Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999995826 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025384)
  • known disease mutation: rs1500 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:73953546C>AN/A show variant in all transcripts   IGV
HGNC symbol ACOX1
Ensembl transcript ID ENST00000537812
Genbank transcript ID NM_001185039
UniProt peptide Q15067
alteration type single base exchange
alteration region CDS
DNA changes c.418G>T
cDNA.1067G>T
g.21970G>T
AA changes G140C Score: 159 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 140
frameshift no
known variant Reference ID: rs118204091
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs1500 (pathogenic for Peroxisomal acyl-CoA oxidase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025384)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025384)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025384)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7341
5.7341
(flanking)-0.2790.977
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 increased21975wt: 0.9156 / mu: 0.9720 (marginal change - not scored)wt: GGTGGGCGTAAGTGA
mu: TGTGGGCGTAAGTGA		 TGGG|cgta
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      140SPTVTSIKWWPGGLGKTSNHAIVL
mutated  not conserved    140SPTVTSIKWWPCGLGKTSNHAIV
Ptroglodytes  all identical  ENSPTRG00000009665  178SPTVTSIKWWPGGLGKTSNHAIV
Mmulatta  all identical  ENSMMUG00000014172  178SPTVTSIKWWPGGLGKTSNHAIV
Fcatus  all identical  ENSFCAG00000005765  179SPTVTSIKWWPGGLGKTSNHAIV
Mmusculus  all identical  ENSMUSG00000020777  178SPTVTSIKWWPGGLGKTSNHAIV
Ggallus  all identical  ENSGALG00000002159  179SPTVTSIKWWPGGLGKTSNHAIV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000014727  178SPTISSIKWWPGGLGKTSNHAIV
Dmelanogaster  all identical  FBgn0027572  191TPSLSAYKWWPGGLGHTANHAVV
Celegans  all identical  F59F4.1  188AAKWWPGGLGKSSNYAVV
Xtropicalis  all identical  ENSXETG00000012601  191SPTVSSIKWWPGGLGKTSNHAVV
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1869 / 1869
position (AA) of stopcodon in wt / mu AA sequence 623 / 623
position of stopcodon in wt / mu cDNA 2518 / 2518
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 650 / 650
chromosome 17
strand -1
last intron/exon boundary 2471
theoretical NMD boundary in CDS 1771
length of CDS 1869
coding sequence (CDS) position 418
cDNA position
(for ins/del: last normal base / first normal base)		 1067
gDNA position
(for ins/del: last normal base / first normal base)		 21970
chromosomal position
(for ins/del: last normal base / first normal base)		 73953546
original gDNA sequence snippet CCTCCATTAAATGGTGGCCTGGTGGGCGTAAGTGAATTTTT
altered gDNA sequence snippet CCTCCATTAAATGGTGGCCTTGTGGGCGTAAGTGAATTTTT
original cDNA sequence snippet CCTCCATTAAATGGTGGCCTGGTGGGCTTGGAAAGACTTCA
altered cDNA sequence snippet CCTCCATTAAATGGTGGCCTTGTGGGCTTGGAAAGACTTCA
wildtype AA sequence MILNDPDFQH EDLNFLTRSQ RYEVAVRKSA IMVKKMREFG IADPDEIMWF KNFVHRGRPE
PLDLHLGMFL PTLLHQATAE QQERFFMPAW NLEIIGTYAQ TEMGHGTHLR GLETTATYDP
ETQEFILNSP TVTSIKWWPG GLGKTSNHAI VLAQLITKGK CYGLHAFIVP IREIGTHKPL
PGITVGDIGP KFGYDEIDNG YLKMDNHRIP RENMLMKYAQ VKPDGTYVKP LSNKLTYGTM
VFVRSFLVGE AARALSKACT IAIRYSAVRH QSEIKPGEPE PQILDFQTQQ YKLFPLLATA
YAFQFVGAYM KETYHRINEG IGQGDLSELP ELHALTAGLK AFTSWTANTG IEACRMACGG
HGYSHCSGLP NIYVNFTPSC TFEGENTVMM LQTARFLMKS YDQVHSGKLV CGMVSYLNDL
PSQRIQPQQV AVWPTMVDIN SPESLTEAYK LRAARLVEIA AKNLQKEVIH RKSKEVAWNL
TSVDLVRASE AHCHYVVVKL FSEKLLKIQD KAIQAVLRSL CLLYSLYGIS QNAGDFLQGS
IMTEPQITQV NQRVKELLTL IRSDAVALVD AFDFQDVTLG SVLGRYDGNV YENLFEWAKN
SPLNKAEVHE SYKHLKSLQS KL*
mutated AA sequence MILNDPDFQH EDLNFLTRSQ RYEVAVRKSA IMVKKMREFG IADPDEIMWF KNFVHRGRPE
PLDLHLGMFL PTLLHQATAE QQERFFMPAW NLEIIGTYAQ TEMGHGTHLR GLETTATYDP
ETQEFILNSP TVTSIKWWPC GLGKTSNHAI VLAQLITKGK CYGLHAFIVP IREIGTHKPL
PGITVGDIGP KFGYDEIDNG YLKMDNHRIP RENMLMKYAQ VKPDGTYVKP LSNKLTYGTM
VFVRSFLVGE AARALSKACT IAIRYSAVRH QSEIKPGEPE PQILDFQTQQ YKLFPLLATA
YAFQFVGAYM KETYHRINEG IGQGDLSELP ELHALTAGLK AFTSWTANTG IEACRMACGG
HGYSHCSGLP NIYVNFTPSC TFEGENTVMM LQTARFLMKS YDQVHSGKLV CGMVSYLNDL
PSQRIQPQQV AVWPTMVDIN SPESLTEAYK LRAARLVEIA AKNLQKEVIH RKSKEVAWNL
TSVDLVRASE AHCHYVVVKL FSEKLLKIQD KAIQAVLRSL CLLYSLYGIS QNAGDFLQGS
IMTEPQITQV NQRVKELLTL IRSDAVALVD AFDFQDVTLG SVLGRYDGNV YENLFEWAKN
SPLNKAEVHE SYKHLKSLQS KL*
speed 1.04 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