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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: ENST00000246024
MT speed 1.17 s - this script 5.46192 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TMX4polymorphism_automatic1.11999298724186e-12simple_aaeaffectedG303Rsingle base exchangers2076015show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999888 (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) chr20:7963041C>TN/A show variant in all transcripts   IGV
HGNC symbol TMX4
Ensembl transcript ID ENST00000246024
Genbank transcript ID NM_021156
UniProt peptide Q9H1E5
alteration type single base exchange
alteration region CDS
DNA changes c.907G>A
cDNA.1123G>A
g.37436G>A
AA changes G303R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
303
frameshift no
known variant Reference ID: rs2076015
databasehomozygous (T/T)heterozygousallele carriers
1000G4927891281
ExAC38301271216542
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0430
-0.1020
(flanking)0.3220
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased37436wt: 0.9578 / mu: 0.9894 (marginal change - not scored)wt: CCCCAGGAGAGGACG
mu: CCCCAAGAGAGGACG
 CCAG|gaga
Donor increased37438wt: 0.38 / mu: 0.76wt: CCAGGAGAGGACGGT
mu: CCAAGAGAGGACGGT
 AGGA|gagg
Donor increased37433wt: 0.71 / mu: 0.79wt: GGCCCCCAGGAGAGG
mu: GGCCCCCAAGAGAGG
 CCCC|cagg
Donor increased37440wt: 0.40 / mu: 0.60wt: AGGAGAGGACGGTGT
mu: AAGAGAGGACGGTGT
 GAGA|ggac
Donor gained374310.74mu: GGGGCCCCCAAGAGA GGCC|ccca
distance from splice site 228
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      303ERSEANDQGPPGEDGVTREEVEPE
mutated  not conserved    303PPREDGVTREEVEP
Ptroglodytes  all identical  ENSPTRG00000013240  303PPGEDGVTREEVEP
Mmulatta  all identical  ENSMMUG00000021137  303PPGEDSVTREEVEP
Fcatus  not conserved  ENSFCAG00000009833  252ERNDVQDQGPLRE---VQEDGEP
Mmusculus  not conserved  ENSMUSG00000034723  299VVKEGSVSPKE---
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000053942  n/a
Dmelanogaster  not conserved  FBgn0034914  299ADSEPEKEEKP--EPKQAGDAAP
Celegans  no alignment  F46E10.9  n/a
Xtropicalis  not conserved  ENSXETG00000026035  321SDGDANNAQNVAKDSDED
protein features
start (aa)end (aa)featuredetails 
224334COMPBIASGlu-rich.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1050 / 1050
position (AA) of stopcodon in wt / mu AA sequence 350 / 350
position of stopcodon in wt / mu cDNA 1266 / 1266
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 217 / 217
chromosome 20
strand -1
last intron/exon boundary 896
theoretical NMD boundary in CDS 629
length of CDS 1050
coding sequence (CDS) position 907
cDNA position
(for ins/del: last normal base / first normal base)
1123
gDNA position
(for ins/del: last normal base / first normal base)
37436
chromosomal position
(for ins/del: last normal base / first normal base)
7963041
original gDNA sequence snippet CCAATGATCAGGGGCCCCCAGGAGAGGACGGTGTGACCCGG
altered gDNA sequence snippet CCAATGATCAGGGGCCCCCAAGAGAGGACGGTGTGACCCGG
original cDNA sequence snippet CCAATGATCAGGGGCCCCCAGGAGAGGACGGTGTGACCCGG
altered cDNA sequence snippet CCAATGATCAGGGGCCCCCAAGAGAGGACGGTGTGACCCGG
wildtype AA sequence MAGGRCGPQL TALLAAWIAA VAATAGPEEA ALPPEQSRVQ PMTASNWTLV MEGEWMLKFY
APWCPSCQQT DSEWEAFAKN GEILQISVGK VDVIQEPGLS GRFFVTTLPA FFHAKDGIFR
RYRGPGIFED LQNYILEKKW QSVEPLTGWK SPASLTMSGM AGLFSISGKI WHLHNYFTVT
LGIPAWCSYV FFVIATLVFG LFMGLVLVVI SECFYVPLPR HLSERSEQNR RSEEAHRAEQ
LQDAEEEKDD SNEEENKDSL VDDEEEKEDL GDEDEAEEEE EEDNLAAGVD EERSEANDQG
PPGEDGVTRE EVEPEEAEEG ISEQPCPADT EVVEDSLRQR KSQHADKGL*
mutated AA sequence MAGGRCGPQL TALLAAWIAA VAATAGPEEA ALPPEQSRVQ PMTASNWTLV MEGEWMLKFY
APWCPSCQQT DSEWEAFAKN GEILQISVGK VDVIQEPGLS GRFFVTTLPA FFHAKDGIFR
RYRGPGIFED LQNYILEKKW QSVEPLTGWK SPASLTMSGM AGLFSISGKI WHLHNYFTVT
LGIPAWCSYV FFVIATLVFG LFMGLVLVVI SECFYVPLPR HLSERSEQNR RSEEAHRAEQ
LQDAEEEKDD SNEEENKDSL VDDEEEKEDL GDEDEAEEEE EEDNLAAGVD EERSEANDQG
PPREDGVTRE EVEPEEAEEG ISEQPCPADT EVVEDSLRQR KSQHADKGL*
speed 1.17 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