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MutationTaster - study a chromosomal position

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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: ENST00000203629
MT speed 0 s - this script 4.513443 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
LAG3polymorphism_automatic0.083881729433425simple_aaeaffectedI455Tsingle base exchangers870849show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.916118270566575 (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) chr12:6887020T>CN/A show variant in all transcripts   IGV
HGNC symbol LAG3
Ensembl transcript ID ENST00000203629
Genbank transcript ID NM_002286
UniProt peptide P18627
alteration type single base exchange
alteration region CDS
DNA changes c.1364T>C
cDNA.1697T>C
g.5343T>C
AA changes I455T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
455
frameshift no
known variant Reference ID: rs870849
databasehomozygous (C/C)heterozygousallele carriers
1000G115010522202
ExAC25163-175597604
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3240.925
-0.1550.924
(flanking)3.1180.989
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 increased5343wt: 0.8080 / mu: 0.8201 (marginal change - not scored)wt: CCACCTCCTGCTGTTTCTCATCCTTGGTGTCCTTTCTCTGC
mu: CCACCTCCTGCTGTTTCTCACCCTTGGTGTCCTTTCTCTGC
 tcat|CCTT
Acc marginally increased5338wt: 0.2885 / mu: 0.3228 (marginal change - not scored)wt: GCAGGCCACCTCCTGCTGTTTCTCATCCTTGGTGTCCTTTC
mu: GCAGGCCACCTCCTGCTGTTTCTCACCCTTGGTGTCCTTTC
 gttt|CTCA
Acc marginally increased5347wt: 0.8563 / mu: 0.8806 (marginal change - not scored)wt: CTCCTGCTGTTTCTCATCCTTGGTGTCCTTTCTCTGCTCCT
mu: CTCCTGCTGTTTCTCACCCTTGGTGTCCTTTCTCTGCTCCT
 cctt|GGTG
Acc marginally increased5344wt: 0.2642 / mu: 0.2856 (marginal change - not scored)wt: CACCTCCTGCTGTTTCTCATCCTTGGTGTCCTTTCTCTGCT
mu: CACCTCCTGCTGTTTCTCACCCTTGGTGTCCTTTCTCTGCT
 catc|CTTG
Acc increased5340wt: 0.32 / mu: 0.44wt: AGGCCACCTCCTGCTGTTTCTCATCCTTGGTGTCCTTTCTC
mu: AGGCCACCTCCTGCTGTTTCTCACCCTTGGTGTCCTTTCTC
 ttct|CATC
distance from splice site 64
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      455ALPAGHLLLFLILGVLSLLLLVTG
mutated  not conserved    455ALPAGHLLLFLTLGVLSLLLLVT
Ptroglodytes  not conserved  ENSPTRG00000024384  455ALPAGHLLLFLTLGVLSLLLLVT
Mmulatta  all identical  ENSMMUG00000013196  455ALRAGHLPLFLILGVLFLLLLVT
Fcatus  all identical  ENSFCAG00000006886  451PLKTGQLPLFLILGILFLLLLMT
Mmusculus  all identical  ENSMUSG00000030124  448DLKGGHLVLVLILGALSLFLLVA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
451471TRANSMEMHelical; (Potential).lost
472525TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
501524REGION12 X 2 AA tandem repeats of E-X.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1578 / 1578
position (AA) of stopcodon in wt / mu AA sequence 526 / 526
position of stopcodon in wt / mu cDNA 1911 / 1911
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 334 / 334
chromosome 12
strand 1
last intron/exon boundary 1765
theoretical NMD boundary in CDS 1381
length of CDS 1578
coding sequence (CDS) position 1364
cDNA position
(for ins/del: last normal base / first normal base)
1697
gDNA position
(for ins/del: last normal base / first normal base)
5343
chromosomal position
(for ins/del: last normal base / first normal base)
6887020
original gDNA sequence snippet CCACCTCCTGCTGTTTCTCATCCTTGGTGTCCTTTCTCTGC
altered gDNA sequence snippet CCACCTCCTGCTGTTTCTCACCCTTGGTGTCCTTTCTCTGC
original cDNA sequence snippet CCACCTCCTGCTGTTTCTCATCCTTGGTGTCCTTTCTCTGC
altered cDNA sequence snippet CCACCTCCTGCTGTTTCTCACCCTTGGTGTCCTTTCTCTGC
wildtype AA sequence MWEAQFLGLL FLQPLWVAPV KPLQPGAEVP VVWAQEGAPA QLPCSPTIPL QDLSLLRRAG
VTWQHQPDSG PPAAAPGHPL APGPHPAAPS SWGPRPRRYT VLSVGPGGLR SGRLPLQPRV
QLDERGRQRG DFSLWLRPAR RADAGEYRAA VHLRDRALSC RLRLRLGQAS MTASPPGSLR
ASDWVILNCS FSRPDRPASV HWFRNRGQGR VPVRESPHHH LAESFLFLPQ VSPMDSGPWG
CILTYRDGFN VSIMYNLTVL GLEPPTPLTV YAGAGSRVGL PCRLPAGVGT RSFLTAKWTP
PGGGPDLLVT GDNGDFTLRL EDVSQAQAGT YTCHIHLQEQ QLNATVTLAI ITVTPKSFGS
PGSLGKLLCE VTPVSGQERF VWSSLDTPSQ RSFSGPWLEA QEAQLLSQPW QCQLYQGERL
LGAAVYFTEL SSPGAQRSGR APGALPAGHL LLFLILGVLS LLLLVTGAFG FHLWRRQWRP
RRFSALEQGI HPPQAQSKIE ELEQEPEPEP EPEPEPEPEP EPEQL*
mutated AA sequence MWEAQFLGLL FLQPLWVAPV KPLQPGAEVP VVWAQEGAPA QLPCSPTIPL QDLSLLRRAG
VTWQHQPDSG PPAAAPGHPL APGPHPAAPS SWGPRPRRYT VLSVGPGGLR SGRLPLQPRV
QLDERGRQRG DFSLWLRPAR RADAGEYRAA VHLRDRALSC RLRLRLGQAS MTASPPGSLR
ASDWVILNCS FSRPDRPASV HWFRNRGQGR VPVRESPHHH LAESFLFLPQ VSPMDSGPWG
CILTYRDGFN VSIMYNLTVL GLEPPTPLTV YAGAGSRVGL PCRLPAGVGT RSFLTAKWTP
PGGGPDLLVT GDNGDFTLRL EDVSQAQAGT YTCHIHLQEQ QLNATVTLAI ITVTPKSFGS
PGSLGKLLCE VTPVSGQERF VWSSLDTPSQ RSFSGPWLEA QEAQLLSQPW QCQLYQGERL
LGAAVYFTEL SSPGAQRSGR APGALPAGHL LLFLTLGVLS LLLLVTGAFG FHLWRRQWRP
RRFSALEQGI HPPQAQSKIE ELEQEPEPEP EPEPEPEPEP EPEQL*
speed 1.21 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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