Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999974 (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) chr16:1536535C>TN/A show variant in all transcripts   IGV
HGNC symbol PTX4
Ensembl transcript ID ENST00000293922
Genbank transcript ID NM_001013658
UniProt peptide Q96A99
alteration type single base exchange
alteration region CDS
DNA changes c.827G>A
cDNA.827G>A
g.2448G>A
AA changes R276K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 276
frameshift no
known variant Reference ID: rs2745098
databasehomozygous (T/T)heterozygousallele carriers
1000G70810701778
ExAC101761241522591
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1020.215
0.8580.156
(flanking)0.0060.007
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained24430.89mu: GCCTCCACCAAGAAC CTCC|acca
distance from splice site 46
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      276GPTLVFPNASTRNVVFLSPGFVTA
mutated  all conserved    276GPTLVFPNASTKNVVFLSPGFVT
Ptroglodytes  all conserved  ENSPTRG00000007595  281GPTLVFPNASTKNVVFLS
Mmulatta  all conserved  ENSMMUG00000007049  281GPTLVFPNASTKNVVFLS
Fcatus  all conserved  ENSFCAG00000010651  239GPVLVFPNASTQNVAFLSPGFPA
Mmusculus  not conserved  ENSMUSG00000044172  281TSTENVIFLSPGFLM
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000038072  329GSMLLFPSTSTENYAIFQKTFQT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000009128  271DSMLVFPNASTENFVTFSKGLRH
protein features
start (aa)end (aa)featuredetails 
271469DOMAINPentaxin.lost
300300DISULFIDBy similarity.might get lost (downstream of altered splice site)
323323METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
364364DISULFIDBy similarity.might get lost (downstream of altered splice site)
406406METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
406406METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
407407METALCalcium 1; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1422 / 1422
position (AA) of stopcodon in wt / mu AA sequence 474 / 474
position of stopcodon in wt / mu cDNA 1422 / 1422
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 1 / 1
chromosome 16
strand -1
last intron/exon boundary 782
theoretical NMD boundary in CDS 731
length of CDS 1422
coding sequence (CDS) position 827
cDNA position
(for ins/del: last normal base / first normal base)		 827
gDNA position
(for ins/del: last normal base / first normal base)		 2448
chromosomal position
(for ins/del: last normal base / first normal base)		 1536535
original gDNA sequence snippet TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC
altered gDNA sequence snippet TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC
original cDNA sequence snippet TTTCCCAAACGCCTCCACCAGGAACGTGGTCTTCCTCAGCC
altered cDNA sequence snippet TTTCCCAAACGCCTCCACCAAGAACGTGGTCTTCCTCAGCC
wildtype AA sequence MGSGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTRNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*
mutated AA sequence MGSGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTKNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*
speed 0.95 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