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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: ENST00000281047
MT speed 0 s - this script 5.785143 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MSGN1polymorphism_automatic0simple_aaeE80Dsingle base exchangers34069439show file

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Prediction

polymorphism

Model: simple_aae, prob: 1 (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) chr2:17998025A>TN/A show variant in all transcripts   IGV
HGNC symbol MSGN1
Ensembl transcript ID ENST00000281047
Genbank transcript ID NM_001105569
UniProt peptide A6NI15
alteration type single base exchange
alteration region CDS
DNA changes c.240A>T
cDNA.263A>T
g.263A>T
AA changes E80D Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS
80
frameshift no
known variant Reference ID: rs34069439
databasehomozygous (T/T)heterozygousallele carriers
1000G3369401276
ExAC14434389918333
regulatory features H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0420
-0.0080
(flanking)0.6190
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 263
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      80CEHGGASSGGSEGCSVGGASGLVE
mutated  all conserved    80CEHGGASSGGSDGCSVGGASGLV
Ptroglodytes  all conserved  ENSPTRG00000011679  80CEHGGASSGGSDGCSVGGASGLV
Mmulatta  all conserved  ENSMMUG00000008141  80CEHGGASSGGSDGCSVGGASGLV
Fcatus  not conserved  ENSFCAG00000013583  80CGHGGANSGGSGACGGRGTGGLG
Mmusculus  all conserved  ENSMUSG00000047002  78CGHSGASTGGSDGYGSHEAAGLV
Ggallus  not conserved  ENSGALG00000016469  69GGGL-----------------
Trubripes  no alignment  ENSTRUG00000008888  n/a
Drerio  not conserved  ENSDARG00000070546  70CEHA---------
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000015571  85----------------SHTQGLE
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 582 / 582
position (AA) of stopcodon in wt / mu AA sequence 194 / 194
position of stopcodon in wt / mu cDNA 605 / 605
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 24 / 24
chromosome 2
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 582
coding sequence (CDS) position 240
cDNA position
(for ins/del: last normal base / first normal base)
263
gDNA position
(for ins/del: last normal base / first normal base)
263
chromosomal position
(for ins/del: last normal base / first normal base)
17998025
original gDNA sequence snippet GCCAGCAGTGGGGGCAGCGAAGGCTGCAGTGTCGGTGGGGC
altered gDNA sequence snippet GCCAGCAGTGGGGGCAGCGATGGCTGCAGTGTCGGTGGGGC
original cDNA sequence snippet GCCAGCAGTGGGGGCAGCGAAGGCTGCAGTGTCGGTGGGGC
altered cDNA sequence snippet GCCAGCAGTGGGGGCAGCGATGGCTGCAGTGTCGGTGGGGC
wildtype AA sequence MDNLRETFLS LEDGLGSSDS PGLLSSWDWK DRAGPFELNQ ASPSQSLSPA PSLESYSSSP
CPAVAGLPCE HGGASSGGSE GCSVGGASGL VEVDYNMLAF QPTHLQGGGG PKAQKGTKVR
MSVQRRRKAS EREKLRMRTL ADALHTLRNY LPPVYSQRGQ PLTKIQTLKY TIKYIGELTD
LLNRGREPRA QSA*
mutated AA sequence MDNLRETFLS LEDGLGSSDS PGLLSSWDWK DRAGPFELNQ ASPSQSLSPA PSLESYSSSP
CPAVAGLPCE HGGASSGGSD GCSVGGASGL VEVDYNMLAF QPTHLQGGGG PKAQKGTKVR
MSVQRRRKAS EREKLRMRTL ADALHTLRNY LPPVYSQRGQ PLTKIQTLKY TIKYIGELTD
LLNRGREPRA QSA*
speed 1.67 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