Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999998167223682 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM121492)
  • protein features (might be) affected
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:80905990C>GN/A show variant in all transcripts   IGV
HGNC symbol ANTXR2
Ensembl transcript ID ENST00000307333
Genbank transcript ID NM_001145794
UniProt peptide P58335
alteration type single base exchange
alteration region CDS
DNA changes c.1069G>C
cDNA.1072G>C
g.140619G>C
AA changes A357P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 357
frameshift no
known variant Reference ID: rs12647691
databasehomozygous (G/G)heterozygousallele carriers
1000G16457302375
ExAC32664-32561103

known disease mutation at this position, please check HGMD for details (HGMD ID CM121492)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7790.611
1.1990.559
(flanking)-1.7390.318
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased140624wt: 0.31 / mu: 0.88wt: CCTCCACCACCACCCGCCCCTGCACCAAAAGAGGTAAGTGA
mu: CCTCCACCACCACCCCCCCCTGCACCAAAAGAGGTAAGTGA		 ccct|GCAC
Acc increased140628wt: 0.56 / mu: 0.90wt: CACCACCACCCGCCCCTGCACCAAAAGAGGTAAGTGAGTGC
mu: CACCACCACCCCCCCCTGCACCAAAAGAGGTAAGTGAGTGC		 gcac|CAAA
Acc increased140630wt: 0.46 / mu: 0.80wt: CCACCACCCGCCCCTGCACCAAAAGAGGTAAGTGAGTGCCT
mu: CCACCACCCCCCCCTGCACCAAAAGAGGTAAGTGAGTGCCT		 acca|AAAG
Acc increased140626wt: 0.52 / mu: 0.88wt: TCCACCACCACCCGCCCCTGCACCAAAAGAGGTAAGTGAGT
mu: TCCACCACCACCCCCCCCTGCACCAAAAGAGGTAAGTGAGT		 ctgc|ACCA
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      357KVVIKDPPPPPAPAPKEEEEEPLP
mutated  not conserved    357KVVIKDPPPPPPPAP
Ptroglodytes  not conserved  ENSPTRG00000016207  357KVVIKDPPPPPPPAP
Mmulatta  not conserved  ENSMMUG00000003333  81KVVIKDPPPPPPPAPKEEEEEPL
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000029338  357KVVIKDPPPPPSAPM
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000060520  347TVVIKDPPPQRPPPPPPKLEPDPE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000021531  354KVVIKDPPPPPPPKPVPVEEPEEVL
protein features
start (aa)end (aa)featuredetails 
342489TOPO_DOMCytoplasmic (Potential).lost
352360COMPBIASPoly-Pro.lost
362366COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1470 / 1470
position (AA) of stopcodon in wt / mu AA sequence 490 / 490
position of stopcodon in wt / mu cDNA 1473 / 1473
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 4 / 4
chromosome 4
strand -1
last intron/exon boundary 1351
theoretical NMD boundary in CDS 1297
length of CDS 1470
coding sequence (CDS) position 1069
cDNA position
(for ins/del: last normal base / first normal base)		 1072
gDNA position
(for ins/del: last normal base / first normal base)		 140619
chromosomal position
(for ins/del: last normal base / first normal base)		 80905990
original gDNA sequence snippet AGGATCCTCCACCACCACCCGCCCCTGCACCAAAAGAGGTA
altered gDNA sequence snippet AGGATCCTCCACCACCACCCCCCCCTGCACCAAAAGAGGTA
original cDNA sequence snippet AGGATCCTCCACCACCACCCGCCCCTGCACCAAAAGAGGAG
altered cDNA sequence snippet AGGATCCTCCACCACCACCCCCCCCTGCACCAAAAGAGGAG
wildtype AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGET LDVSVSFNGG
KSVISGSLIV TATECSNGIA AIIVILVLLL LLGIGLMWWF WPLCCKVVIK DPPPPPAPAP
KEEEEEPLPT KKWPTVDASY YGGRGVGGIK RMEVRWGDKG STEEGARLEK AKNAVVKIPE
ETEEPIRPRP PRPKPTHQPP QTKWYTPIKG RLDALWALLR RQYDRVSLMR PQEGDEVCIW
ECIEKELTA*
mutated AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGET LDVSVSFNGG
KSVISGSLIV TATECSNGIA AIIVILVLLL LLGIGLMWWF WPLCCKVVIK DPPPPPPPAP
KEEEEEPLPT KKWPTVDASY YGGRGVGGIK RMEVRWGDKG STEEGARLEK AKNAVVKIPE
ETEEPIRPRP PRPKPTHQPP QTKWYTPIKG RLDALWALLR RQYDRVSLMR PQEGDEVCIW
ECIEKELTA*
speed 0.87 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