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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: ENST00000374280
MT speed 1.15 s - this script 5.091977 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EXTL1polymorphism_automatic0.442948808761009simple_aaeaffectedH379Nsingle base exchangers2736831show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.557051191238991 (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) chr1:26357656C>AN/A show variant in all transcripts   IGV
HGNC symbol EXTL1
Ensembl transcript ID ENST00000374280
Genbank transcript ID NM_004455
UniProt peptide Q92935
alteration type single base exchange
alteration region CDS
DNA changes c.1135C>A
cDNA.2002C>A
g.11282C>A
AA changes H379N Score: 68 explain score(s)
position(s) of altered AA
if AA alteration in CDS
379
frameshift no
known variant Reference ID: rs2736831
databasehomozygous (A/A)heterozygousallele carriers
1000G10309161946
ExAC28686-246054081
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1190.567
3.7120.776
(flanking)1.1540.715
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased11278wt: 0.31 / mu: 1.00wt: ACATCAGCTCACCCC
mu: ACATCAGCTAACCCC
 ATCA|gctc
distance from splice site 34
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      379VIQDRIFGTSAHPSLLWNSPPGAL
mutated  all conserved    379VIQDRIFGTSANPSLLWNSPPGA
Ptroglodytes  all identical  ENSPTRG00000000371  379VIQDRIFGTSAHPSLLWNSPPGA
Mmulatta  all identical  ENSMMUG00000012329  378VIQDRIFGTSAHPSLLWNSPPGA
Fcatus  all identical  ENSFCAG00000012799  375VQGQK--SRSGH-VLVWSNPPHW
Mmusculus  all identical  ENSMUSG00000028838  372IIQDRIWGASGHPSLMWNSPPGA
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000002944  122IIKDRVFSHVSRNKYM
Drerio  no alignment  ENSDARG00000035649  n/a
Dmelanogaster  not conserved  FBgn0020245  437IIRERLPDYPVRSSLVWNSSPGA
Celegans  no alignment  F12F6.3  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
31676TOPO_DOMLumenal (Potential).lost
584584DISULFIDBy similarity.might get lost (downstream of altered splice site)
634634DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2031 / 2031
position (AA) of stopcodon in wt / mu AA sequence 677 / 677
position of stopcodon in wt / mu cDNA 2898 / 2898
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 868 / 868
chromosome 1
strand 1
last intron/exon boundary 2716
theoretical NMD boundary in CDS 1798
length of CDS 2031
coding sequence (CDS) position 1135
cDNA position
(for ins/del: last normal base / first normal base)
2002
gDNA position
(for ins/del: last normal base / first normal base)
11282
chromosomal position
(for ins/del: last normal base / first normal base)
26357656
original gDNA sequence snippet GGATTTTTGGAACATCAGCTCACCCCTCACTGCTGTGGAAC
altered gDNA sequence snippet GGATTTTTGGAACATCAGCTAACCCCTCACTGCTGTGGAAC
original cDNA sequence snippet GGATTTTTGGAACATCAGCTCACCCCTCACTGCTGTGGAAC
altered cDNA sequence snippet GGATTTTTGGAACATCAGCTAACCCCTCACTGCTGTGGAAC
wildtype AA sequence MQSWRRRKSL WLALSASWLL LVLLGGFSLL RLALPPRPRP GASQGWPRWL DAELLQSFSQ
PGELPEDAVS PPQAPHGGSC NWESCFDTSK CRGDGLKVFV YPAVGTISET HRRILASIEG
SRFYTFSPAG ACLLLLLSLD AQTGECSSMP LQWNRGRNHL VLRLHPAPCP RTFQLGQAMV
AEASPTVDSF RPGFDVALPF LPEAHPLRGG APGQLRQHSP QPGVALLALE EERGGWRTAD
TGSSACPWDG RCEQDPGPGQ TQRQETLPNA TFCLISGHRP EAASRFLQAL QAGCIPVLLS
PRWELPFSEV IDWTKAAIVA DERLPLQVLA ALQEMSPARV LALRQQTQFL WDAYFSSVEK
VIHTTLEVIQ DRIFGTSAHP SLLWNSPPGA LLALSTFSTS PQDFPFYYLQ QGSRPEGRFS
ALIWVGPPGQ PPLKLIQAVA GSQHCAQILV LWSNERPLPS RWPETAVPLT VIDGHRKVSD
RFYPYSTIRT DAILSLDARS SLSTSEVDFA FLVWQSFPER MVGFLTSSHF WDEAHGGWGY
TAERTNEFSM VLTTAAFYHR YYHTLFTHSL PKALRTLADE APTCVDVLMN FIVAAVTKLP
PIKVPYGKQR QEAAPLAPGG PGPRPKPPAP APDCINQIAA AFGHMPLLSS RLRLDPVLFK
DPVSVQRKKY RSLEKP*
mutated AA sequence MQSWRRRKSL WLALSASWLL LVLLGGFSLL RLALPPRPRP GASQGWPRWL DAELLQSFSQ
PGELPEDAVS PPQAPHGGSC NWESCFDTSK CRGDGLKVFV YPAVGTISET HRRILASIEG
SRFYTFSPAG ACLLLLLSLD AQTGECSSMP LQWNRGRNHL VLRLHPAPCP RTFQLGQAMV
AEASPTVDSF RPGFDVALPF LPEAHPLRGG APGQLRQHSP QPGVALLALE EERGGWRTAD
TGSSACPWDG RCEQDPGPGQ TQRQETLPNA TFCLISGHRP EAASRFLQAL QAGCIPVLLS
PRWELPFSEV IDWTKAAIVA DERLPLQVLA ALQEMSPARV LALRQQTQFL WDAYFSSVEK
VIHTTLEVIQ DRIFGTSANP SLLWNSPPGA LLALSTFSTS PQDFPFYYLQ QGSRPEGRFS
ALIWVGPPGQ PPLKLIQAVA GSQHCAQILV LWSNERPLPS RWPETAVPLT VIDGHRKVSD
RFYPYSTIRT DAILSLDARS SLSTSEVDFA FLVWQSFPER MVGFLTSSHF WDEAHGGWGY
TAERTNEFSM VLTTAAFYHR YYHTLFTHSL PKALRTLADE APTCVDVLMN FIVAAVTKLP
PIKVPYGKQR QEAAPLAPGG PGPRPKPPAP APDCINQIAA AFGHMPLLSS RLRLDPVLFK
DPVSVQRKKY RSLEKP*
speed 1.15 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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