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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: ENST00000333822
MT speed 1.83 s - this script 7.275302 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRTAP4-8polymorphism_automatic4.36919003190539e-05simple_aaeaffectedN123Tsingle base exchangers147906218show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999956308099681 (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) chr17:39253969T>GN/A show variant in all transcripts   IGV
HGNC symbol KRTAP4-8
Ensembl transcript ID ENST00000333822
Genbank transcript ID NM_031960
UniProt peptide Q9BYQ9
alteration type single base exchange
alteration region CDS
DNA changes c.368A>C
cDNA.425A>C
g.425A>C
AA changes N123T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS
123
frameshift no
known variant Reference ID: rs147906218
databasehomozygous (G/G)heterozygousallele carriers
1000G60912751884
ExAC39237276
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2280.617
-1.0570.515
(flanking)1.2020.833
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased419wt: 0.2923 / mu: 0.3239 (marginal change - not scored)wt: CTGCCAGTCTGTGTGCTGCCAGCCCAACTGCTGCCGCCCCA
mu: CTGCCAGTCTGTGTGCTGCCAGCCCACCTGCTGCCGCCCCA
 gcca|GCCC
Acc gained4270.40mu: CTGTGTGCTGCCAGCCCACCTGCTGCCGCCCCAGCTGCAGC acct|GCTG
distance from splice site 425
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      123PQCCQSVCCQPNCCRPSCSISSCC
mutated  not conserved    123QPTCCRPSCSISSC
Ptroglodytes  all identical  ENSPTRG00000030935  143PQCCQSVCCQPNCCHPSCSISSC
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000069718  118SSSCCGSSCCRP------C
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 
14164REGION25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].lost
119123REPEAT20.lost
123123CONFLICTN -> T (in Ref. 2; CAC27579).lost
124128REPEAT21.might get lost (downstream of altered splice site)
126126CONFLICTR -> H (in Ref. 2; CAC27579).might get lost (downstream of altered splice site)
134138REPEAT22.might get lost (downstream of altered splice site)
139143REPEAT23.might get lost (downstream of altered splice site)
144148REPEAT24.might get lost (downstream of altered splice site)
149164REPEAT25.might get lost (downstream of altered splice site)
151151CONFLICTL -> V (in Ref. 2; CAC27579).might get lost (downstream of altered splice site)
168168CONFLICTA -> T (in Ref. 2; CAC27579).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 558 / 558
position (AA) of stopcodon in wt / mu AA sequence 186 / 186
position of stopcodon in wt / mu cDNA 615 / 615
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 58 / 58
chromosome 17
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 558
coding sequence (CDS) position 368
cDNA position
(for ins/del: last normal base / first normal base)
425
gDNA position
(for ins/del: last normal base / first normal base)
425
chromosomal position
(for ins/del: last normal base / first normal base)
39253969
original gDNA sequence snippet GTCTGTGTGCTGCCAGCCCAACTGCTGCCGCCCCAGCTGCA
altered gDNA sequence snippet GTCTGTGTGCTGCCAGCCCACCTGCTGCCGCCCCAGCTGCA
original cDNA sequence snippet GTCTGTGTGCTGCCAGCCCAACTGCTGCCGCCCCAGCTGCA
altered cDNA sequence snippet GTCTGTGTGCTGCCAGCCCACCTGCTGCCGCCCCAGCTGCA
wildtype AA sequence MVNSCCGSVC SDQGCGQDLC QETCCCPSCC QTTCCRTTCY RPSYSVSCCC RPQCCQSVCC
QPTCCRPSCC VSSCCKPQCC QSVCCQPTCC HPSCCISSCC RPSCCVSSCC KPQCCQSVCC
QPNCCRPSCS ISSCCRPSCC ESSCCRPCCC LRPVCGRVSC HTTCYRPACV ISTCPRPVCC
ASSCC*
mutated AA sequence MVNSCCGSVC SDQGCGQDLC QETCCCPSCC QTTCCRTTCY RPSYSVSCCC RPQCCQSVCC
QPTCCRPSCC VSSCCKPQCC QSVCCQPTCC HPSCCISSCC RPSCCVSSCC KPQCCQSVCC
QPTCCRPSCS ISSCCRPSCC ESSCCRPCCC LRPVCGRVSC HTTCYRPACV ISTCPRPVCC
ASSCC*
speed 1.83 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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