Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999998513054 (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 ENST00000440447
Genbank transcript ID N/A
UniProt peptide Q96A99
alteration type single base exchange
alteration region CDS
DNA changes c.397G>A
cDNA.469G>A
g.2448G>A
AA changes G133R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 133
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      133APPSFSQTPPPGTWSSSALVSSLP
mutated  not conserved    133APPSFSQTPPPRTWSSSALVSSL
Ptroglodytes  no alignment  ENSPTRG00000007595  n/a
Mmulatta  no alignment  ENSMMUG00000007049  n/a
Fcatus  no alignment  ENSFCAG00000010651  n/a
Mmusculus  no alignment  ENSMUSG00000044172  n/a
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000038072  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000009128  n/a
protein features
start (aa)end (aa)featuredetails 
271469DOMAINPentaxin.might get lost (downstream of altered splice site)
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 579 / 579
position (AA) of stopcodon in wt / mu AA sequence 193 / 193
position of stopcodon in wt / mu cDNA 651 / 651
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 73 / 73
chromosome 16
strand -1
last intron/exon boundary 424
theoretical NMD boundary in CDS 301
length of CDS 579
coding sequence (CDS) position 397
cDNA position
(for ins/del: last normal base / first normal base)		 469
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 LQRRGRKFAA
WAPPSFSQTP PPGTWSSSAL VSSLPCEPCP SAAGSARPPA AWAPSCPTPP RTMTTSWCCT
AETPCCPDPS TS*
mutated AA sequence MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKFAA
WAPPSFSQTP PPRTWSSSAL VSSLPCEPCP SAAGSARPPA AWAPSCPTPP RTMTTSWCCT
AETPCCPDPS TS*
speed 0.92 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