Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999522368 (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 ENST00000377238
Genbank transcript ID N/A
UniProt peptide Q6UX71
alteration type single base exchange
alteration region CDS
DNA changes c.775G>A
cDNA.2126G>A
g.401251G>A
AA changes V259I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 259
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      259PVETSSRTTTTVGATTTQFRVLTT
mutated  all conserved    259PVETSSRTTTTIGATTTQFRVLT
Ptroglodytes  all identical  ENSPTRG00000002342  396PVETSSRTTTTVGATTTQFRVLT
Mmulatta  all identical  ENSMMUG00000015370  396PVETSSRTTTTVGATTTQFRVLT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000026748  398PGET-SQTTTTSHTTTMQFRVLT
Ggallus  all conserved  ENSGALG00000007956  395TTEALLYSTTTLQPTTTKFRVLT
Trubripes  not conserved  ENSTRUG00000008838  350PDTTVLYPVTTAAKTTPRSREVT
Drerio  all identical  ENSDARG00000059950  390TTNMDLLTTASVVKMSTRNRGTT
Dmelanogaster  not conserved  FBgn0028331  497AAGQGKNGSANSGASAN--GATN
Celegans  not conserved  C36E8.3  397EDETYDEED-------------Y
Xtropicalis  all conserved  ENSXETG00000016596  371TTGVSHHATTGLHATTSIYSFTT
protein features
start (aa)end (aa)featuredetails 
31454TOPO_DOMExtracellular (Potential).lost
327372DOMAINPSI.might get lost (downstream of altered splice site)
383427COMPBIASThr-rich.might get lost (downstream of altered splice site)
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 1179 / 1179
position (AA) of stopcodon in wt / mu AA sequence 393 / 393
position of stopcodon in wt / mu cDNA 2530 / 2530
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 1352 / 1352
chromosome 10
strand 1
last intron/exon boundary 2414
theoretical NMD boundary in CDS 1012
length of CDS 1179
coding sequence (CDS) position 775
cDNA position
(for ins/del: last normal base / first normal base)		 2126
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 MEKDKVKIHG ILSNTHRQAA RVNLSFDFPF YGHFLREITV ATGGFIYTGE VVHRMLTATQ
YIAPLMANFD PSVSRNSTVR YFDNGTALVV QWDHVHLQDN YNLGSFTFQA TLLMDGRIIF
GYKEIPVLVT QISSTNHPVK VGLSDAFVVV HRIQQIPNVR RRTIYEYHRV ELQMSKITNI
SAVEMTPLPT CLQFNRCGPC VSSQIGFNCS WCSKLQRCSS GFDRHRQDWV DSGCPEESKE
KMCENTEPVE TSSRTTTTVG ATTTQFRVLT TTRRAVTSQF PTSLPTEDDT KIALHLKDNG
ASTDDSAAEK KGGTLHAGLI IGILILVLIV ATAILVTVYM YHHPTSAASI FFIERRPSRW
PAMKFRRGSG HPAYAEVEPV GEKEGFIVSE QC*
mutated AA sequence MEKDKVKIHG ILSNTHRQAA RVNLSFDFPF YGHFLREITV ATGGFIYTGE VVHRMLTATQ
YIAPLMANFD PSVSRNSTVR YFDNGTALVV QWDHVHLQDN YNLGSFTFQA TLLMDGRIIF
GYKEIPVLVT QISSTNHPVK VGLSDAFVVV HRIQQIPNVR RRTIYEYHRV ELQMSKITNI
SAVEMTPLPT CLQFNRCGPC VSSQIGFNCS WCSKLQRCSS GFDRHRQDWV DSGCPEESKE
KMCENTEPVE TSSRTTTTIG ATTTQFRVLT TTRRAVTSQF PTSLPTEDDT KIALHLKDNG
ASTDDSAAEK KGGTLHAGLI IGILILVLIV ATAILVTVYM YHHPTSAASI FFIERRPSRW
PAMKFRRGSG HPAYAEVEPV GEKEGFIVSE QC*
speed 1.30 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