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 ENST00000447419
Genbank transcript ID N/A
UniProt peptide Q96A99
alteration type single base exchange
alteration region CDS
DNA changes c.842G>A
cDNA.868G>A
g.2448G>A
AA changes R281K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 281
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      281GPTLVFPNASTRNVVFLSPGFVTA
mutated  all conserved    281GPTLVFPNASTKNVVFLSPGFVT
Ptroglodytes  all conserved  ENSPTRG00000007595  281GPTLVFPNASTKNVVFLSPGFVT
Mmulatta  all conserved  ENSMMUG00000007049  281GPTLVFPNASTKNVVFLSPGFVT
Fcatus  all conserved  ENSFCAG00000010651  239GPVLVFPNASTQNVAFLSPGFPA
Mmusculus  not conserved  ENSMUSG00000044172  291DPVLIFPNTSTENVIFLSPGF
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000038072  334STSTENYAIFQKTFQT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000009128  283VFPNASTENFVTFSKGLRH
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 1437 / 1437
position (AA) of stopcodon in wt / mu AA sequence 479 / 479
position of stopcodon in wt / mu cDNA 1463 / 1463
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 27 / 27
chromosome 16
strand -1
last intron/exon boundary 823
theoretical NMD boundary in CDS 746
length of CDS 1437
coding sequence (CDS) position 842
cDNA position
(for ins/del: last normal base / first normal base)		 868
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 MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKVDT
RLRALDLTLG ERSQQRARER KAHKAQRDAL QDSLARLEGL VHSQGARLAA LEGRLPVAHP
GTAALGPALV PTPTQPEELG PTSLKLQRDR QELRAASEHR GPPQDSSAPL QGRREPPASG
SHRVLSGTAP KDPRQQAWSP QVPGEICGVG PTLVFPNAST RNVVFLSPGF VTALRALSFC
SWVRTASGRL GTLLSYATED NDNKLVLHGR DSLLPGSIHF VIGDPAFREL PLQLLLDGQW
HHICVIWTST QGRYWLHVDR RLVATGSRFR EGYEIPPGGS LVLGQEQDSV GGGFDSSEAF
VGSMSGLAIW DRALVPGEVA NLAIGKEFPT GAILTLANAA LAGGFVQGAN CTCLERCP*
mutated AA sequence MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKVDT
RLRALDLTLG ERSQQRARER KAHKAQRDAL QDSLARLEGL VHSQGARLAA LEGRLPVAHP
GTAALGPALV PTPTQPEELG PTSLKLQRDR QELRAASEHR GPPQDSSAPL QGRREPPASG
SHRVLSGTAP KDPRQQAWSP QVPGEICGVG PTLVFPNAST KNVVFLSPGF VTALRALSFC
SWVRTASGRL GTLLSYATED NDNKLVLHGR DSLLPGSIHF VIGDPAFREL PLQLLLDGQW
HHICVIWTST QGRYWLHVDR RLVATGSRFR EGYEIPPGGS LVLGQEQDSV GGGFDSSEAF
VGSMSGLAIW DRALVPGEVA NLAIGKEFPT GAILTLANAA LAGGFVQGAN CTCLERCP*
speed 1.01 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