Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999998848583 (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) chr9:140262426C>TN/A show variant in all transcripts   IGV
HGNC symbol EXD3
Ensembl transcript ID ENST00000479452
Genbank transcript ID N/A
UniProt peptide Q8N9H8
alteration type single base exchange
alteration region CDS
DNA changes c.478G>A
cDNA.567G>A
g.55289G>A
AA changes A160T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 160
frameshift no
known variant Reference ID: rs11533158
databasehomozygous (T/T)heterozygousallele carriers
1000G12939502243
ExAC29158-255493609
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2110.211
-0.2390.211
(flanking)1.8730.257
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 increased55294wt: 0.9405 / mu: 0.9766 (marginal change - not scored)wt: GCGACGTTGAAGCTG
mu: ACGACGTTGAAGCTG		 GACG|ttga
Donor increased55281wt: 0.55 / mu: 0.78wt: AGCCACGCTGGGCGC
mu: AGCCACGCTGGGCAC		 CCAC|gctg
Donor gained552850.81mu: ACGCTGGGCACGACG GCTG|ggca
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      160EGRFREAATLGATLKLQSELGVEK
mutated  not conserved    160EGRFREAATLGTTLKLQSELGVE
Ptroglodytes  no homologue    
Mmulatta  no alignment  ENSMMUG00000032154  n/a
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000063140  152CCCFKEALVFSVKMELQSDLDME
Dmelanogaster  not conserved  FBgn0032924  194NGLYKEVTQWSISLQLTHEFDML
Celegans  not conserved  ZK1098.3  187KFKEAAEIVMKHEVVDDYSFE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
160160CONFLICTA -> T (in Ref. 2; BAC04356 and 4; AAH37355/AAI10880).lost
249249CONFLICTG -> S (in Ref. 2; BAC04356).might get lost (downstream of altered splice site)
322322CONFLICTE -> D (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).might get lost (downstream of altered splice site)
517571DOMAIN3'-5' exonuclease.might get lost (downstream of altered splice site)
519519CONFLICTS -> T (in Ref. 1; BAC10986).might get lost (downstream of altered splice site)
545545CONFLICTC -> Y (in Ref. 1; BAC10986 and 2; BAC04356/BAB70838).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 741 / 741
position (AA) of stopcodon in wt / mu AA sequence 247 / 247
position of stopcodon in wt / mu cDNA 830 / 830
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 90 / 90
chromosome 9
strand -1
last intron/exon boundary 746
theoretical NMD boundary in CDS 606
length of CDS 741
coding sequence (CDS) position 478
cDNA position
(for ins/del: last normal base / first normal base)		 567
gDNA position
(for ins/del: last normal base / first normal base)		 55289
chromosomal position
(for ins/del: last normal base / first normal base)		 140262426
original gDNA sequence snippet GCCAGGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG
altered gDNA sequence snippet GCCAGGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG
original cDNA sequence snippet GAGAAGCAGCCACGCTGGGCGCGACGTTGAAGCTGCAGTCG
altered cDNA sequence snippet GAGAAGCAGCCACGCTGGGCACGACGTTGAAGCTGCAGTCG
wildtype AA sequence MDPGDPAGDP AAGERHRMGR DPLLLLQALQ TLWSTRERKQ LREEAWRGFA ALDDPLAGLL
DMLESCRGQR GEGPSLAAWI SHQLQCWLQA QPCPSLAQHS LRLKQLQARA VKVLTESPPS
LAAPLASIFQ LQDADRSCLL AHVHRLHHEG RFREAATLGA TLKLQSELGV EKMSIPLLLQ
DKVALVERYV AGFPDLQRRL LVLMDSWCQP GFDIKDVASC HVTAAGAAAS GEERLGLAGA
QPSSPE*
mutated AA sequence MDPGDPAGDP AAGERHRMGR DPLLLLQALQ TLWSTRERKQ LREEAWRGFA ALDDPLAGLL
DMLESCRGQR GEGPSLAAWI SHQLQCWLQA QPCPSLAQHS LRLKQLQARA VKVLTESPPS
LAAPLASIFQ LQDADRSCLL AHVHRLHHEG RFREAATLGT TLKLQSELGV EKMSIPLLLQ
DKVALVERYV AGFPDLQRRL LVLMDSWCQP GFDIKDVASC HVTAAGAAAS GEERLGLAGA
QPSSPE*
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