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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: ENST00000429849
MT speed 1.44 s - this script 6.039246 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
C12orf71polymorphism_automatic4.00013355772444e-13simple_aaeaffectedI140Vsingle base exchangers708167show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.9999999999996 (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) chr12:27234999T>CN/A show variant in all transcripts   IGV
HGNC symbol C12orf71
Ensembl transcript ID ENST00000429849
Genbank transcript ID NM_001080406
UniProt peptide A8MTZ7
alteration type single base exchange
alteration region CDS
DNA changes c.418A>G
cDNA.449A>G
g.449A>G
AA changes I140V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
140
frameshift no
known variant Reference ID: rs708167
databasehomozygous (C/C)heterozygousallele carriers
1000G145604749
ExAC71851839725582
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.7580.012
0.6510.015
(flanking)0.0370.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained4430.51mu: AAGAGTTTCAGGTAT GAGT|ttca
distance from splice site 99
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      140GKLNNLVQEFQIFLENLKDDDAVF
mutated  all conserved    140GKLNNLVQEFQVFLENLKDDDAV
Ptroglodytes  all identical  ENSPTRG00000034261  140GKLNNLVQEFQIFLENLKDDDAV
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000040163  144CKLYNLVQKLETFLGKEKGGQHDGCV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
218218MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 810 / 810
position (AA) of stopcodon in wt / mu AA sequence 270 / 270
position of stopcodon in wt / mu cDNA 841 / 841
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 32 / 32
chromosome 12
strand -1
last intron/exon boundary 548
theoretical NMD boundary in CDS 466
length of CDS 810
coding sequence (CDS) position 418
cDNA position
(for ins/del: last normal base / first normal base)
449
gDNA position
(for ins/del: last normal base / first normal base)
449
chromosomal position
(for ins/del: last normal base / first normal base)
27234999
original gDNA sequence snippet ATCTTGTGCAAGAGTTTCAGATATTTCTAGAAAATCTGAAA
altered gDNA sequence snippet ATCTTGTGCAAGAGTTTCAGGTATTTCTAGAAAATCTGAAA
original cDNA sequence snippet ATCTTGTGCAAGAGTTTCAGATATTTCTAGAAAATCTGAAA
altered cDNA sequence snippet ATCTTGTGCAAGAGTTTCAGGTATTTCTAGAAAATCTGAAA
wildtype AA sequence MAYSSSNSDI EDDSSKSNSN LSLSVGYFPC EDTPCEDTTS WEDAPSKGPS IHFLPPVQGA
WGTERIGRRM KRQDQIQDEP EQFCKLSIFL AWDVDIGSDN TDSRANRLLN GDNLWIDKLP
KERTKLSVGK LNNLVQEFQI FLENLKDDDA VFPETAQQDF QLSSGSPPEM VQMISQATAS
QRTSAPEISS ILSEQPEKDD TPSHTQAQCC LNFGWAFSWL RQRILPSLLR RDHPVNATKS
PHRSAPTKRL FHRGKRIQPQ ETLELGHPI*
mutated AA sequence MAYSSSNSDI EDDSSKSNSN LSLSVGYFPC EDTPCEDTTS WEDAPSKGPS IHFLPPVQGA
WGTERIGRRM KRQDQIQDEP EQFCKLSIFL AWDVDIGSDN TDSRANRLLN GDNLWIDKLP
KERTKLSVGK LNNLVQEFQV FLENLKDDDA VFPETAQQDF QLSSGSPPEM VQMISQATAS
QRTSAPEISS ILSEQPEKDD TPSHTQAQCC LNFGWAFSWL RQRILPSLLR RDHPVNATKS
PHRSAPTKRL FHRGKRIQPQ ETLELGHPI*
speed 1.44 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