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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: ENST00000304748
MT speed 0.89 s - this script 3.957969 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FPR1polymorphism_automatic1.99840144432528e-15simple_aaeaffectedV101Lsingle base exchangers2070745show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999998 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM074876)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:52249947C>GN/A show variant in all transcripts   IGV
HGNC symbol FPR1
Ensembl transcript ID ENST00000304748
Genbank transcript ID NM_002029
UniProt peptide P21462
alteration type single base exchange
alteration region CDS
DNA changes c.301G>C
cDNA.396G>C
g.5204G>C
AA changes V101L Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS
101
frameshift no
known variant Reference ID: rs2070745
databasehomozygous (G/G)heterozygousallele carriers
1000G40711581565
ExAC98341309922933

known disease mutation at this position, please check HGMD for details (HGMD ID CM074876)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3050.001
-0.1870.001
(flanking)-0.330.005
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased5213wt: 0.68 / mu: 0.88wt: TGTGCAAATTCGTCTTTACCATAGTGGACATCAACTTGTTC
mu: TGTGCAAATTCCTCTTTACCATAGTGGACATCAACTTGTTC
 acca|TAGT
Acc marginally increased5199wt: 0.8481 / mu: 0.8655 (marginal change - not scored)wt: TTTCGGCTGGTTCCTGTGCAAATTCGTCTTTACCATAGTGG
mu: TTTCGGCTGGTTCCTGTGCAAATTCCTCTTTACCATAGTGG
 gcaa|ATTC
Acc increased5214wt: 0.20 / mu: 0.37wt: GTGCAAATTCGTCTTTACCATAGTGGACATCAACTTGTTCG
mu: GTGCAAATTCCTCTTTACCATAGTGGACATCAACTTGTTCG
 ccat|AGTG
Acc increased5211wt: 0.25 / mu: 0.65wt: CCTGTGCAAATTCGTCTTTACCATAGTGGACATCAACTTGT
mu: CCTGTGCAAATTCCTCTTTACCATAGTGGACATCAACTTGT
 ttac|CATA
Donor marginally increased5195wt: 0.9142 / mu: 0.9676 (marginal change - not scored)wt: TCCTGTGCAAATTCG
mu: TCCTGTGCAAATTCC
 CTGT|gcaa
distance from splice site 312
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      101HWPFGWFLCKFVFTIVDINLFGSV
mutated  all conserved    101HWPFGWFLCKFLFTIVDINLFGS
Ptroglodytes  all conserved  ENSPTRG00000011395  101HWPFGWFLCKFIFTIVDINLFGS
Mmulatta  all conserved  ENSMMUG00000013049  101HWPFGWFLCKFIFSIVDINLFGS
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000045551  109HWPFGWFMCKFIYTVIDINLFGS
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 
101121TRANSMEMHelical; Name=3; (Potential).lost
122140TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
141162TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
163205TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
176176DISULFIDPotential.might get lost (downstream of altered splice site)
206226TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
227242TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
238238CONFLICTR -> P (in Ref. 1; AAA36362).might get lost (downstream of altered splice site)
243266TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
267285TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
286305TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
306350TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
328328MOD_RESPhosphoserine (Potential).might get lost (downstream of altered splice site)
329329MOD_RESPhosphothreonine (Potential).might get lost (downstream of altered splice site)
331331MOD_RESPhosphothreonine (Potential).might get lost (downstream of altered splice site)
332332MOD_RESPhosphoserine (Potential).might get lost (downstream of altered splice site)
334334MOD_RESPhosphothreonine (Potential).might get lost (downstream of altered splice site)
336336MOD_RESPhosphothreonine (Potential).might get lost (downstream of altered splice site)
338338MOD_RESPhosphoserine (Potential).might get lost (downstream of altered splice site)
339339MOD_RESPhosphothreonine (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1053 / 1053
position (AA) of stopcodon in wt / mu AA sequence 351 / 351
position of stopcodon in wt / mu cDNA 1148 / 1148
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 96 / 96
chromosome 19
strand -1
last intron/exon boundary 85
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1053
coding sequence (CDS) position 301
cDNA position
(for ins/del: last normal base / first normal base)
396
gDNA position
(for ins/del: last normal base / first normal base)
5204
chromosomal position
(for ins/del: last normal base / first normal base)
52249947
original gDNA sequence snippet GCTGGTTCCTGTGCAAATTCGTCTTTACCATAGTGGACATC
altered gDNA sequence snippet GCTGGTTCCTGTGCAAATTCCTCTTTACCATAGTGGACATC
original cDNA sequence snippet GCTGGTTCCTGTGCAAATTCGTCTTTACCATAGTGGACATC
altered cDNA sequence snippet GCTGGTTCCTGTGCAAATTCCTCTTTACCATAGTGGACATC
wildtype AA sequence METNSSLPTN ISGGTPAVSA GYLFLDIITY LVFAVTFVLG VLGNGLVIWV AGFRMTHTVT
TISYLNLAVA DFCFTSTLPF FMVRKAMGGH WPFGWFLCKF VFTIVDINLF GSVFLIALIA
LDRCVCVLHP VWTQNHRTVS LAKKVIIGPW VMALLLTLPV IIRVTTVPGK TGTVACTFNF
SPWTNDPKER INVAVAMLTV RGIIRFIIGF SAPMSIVAVS YGLIATKIHK QGLIKSSRPL
RVLSFVAAAF FLCWSPYQVV ALIATVRIRE LLQGMYKEIG IAVDVTSALA FFNSCLNPML
YVFMGQDFRE RLIHALPASL ERALTEDSTQ TSDTATNSTL PSAEVELQAK *
mutated AA sequence METNSSLPTN ISGGTPAVSA GYLFLDIITY LVFAVTFVLG VLGNGLVIWV AGFRMTHTVT
TISYLNLAVA DFCFTSTLPF FMVRKAMGGH WPFGWFLCKF LFTIVDINLF GSVFLIALIA
LDRCVCVLHP VWTQNHRTVS LAKKVIIGPW VMALLLTLPV IIRVTTVPGK TGTVACTFNF
SPWTNDPKER INVAVAMLTV RGIIRFIIGF SAPMSIVAVS YGLIATKIHK QGLIKSSRPL
RVLSFVAAAF FLCWSPYQVV ALIATVRIRE LLQGMYKEIG IAVDVTSALA FFNSCLNPML
YVFMGQDFRE RLIHALPASL ERALTEDSTQ TSDTATNSTL PSAEVELQAK *
speed 0.89 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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