSTVTE TNSTQPNPKG SQGGNDTSPT GNSTPGLNTG NNPPAQNGIG PLPAVNASGQ
GGPGSQIPWR PSQPNIRENH PYPNIRNFPS GRQWYFTGTV MGHRQNRPFY RNQQVQRGPR
WNFFAWERKQ VARPGNPVYH KAYPPTSRGN YPNYAGNPAN LRRKPQGPNK HPVGTTVAPL
GPKPGPVVRN EKIQNPKEKP LGPKEQIIVP TKNPTSPWRN SQQYEVNKSN YKLPHSEGYM
PVPNFNSVDQ HENSYYPRGD SRKVPNSDGQ TQSQNLPKGI VLGSRRMPYE SETNQSELKH
SSYQPAVYPE EIPSPAKEHF PAGRNTWDHQ EISPPFKEDP GRQEEHLPHP SHGSRGSVFY
PEYNPYDPRE NSPYLRGNTW DERDDSPNTM GQKESPLYPI NTPDQKEIVP YNEEDPVDPT
GDEVFPGQNR WGEELSFKGG PTVRHYEGEQ YTSNQPKEYL PYSLDNPSKP REDFYYSEFY
PWSPDENFPS YNTASTMPPP IESRGYYVNN AAGPEESTLF PSRNSWDHRI QAQGQRERRP
YFNRNIWDQA THLQKAPARP PDQKGNQPYY SNTPAGLQKN PIWHEGENLN YGMQITRMNS
PEREHSSFPN FIPPSYPSGQ KEAHLFHLSQ RGSCCAGSST GPKDNPLALQ DYTPSYGLAP
GENQDTSPLY TDGSHTKQTR DIISPTSILP GQRNSSEKRE SQNPFRDDVS TLRRNTPCSI
KNQLGQKEIM PFPEASSLQS KNTPCLKNDL GGDGNNILEQ VFEDNQLNER TVDLTPEQLV
IGTPDEGSNP EGIQSQVQEN ESERQQQRPS NILHLPCFGS KLAKHHSSTT GTPSSDGRQS
PFDGDSITPT ENPNTLVELA TEEQFKSINV DPLDADEHSP FEFLQRGTNV QDQVQDCLLL
QA*
mutated AA sequence MLVLRCRLGT SFPKLDNLVP KGKMKILLVF LGLLGNSVAM PMHMPRMPGF SSKSEEMMRY
NQFNFMNGPH MAHLGPFFGN GLPQQFPQYQ MPMWPQPPPN TWHPRKSSAP KRHNKTDQTQ
ETQKPNQTQS KKPPQKRPLK QPSHNQPQPE EEAQPPQAFP PFGNGLFPYQ QPPWQIPQRL
PPPGYGRPPI SNEEGGNPYF GYFGYHGFGG RPPYYSEEMF EQDFEKPKEE DPPKAESPGT
EPTANSTVTE TNSTQPNPKG SQGGNDTSPT GNSTPGLNTG NNPPAQNGIG PLPAVNASGQ
GGPGSQIPWR PSQPNIRENH PYPNIRNFPS GRQWYFTGTV MGHRQNRPFY RNQQVQRGPR
WNFFAWERKQ VARPGNPVYH KAYPPTSRGN YPNYAGNPAN LRRKPQGPNK HPVGTTVAPL
GPKPGPVVRN EKIQNPKEKP LGPKEQIIVP TKNPTSPWRN SQQYEVNKSN YKLPHSEGYM
PVPNFNSVDQ HENSYYPRGD SRKVPNSDGQ TQSQNLPKGI VLGSRRMPYE SETNQSELKH
SSYQPAVYPE EIPSPAKEHF PAGRNTWDHQ EISPPFKEDP GRQEEHLPHP SHGSRGSVFY
PEYNPYDPRE NSPYLRGNTW DERDDSPNTM GQKESPLYPI NTPDQKETVP YNEEDPVDPT
GDEVFPGQNR WGEELSFKGG PTVRHYEGEQ YTSNQPKEYL PYSLDNPSKP REDFYYSEFY
PWSPDENFPS YNTASTMPPP IESRGYYVNN AAGPEESTLF PSRNSWDHRI QAQGQRERRP
YFNRNIWDQA THLQKAPARP PDQKGNQPYY SNTPAGLQKN PIWHEGENLN YGMQITRMNS
PEREHSSFPN FIPPSYPSGQ KEAHLFHLSQ RGSCCAGSST GPKDNPLALQ DYTPSYGLAP
GENQDTSPLY TDGSHTKQTR DIISPTSILP GQRNSSEKRE SQNPFRDDVS TLRRNTPCSI
KNQLGQKEIM PFPEASSLQS KNTPCLKNDL GGDGNNILEQ VFEDNQLNER TVDLTPEQLV
IGTPDEGSNP EGIQSQVQEN ESERQQQRPS NILHLPCFGS KLAKHHSSTT GTPSSDGRQS
PFDGDSITPT ENPNTLVELA TEEQFKSINV DPLDADEHSP FEFLQRGTNV QDQVQDCLLL
QA*
speed 1.01 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