Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000264387
Querying Taster for transcript #2: ENST00000409066
MT speed 0 s - this script 3.770014 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
C2orf83polymorphism_automatic1.18105525359624e-12simple_aaeS45Lsingle base exchangers28739019show file
C2orf83polymorphism_automatic1.18105525359624e-12simple_aaeS45Lsingle base exchangers28739019show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999998819 (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) chr2:228493211G>AN/A show variant in all transcripts   IGV
HGNC symbol C2orf83
Ensembl transcript ID ENST00000264387
Genbank transcript ID NM_020161
UniProt peptide Q53S99
alteration type single base exchange
alteration region CDS
DNA changes c.134C>T
cDNA.221C>T
g.4826C>T
AA changes S45L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 45
frameshift no
known variant Reference ID: rs28739019
databasehomozygous (A/A)heterozygousallele carriers
1000G31010821392
ExAC133445755909
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9710
-0.7270
(flanking)-0.2490
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 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      45LPVDIQHKAKPSPKASQMLPPDLG
mutated  not conserved    45LPVDIQHKAKPLPKASQMLPPDL
Ptroglodytes  all identical  ENSPTRG00000012996  45LPVDIQHKAKPSPKASQMLPPDL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
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 453 / 453
position (AA) of stopcodon in wt / mu AA sequence 151 / 151
position of stopcodon in wt / mu cDNA 540 / 540
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 88 / 88
chromosome 2
strand -1
last intron/exon boundary 278
theoretical NMD boundary in CDS 140
length of CDS 453
coding sequence (CDS) position 134
cDNA position
(for ins/del: last normal base / first normal base)		 221
gDNA position
(for ins/del: last normal base / first normal base)		 4826
chromosomal position
(for ins/del: last normal base / first normal base)		 228493211
original gDNA sequence snippet ACAGCACAAAGCAAAGCCCTCGCCAAAAGCCAGCCAGATGC
altered gDNA sequence snippet ACAGCACAAAGCAAAGCCCTTGCCAAAAGCCAGCCAGATGC
original cDNA sequence snippet TCAGCACAAAGCAAAGCCCTCGCCAAAAGCCAGCCAGATGC
altered cDNA sequence snippet TCAGCACAAAGCAAAGCCCTTGCCAAAAGCCAGCCAGATGC
wildtype AA sequence MEDYALTFGI NPFIALMIQP IVTMTVVDNQ GLGLPVDIQH KAKPSPKASQ MLPPDLGPPS
FQNLLSPSEK LEPWDPGMRK LTVQTCGLTF IHPAGHGLCH PTAEASAETL SSTALNRPSV
REGACNEKST ENKKPQDSVL WSHSRWFQGN *
mutated AA sequence MEDYALTFGI NPFIALMIQP IVTMTVVDNQ GLGLPVDIQH KAKPLPKASQ MLPPDLGPPS
FQNLLSPSEK LEPWDPGMRK LTVQTCGLTF IHPAGHGLCH PTAEASAETL SSTALNRPSV
REGACNEKST ENKKPQDSVL WSHSRWFQGN *
speed 0.78 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999998819 (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) chr2:228493211G>AN/A show variant in all transcripts   IGV
HGNC symbol C2orf83
Ensembl transcript ID ENST00000409066
Genbank transcript ID NM_001162483
UniProt peptide Q53S99
alteration type single base exchange
alteration region CDS
DNA changes c.134C>T
cDNA.369C>T
g.4826C>T
AA changes S45L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 45
frameshift no
known variant Reference ID: rs28739019
databasehomozygous (A/A)heterozygousallele carriers
1000G31010821392
ExAC133445755909
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9710
-0.7270
(flanking)-0.2490
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 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      45LPVDIQHKAKPSPKASQMLPPDLG
mutated  not conserved    45LPVDIQHKAKPLPKASQMLPPDL
Ptroglodytes  all identical  ENSPTRG00000012996  45LPVDIQHKAKPSPKASQMLPPDL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
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 291 / 291
position (AA) of stopcodon in wt / mu AA sequence 97 / 97
position of stopcodon in wt / mu cDNA 526 / 526
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 236 / 236
chromosome 2
strand -1
last intron/exon boundary 521
theoretical NMD boundary in CDS 235
length of CDS 291
coding sequence (CDS) position 134
cDNA position
(for ins/del: last normal base / first normal base)		 369
gDNA position
(for ins/del: last normal base / first normal base)		 4826
chromosomal position
(for ins/del: last normal base / first normal base)		 228493211
original gDNA sequence snippet ACAGCACAAAGCAAAGCCCTCGCCAAAAGCCAGCCAGATGC
altered gDNA sequence snippet ACAGCACAAAGCAAAGCCCTTGCCAAAAGCCAGCCAGATGC
original cDNA sequence snippet TCAGCACAAAGCAAAGCCCTCGCCAAAAGCCAGCCAGATGC
altered cDNA sequence snippet TCAGCACAAAGCAAAGCCCTTGCCAAAAGCCAGCCAGATGC
wildtype AA sequence MEDYALTFGI NPFIALMIQP IVTMTVVDNQ GLGLPVDIQH KAKPSPKASQ MLPPDLGPPS
FQNCFTCRTA PSLVMVLSWK SGVRREVPVH PSYAKY*
mutated AA sequence MEDYALTFGI NPFIALMIQP IVTMTVVDNQ GLGLPVDIQH KAKPLPKASQ MLPPDLGPPS
FQNCFTCRTA PSLVMVLSWK SGVRREVPVH PSYAKY*
speed 1.04 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
back to results table

Problems