Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999992 (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)
  • protein features (might be) affected
 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 ENST00000293217
Genbank transcript ID NM_004035
UniProt peptide Q15067
alteration type single base exchange
alteration region CDS
DNA changes c.532G>T
cDNA.822G>T
g.21970G>T
AA changes G178C Score: 159 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 178
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      178SPTVTSIKWWPGGLGKTSNHAIVL
mutated  not conserved    178SPTVTSIKWWPCGL
Ptroglodytes  all identical  ENSPTRG00000009665  178SPTVTSIKWWPGGL
Mmulatta  all identical  ENSMMUG00000014172  178SPTVTSIKWWPGGL
Fcatus  all identical  ENSFCAG00000005765  179SPTVTSIKWWPGGLGKTSNHAIV
Mmusculus  all identical  ENSMUSG00000020777  178SPTVTSIKWWPGGL
Ggallus  all identical  ENSGALG00000002159  179SPTVTSIKWWPGGL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000014727  178SPTISSIKWWPGGL
Dmelanogaster  all identical  FBgn0027572  191YKWWPGGLGHTANHAVV
Celegans  all identical  F59F4.1  188SPTITAAKWWPGGLGKSSNYAVV
Xtropicalis  all identical  ENSXETG00000012601  191SPTVSSIKWWPGGL
protein features
start (aa)end (aa)featuredetails 
178178BINDINGFAD; via amide nitrogen (By similarity).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1983 / 1983
position (AA) of stopcodon in wt / mu AA sequence 661 / 661
position of stopcodon in wt / mu cDNA 2273 / 2273
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 291 / 291
chromosome 17
strand -1
last intron/exon boundary 2226
theoretical NMD boundary in CDS 1885
length of CDS 1983
coding sequence (CDS) position 532
cDNA position
(for ins/del: last normal base / first normal base)		 822
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 MNPDLRRERD SASFNPELLT HILDGSPEKT RRRREIENMI LNDPDFQHED LNFLTRSQRY
EVAVRKSAIM VKKMREFGIA DPDEIMWFKN FVHRGRPEPL DLHLGMFLPT LLHQATAEQQ
ERFFMPAWNL EIIGTYAQTE MGHGTHLRGL ETTATYDPET QEFILNSPTV TSIKWWPGGL
GKTSNHAIVL AQLITKGKCY GLHAFIVPIR EIGTHKPLPG ITVGDIGPKF GYDEIDNGYL
KMDNHRIPRE NMLMKYAQVK PDGTYVKPLS NKLTYGTMVF VRSFLVGEAA RALSKACTIA
IRYSAVRHQS EIKPGEPEPQ ILDFQTQQYK LFPLLATAYA FQFVGAYMKE TYHRINEGIG
QGDLSELPEL HALTAGLKAF TSWTANTGIE ACRMACGGHG YSHCSGLPNI YVNFTPSCTF
EGENTVMMLQ TARFLMKSYD QVHSGKLVCG MVSYLNDLPS QRIQPQQVAV WPTMVDINSP
ESLTEAYKLR AARLVEIAAK NLQKEVIHRK SKEVAWNLTS VDLVRASEAH CHYVVVKLFS
EKLLKIQDKA IQAVLRSLCL LYSLYGISQN AGDFLQGSIM TEPQITQVNQ RVKELLTLIR
SDAVALVDAF DFQDVTLGSV LGRYDGNVYE NLFEWAKNSP LNKAEVHESY KHLKSLQSKL
*
mutated AA sequence MNPDLRRERD SASFNPELLT HILDGSPEKT RRRREIENMI LNDPDFQHED LNFLTRSQRY
EVAVRKSAIM VKKMREFGIA DPDEIMWFKN FVHRGRPEPL DLHLGMFLPT LLHQATAEQQ
ERFFMPAWNL EIIGTYAQTE MGHGTHLRGL ETTATYDPET QEFILNSPTV TSIKWWPCGL
GKTSNHAIVL AQLITKGKCY GLHAFIVPIR EIGTHKPLPG ITVGDIGPKF GYDEIDNGYL
KMDNHRIPRE NMLMKYAQVK PDGTYVKPLS NKLTYGTMVF VRSFLVGEAA RALSKACTIA
IRYSAVRHQS EIKPGEPEPQ ILDFQTQQYK LFPLLATAYA FQFVGAYMKE TYHRINEGIG
QGDLSELPEL HALTAGLKAF TSWTANTGIE ACRMACGGHG YSHCSGLPNI YVNFTPSCTF
EGENTVMMLQ TARFLMKSYD QVHSGKLVCG MVSYLNDLPS QRIQPQQVAV WPTMVDINSP
ESLTEAYKLR AARLVEIAAK NLQKEVIHRK SKEVAWNLTS VDLVRASEAH CHYVVVKLFS
EKLLKIQDKA IQAVLRSLCL LYSLYGISQN AGDFLQGSIM TEPQITQVNQ RVKELLTLIR
SDAVALVDAF DFQDVTLGSV LGRYDGNVYE NLFEWAKNSP LNKAEVHESY KHLKSLQSKL
*
speed 0.75 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