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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: ENST00000367288
MT speed 1.41 s - this script 3.613625 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
LMOD1polymorphism_automatic4.9960036108132e-15simple_aaeT295Msingle base exchangers2820312show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:201869257G>AN/A show variant in all transcripts   IGV
HGNC symbol LMOD1
Ensembl transcript ID ENST00000367288
Genbank transcript ID NM_012134
UniProt peptide P29536
alteration type single base exchange
alteration region CDS
DNA changes c.884C>T
cDNA.1131C>T
g.46459C>T
AA changes T295M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS
295
frameshift no
known variant Reference ID: rs2820312
databasehomozygous (A/A)heterozygousallele carriers
1000G131829960
ExAC49462287527821
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
SP1, Transcription Factor, SP1 Transcription Factor Binding
PU1, Transcription Factor, PU1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3410.001
0.1340
(flanking)-1.4790
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 623
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      295DDSKTKTPEKQTPSGPTKPSEGPA
mutated  not conserved    295DDSKTKTPEKQMPSGPT
Ptroglodytes  not conserved  ENSPTRG00000001841  295DDSKTKTPEKQMPSGPT
Mmulatta  not conserved  ENSMMUG00000001923  295EDSKTKTPEKQMPSGPT
Fcatus  not conserved  ENSFCAG00000000446  289EENKTQALEKQAPASPT
Mmusculus  not conserved  ENSMUSG00000048096  293EESKTKAPEKQAPSCPN
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000012878  300NVGNCLGATTTPNSK
Drerio  not conserved  ENSDARG00000056111  296ENSKAKIFTSSFHESSGNCHGADTCSLTTEEDESY
Dmelanogaster  no alignment  FBgn0082582  n/a
Celegans  no alignment  C06A5.7  n/a
Xtropicalis  all identical  ENSXETG00000007976  270ET------QNQTEE
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1803 / 1803
position (AA) of stopcodon in wt / mu AA sequence 601 / 601
position of stopcodon in wt / mu cDNA 2050 / 2050
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 248 / 248
chromosome 1
strand -1
last intron/exon boundary 2024
theoretical NMD boundary in CDS 1726
length of CDS 1803
coding sequence (CDS) position 884
cDNA position
(for ins/del: last normal base / first normal base)
1131
gDNA position
(for ins/del: last normal base / first normal base)
46459
chromosomal position
(for ins/del: last normal base / first normal base)
201869257
original gDNA sequence snippet CAAAACACCCGAGAAACAGACGCCCAGTGGCCCCACCAAGC
altered gDNA sequence snippet CAAAACACCCGAGAAACAGATGCCCAGTGGCCCCACCAAGC
original cDNA sequence snippet CAAAACACCCGAGAAACAGACGCCCAGTGGCCCCACCAAGC
altered cDNA sequence snippet CAAAACACCCGAGAAACAGATGCCCAGTGGCCCCACCAAGC
wildtype AA sequence MSRVAKYRRQ VSEDPDIDSL LETLSPEEME ELEKELDVVD PDGSVPVGLR QRNQTEKQST
GVYNREAMLN FCEKETKKLM QREMSMDESK QVETKTDAKN GEERGRDASK KALGPRRDSD
LGKEPKRGGL KKSFSRDRDE AGGKSGEKPK EEKIIRGIDK GRVRAAVDKK EAGKDGRGEE
RAVATKKEEE KKGSDRNTGL SRDKDKKREE MKEVAKKEDD EKVKGERRNT DTRKEGEKMK
RAGGNTDMKK EDEKVKRGTG NTDTKKDDEK VKKNEPLHEK EAKDDSKTKT PEKQTPSGPT
KPSEGPAKVE EEAAPSIFDE PLERVKNNDP EMTEVNVNNS DCITNEILVR FTEALEFNTV
VKLFALANTR ADDHVAFAIA IMLKANKTIT SLNLDSNHIT GKGILAIFRA LLQNNTLTEL
RFHNQRHICG GKTEMEIAKL LKENTTLLKL GYHFELAGPR MTVTNLLSRN MDKQRQKRLQ
EQRQAQEAKG EKKDLLEVPK AGAVAKGSPK PSPQPSPKPS PKNSPKKGGA PAAPPPPPPP
LAPPLIMENL KNSLSPATQR KMGDKVLPAQ EKNSRDQLLA AIRSSNLKQL KKVEVPKLLQ
*
mutated AA sequence MSRVAKYRRQ VSEDPDIDSL LETLSPEEME ELEKELDVVD PDGSVPVGLR QRNQTEKQST
GVYNREAMLN FCEKETKKLM QREMSMDESK QVETKTDAKN GEERGRDASK KALGPRRDSD
LGKEPKRGGL KKSFSRDRDE AGGKSGEKPK EEKIIRGIDK GRVRAAVDKK EAGKDGRGEE
RAVATKKEEE KKGSDRNTGL SRDKDKKREE MKEVAKKEDD EKVKGERRNT DTRKEGEKMK
RAGGNTDMKK EDEKVKRGTG NTDTKKDDEK VKKNEPLHEK EAKDDSKTKT PEKQMPSGPT
KPSEGPAKVE EEAAPSIFDE PLERVKNNDP EMTEVNVNNS DCITNEILVR FTEALEFNTV
VKLFALANTR ADDHVAFAIA IMLKANKTIT SLNLDSNHIT GKGILAIFRA LLQNNTLTEL
RFHNQRHICG GKTEMEIAKL LKENTTLLKL GYHFELAGPR MTVTNLLSRN MDKQRQKRLQ
EQRQAQEAKG EKKDLLEVPK AGAVAKGSPK PSPQPSPKPS PKNSPKKGGA PAAPPPPPPP
LAPPLIMENL KNSLSPATQR KMGDKVLPAQ EKNSRDQLLA AIRSSNLKQL KKVEVPKLLQ
*
speed 1.41 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