Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 4.03644766828775e-30 (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) chr16:15131962A>GN/A show variant in all transcripts   IGV
HGNC symbol PDXDC1
Ensembl transcript ID ENST00000535621
Genbank transcript ID N/A
UniProt peptide Q6P996
alteration type single base exchange
alteration region intron
DNA changes g.63515A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs1135999
databasehomozygous (G/G)heterozygousallele carriers
1000G33410551389
ExAC76091754925158
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3791
3.3931
(flanking)0.7761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased63513wt: 0.41 / mu: 0.52wt: TAGAGTAGGGCTTTATTTCCAGAAAACAGTGTGTGAGCTGG
mu: TAGAGTAGGGCTTTATTTCCAGGAAACAGTGTGTGAGCTGG		 tcca|GAAA
Acc increased63514wt: 0.53 / mu: 0.75wt: AGAGTAGGGCTTTATTTCCAGAAAACAGTGTGTGAGCTGGA
mu: AGAGTAGGGCTTTATTTCCAGGAAACAGTGTGTGAGCTGGA		 ccag|AAAA
Donor gained635140.50mu: TTCCAGGAAACAGTG CCAG|gaaa
distance from splice site 8049
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
687687MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
691691MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
718718MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
720720MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
721721MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
722722MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
724724MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
737737MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
757757MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
779779MOD_RESPhosphoserine.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 189 / 189
chromosome 16
strand 1
last intron/exon boundary 1588
theoretical NMD boundary in CDS 1349
length of CDS 1497
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)		 63515
chromosomal position
(for ins/del: last normal base / first normal base)		 15131962
original gDNA sequence snippet GAGTAGGGCTTTATTTCCAGAAAACAGTGTGTGAGCTGGAG
altered gDNA sequence snippet GAGTAGGGCTTTATTTCCAGGAAACAGTGTGTGAGCTGGAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDASLEKIAD PTLAEMGKNL KEAVKMLEDS QRRTEEENGK KLISGDIPGP LQGSGQDMVS
ILQLVQNLMH GDEDEEPQSP RIQNIGEQGH MALLGHSLGA YISTLDKEKL RKLTTRILSD
TTLWLCRIFR YENGCAYFHE EEREGLAKIC RLAIHSRYED FVVDGFNVLY NKKPVIYLSA
AARPGLGQYL CNQLGLPFPC LCRVPCNTVF GSQHQMDVAF LEKLIKDDIE RGRLPLLLVA
NAGTAAVGHT DKIGRLKELC EQYGIWLHVE GVNLATLALG YVSSSVLAAA KCDSMTMTPG
PWLGLPAVPA VTLYKHDDPA LTLVAGLTSN KPTDKLRALP LWLSLQYLGL DGFVERIKHA
CQLSQRLQES LKKVNYIKIL VEDELSSPVV VFRFFQELPG SDPVFKAVPV PNMTPSGVGR
ERHSCDALNR WLGEQLKQLV PASGLTVMDL EAEGTCLRFS PLMTAAGWSH CGTTTRYDCV
RSRLTTRLPG STGEQAPP*
mutated AA sequence N/A
speed 0.97 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