Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999839117028 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr16:1538464C>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 intron
DNA changes g.519G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2745103
databasehomozygous (T/T)heterozygousallele carriers
1000G2108711081
ExAC39802138725367
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5350
0.5360.003
(flanking)0.1050.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased516wt: 0.9532 / mu: 0.9560 (marginal change - not scored)wt: TGTCATGGGGAGTGG
mu: TGTCATGGAGAGTGG		 TCAT|gggg
Donor increased511wt: 0.80 / mu: 0.91wt: GGTAGTGTCATGGGG
mu: GGTAGTGTCATGGAG		 TAGT|gtca
Donor increased523wt: 0.47 / mu: 0.63wt: GGGAGTGGAAACTGG
mu: GAGAGTGGAAACTGG		 GAGT|ggaa
distance from splice site 306
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
6767CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9191CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
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 2 (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 519
chromosomal position
(for ins/del: last normal base / first normal base)		 1538464
original gDNA sequence snippet GGGGCCGGGTAGTGTCATGGGGAGTGGAAACTGGGAGGTCA
altered gDNA sequence snippet GGGGCCGGGTAGTGTCATGGAGAGTGGAAACTGGGAGGTCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
speed 0.35 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