Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999470892712 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990104)
  • known disease mutation: rs21017 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7127359C>TN/A show variant in all transcripts   IGV
HGNC symbol ACADVL
Ensembl transcript ID ENST00000356839
Genbank transcript ID NM_000018
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1405C>T
cDNA.1584C>T
g.6916C>T
AA changes R469W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 469
frameshift no
known variant Reference ID: rs113994170
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs21017 (pathogenic for Very long chain acyl-CoA dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990104)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990104)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990104)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0210.988
0.4650.993
(flanking)4.6931
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased6926wt: 0.9341 / mu: 0.9518 (marginal change - not scored)wt: TGACATTCTTCGGCTGTTTGTGGCTCTGCAGGGCTGTATGG
mu: TGACATTCTTTGGCTGTTTGTGGCTCTGCAGGGCTGTATGG		 ttgt|GGCT
Acc marginally increased6924wt: 0.8873 / mu: 0.9595 (marginal change - not scored)wt: AATGACATTCTTCGGCTGTTTGTGGCTCTGCAGGGCTGTAT
mu: AATGACATTCTTTGGCTGTTTGTGGCTCTGCAGGGCTGTAT		 gttt|GTGG
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      469FRIFEGTNDILRLFVALQGCMDKG
mutated  not conserved    469FRIFEGTNDILWLFVALQGCMDK
Ptroglodytes  all identical  ENSPTRG00000008664  492FRIFEGTNDILRLFVALQGCMDK
Mmulatta  all identical  ENSMMUG00000010538  491RIFEGTNDILRLFVALQGCMDK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  470FRIFEGANDILRLFVALQGCMD
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  471FRIFEGTNDILRLFVALNGFQNA
Drerio  all identical  ENSDARG00000016687  474FRIFEGTNDILRLFVALNGFQNA
Dmelanogaster  all identical  FBgn0034432  442FRIFEGTNDILRLFIALTGIQYA
Celegans  all identical  E04F6.5  437FRIFEGANDVLRLFIALTGAQHA
Xtropicalis  not conserved  ENSXETG00000031271  266CGLIPWAINPFL-----VPPMQSA
protein features
start (aa)end (aa)featuredetails 
41482REGIONCatalytic.lost
465485HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1968 / 1968
position (AA) of stopcodon in wt / mu AA sequence 656 / 656
position of stopcodon in wt / mu cDNA 2147 / 2147
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 180 / 180
chromosome 17
strand 1
last intron/exon boundary 2007
theoretical NMD boundary in CDS 1777
length of CDS 1968
coding sequence (CDS) position 1405
cDNA position
(for ins/del: last normal base / first normal base)		 1584
gDNA position
(for ins/del: last normal base / first normal base)		 6916
chromosomal position
(for ins/del: last normal base / first normal base)		 7127359
original gDNA sequence snippet AGGGGACAAATGACATTCTTCGGCTGTTTGTGGCTCTGCAG
altered gDNA sequence snippet AGGGGACAAATGACATTCTTTGGCTGTTTGTGGCTCTGCAG
original cDNA sequence snippet AGGGGACAAATGACATTCTTCGGCTGTTTGTGGCTCTGCAG
altered cDNA sequence snippet AGGGGACAAATGACATTCTTTGGCTGTTTGTGGCTCTGCAG
wildtype AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFT VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRIFRI FEGTNDILRL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AARIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*
mutated AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFT VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRIFRI FEGTNDILWL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AARIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*
speed 0.56 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