Yum, tasty mutations...

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: ENST00000376168
MT speed 0.42 s - this script 2.415102 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PRAMEF5polymorphism3.47000206346593e-12simple_aaeT5Isingle base exchangeshow file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999653      (explain)
Summary
  • amino acid sequence changed
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:13364904C>TN/A show variant in all transcripts   IGV
HGNC symbol PRAMEF5
Ensembl transcript ID ENST00000376168
Genbank transcript ID NM_001013407
UniProt peptide Q5VXH4
alteration type single base exchange
alteration region CDS
DNA changes c.14C>T
cDNA.114C>T
g.5086C>T
AA changes T5I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 5
frameshift no
known variant Variant was neither found in ExAC nor 1000G.
Search ExAC.
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.8890.001
0.8790.008
(flanking)-0.0260.011
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 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      5 MSIRTPPRLLELAGRSL
mutated  not conserved    5 MSIRIPPRLLELAGRSLLRDQA
Ptroglodytes  all identical  ENSPTRG00000029626  5 MSIQTPPRLLELAGRSLLRDQA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000028591  5 MSLRATPTLLQLAMQSLLRDEA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1431 / 1431
position (AA) of stopcodon in wt / mu AA sequence 477 / 477
position of stopcodon in wt / mu cDNA 1531 / 1531
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 101 / 101
chromosome 1
strand 1
last intron/exon boundary 970
theoretical NMD boundary in CDS 819
length of CDS 1431
coding sequence (CDS) position 14
cDNA position
(for ins/del: last normal base / first normal base)		 114
gDNA position
(for ins/del: last normal base / first normal base)		 5086
chromosomal position
(for ins/del: last normal base / first normal base)		 13364904
original gDNA sequence snippet CGTGAAGATGAGCATCCGGACTCCACCCAGACTCCTGGAGC
altered gDNA sequence snippet CGTGAAGATGAGCATCCGGATTCCACCCAGACTCCTGGAGC
original cDNA sequence snippet CGTGAAGATGAGCATCCGGACTCCACCCAGACTCCTGGAGC
altered cDNA sequence snippet CGTGAAGATGAGCATCCGGATTCCACCCAGACTCCTGGAGC
wildtype AA sequence MSIRTPPRLL ELAGRSLLRD QALAMSTLEE LPTELFPPLF MEAFSRRRCE ALKLMVQAWP
FRRLPLRPLI KMPCLEAFQA VLDGLDALLT QGVHPRRWKL QVLDLQDVCE NFWMVWSEAM
AHGCFLNAKR NKKPVQDCPR MRGQQPLTVF VELWLKNRTL DEYLTCLLLW VKQRKDLLHL
CCKKLKILGM PFRNIRSILK MVNLDCIQEV EVNCKWVLPI LTQFTPYLGH MRNLQKLVLS
HMDVSRYVSP EQKKEIVTQF TTQFLKLCCL QKLSMNSVSF LEGHLDQLLS CLKTSLKVLT
ITNCVLLESD LKHLSQCPSI SQLKTLDLSG IRLTNYSLVP LQILLEKVAA TLEYLDLDDC
GIIDSQVNAI LPALSRCFEL NTFSFCGNPI SMATLENLLS HTIILKNLCV ELYPAPRESY
DADGTLCWSR FAQIRAELMK RVRDLRHPKR ILFCTDCCPD CGNRSFYDLE ADQCCC*
mutated AA sequence MSIRIPPRLL ELAGRSLLRD QALAMSTLEE LPTELFPPLF MEAFSRRRCE ALKLMVQAWP
FRRLPLRPLI KMPCLEAFQA VLDGLDALLT QGVHPRRWKL QVLDLQDVCE NFWMVWSEAM
AHGCFLNAKR NKKPVQDCPR MRGQQPLTVF VELWLKNRTL DEYLTCLLLW VKQRKDLLHL
CCKKLKILGM PFRNIRSILK MVNLDCIQEV EVNCKWVLPI LTQFTPYLGH MRNLQKLVLS
HMDVSRYVSP EQKKEIVTQF TTQFLKLCCL QKLSMNSVSF LEGHLDQLLS CLKTSLKVLT
ITNCVLLESD LKHLSQCPSI SQLKTLDLSG IRLTNYSLVP LQILLEKVAA TLEYLDLDDC
GIIDSQVNAI LPALSRCFEL NTFSFCGNPI SMATLENLLS HTIILKNLCV ELYPAPRESY
DADGTLCWSR FAQIRAELMK RVRDLRHPKR ILFCTDCCPD CGNRSFYDLE ADQCCC*
speed 0.42 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