Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999880881 (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) chr10:20506418G>AN/A show variant in all transcripts   IGV
HGNC symbol PLXDC2
Ensembl transcript ID ENST00000377252
Genbank transcript ID NM_032812
UniProt peptide Q6UX71
alteration type single base exchange
alteration region CDS
DNA changes c.1186G>A
cDNA.2027G>A
g.401251G>A
AA changes V396I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 396
frameshift no
known variant Reference ID: rs3817405
databasehomozygous (A/A)heterozygousallele carriers
1000G89810401938
ExAC24194-156218573
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3910.218
-2.4850
(flanking)-0.2780
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 increased401251wt: 0.8847 / mu: 0.9345 (marginal change - not scored)wt: CAACCGTAGGAGCGA
mu: CAACCATAGGAGCGA		 ACCG|tagg
Donor increased401256wt: 0.72 / mu: 0.88wt: GTAGGAGCGACAACC
mu: ATAGGAGCGACAACC		 AGGA|gcga
Donor increased401253wt: 0.54 / mu: 0.89wt: ACCGTAGGAGCGACA
mu: ACCATAGGAGCGACA		 CGTA|ggag
Donor increased401243wt: 0.44 / mu: 0.66wt: AACCACCACAACCGT
mu: AACCACCACAACCAT		 CCAC|caca
distance from splice site 64
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      396PVETSSRTTTTVGATTTQFRVLTT
mutated  all conserved    396PVETSSRTTTTIGATTTQFRVLT
Ptroglodytes  all identical  ENSPTRG00000002342  396PVETSSRTTTTVGATTTQFRVLT
Mmulatta  all identical  ENSMMUG00000015370  396PVETSSRTTTTVGATTTQFRVLT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000026748  396PGET-SQTTTTSHTTTMQFRVLT
Ggallus  all conserved  ENSGALG00000007956  395TTEALLYSTTTLQPTTTKFRVLT
Trubripes  not conserved  ENSTRUG00000008838  348PDTTVLYPVTTAAKTTPRSREV
Drerio  all identical  ENSDARG00000059950  390NMDLLTTASVVKMSTRNRGTT
Dmelanogaster  not conserved  FBgn0028331  497SGASAN--GATN
Celegans  not conserved  C36E8.3  397EDETYDEED-------------Y
Xtropicalis  all conserved  ENSXETG00000016596  371TTGVSHHATTGLHATTSIYSFTT
protein features
start (aa)end (aa)featuredetails 
31454TOPO_DOMExtracellular (Potential).lost
383427COMPBIASThr-rich.lost
455475TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
476529TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
506506MOD_RESPhosphoserine (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 1590 / 1590
position (AA) of stopcodon in wt / mu AA sequence 530 / 530
position of stopcodon in wt / mu cDNA 2431 / 2431
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 842 / 842
chromosome 10
strand 1
last intron/exon boundary 2315
theoretical NMD boundary in CDS 1423
length of CDS 1590
coding sequence (CDS) position 1186
cDNA position
(for ins/del: last normal base / first normal base)		 2027
gDNA position
(for ins/del: last normal base / first normal base)		 401251
chromosomal position
(for ins/del: last normal base / first normal base)		 20506418
original gDNA sequence snippet CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG
altered gDNA sequence snippet CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG
original cDNA sequence snippet CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG
altered cDNA sequence snippet CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG
wildtype AA sequence MARFPKADLA AAGVMLLCHF FTDQFQFADG KPGDQILDWQ YGVTQAFPHT EEEVEVDSHA
YSHRWKRNLD FLKAVDTNRA SVGQDSPEPR SFTDLLLDDG QDNNTQIEED TDHNYYISRI
YGPSDSASRD LWVNIDQMEK DKVKIHGILS NTHRQAARVN LSFDFPFYGH FLREITVATG
GFIYTGEVVH RMLTATQYIA PLMANFDPSV SRNSTVRYFD NGTALVVQWD HVHLQDNYNL
GSFTFQATLL MDGRIIFGYK EIPVLVTQIS STNHPVKVGL SDAFVVVHRI QQIPNVRRRT
IYEYHRVELQ MSKITNISAV EMTPLPTCLQ FNRCGPCVSS QIGFNCSWCS KLQRCSSGFD
RHRQDWVDSG CPEESKEKMC ENTEPVETSS RTTTTVGATT TQFRVLTTTR RAVTSQFPTS
LPTEDDTKIA LHLKDNGAST DDSAAEKKGG TLHAGLIIGI LILVLIVATA ILVTVYMYHH
PTSAASIFFI ERRPSRWPAM KFRRGSGHPA YAEVEPVGEK EGFIVSEQC*
mutated AA sequence MARFPKADLA AAGVMLLCHF FTDQFQFADG KPGDQILDWQ YGVTQAFPHT EEEVEVDSHA
YSHRWKRNLD FLKAVDTNRA SVGQDSPEPR SFTDLLLDDG QDNNTQIEED TDHNYYISRI
YGPSDSASRD LWVNIDQMEK DKVKIHGILS NTHRQAARVN LSFDFPFYGH FLREITVATG
GFIYTGEVVH RMLTATQYIA PLMANFDPSV SRNSTVRYFD NGTALVVQWD HVHLQDNYNL
GSFTFQATLL MDGRIIFGYK EIPVLVTQIS STNHPVKVGL SDAFVVVHRI QQIPNVRRRT
IYEYHRVELQ MSKITNISAV EMTPLPTCLQ FNRCGPCVSS QIGFNCSWCS KLQRCSSGFD
RHRQDWVDSG CPEESKEKMC ENTEPVETSS RTTTTIGATT TQFRVLTTTR RAVTSQFPTS
LPTEDDTKIA LHLKDNGAST DDSAAEKKGG TLHAGLIIGI LILVLIVATA ILVTVYMYHH
PTSAASIFFI ERRPSRWPAM KFRRGSGHPA YAEVEPVGEK EGFIVSEQC*
speed 0.94 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