Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999996775363195 (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 ENST00000543245
Genbank transcript ID NM_001270447
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1474C>T
cDNA.1495C>T
g.6916C>T
AA changes R492W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 492
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      492FRIFEGTNDILRLFVALQGCMDKG
mutated  not conserved    492FRIFEGTNDILWLFVALQGCMDK
Ptroglodytes  all identical  ENSPTRG00000008664  492EGTNDILRLFVALQGCMDK
Mmulatta  all identical  ENSMMUG00000010538  490FRIFEGTNDILRLFVALQGCM
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  470FRIFEGANDILRLFVALQGCMDK
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 
483516REGIONMembrane-anchoring (Probable).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2037 / 2037
position (AA) of stopcodon in wt / mu AA sequence 679 / 679
position of stopcodon in wt / mu cDNA 2058 / 2058
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 22 / 22
chromosome 17
strand 1
last intron/exon boundary 1918
theoretical NMD boundary in CDS 1846
length of CDS 2037
coding sequence (CDS) position 1474
cDNA position
(for ins/del: last normal base / first normal base)		 1495
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 MLGGLAAAAG TRIMGKEIEA EAQRPLRQTW RPGQPPAMTA KTMSSRLTAL LGQPRPGPAR
RPYAGGAAQL ALDKSDSHPS DALTRKKPAK AESKSFAVGM FKGQLTTDQV FPYPSVLNEE
QTQFLKELVE PVSRFFEEVN DPAKNDALEM VEETTWQGLK ELGAFGLQVP SELGGVGLCN
TQYARLVEIV GMHDLGVGIT LGAHQSIGFK GILLFGTKAQ KEKYLPKLAS GETVAAFCLT
EPSSGSDAAS IRTSAVPSPC GKYYTLNGSK LWISNGGLAD IFTVFAKTPV TDPATGAVKE
KITAFVVERG FGGITHGPPE KKMGIKASNT AEVFFDGVRV PSENVLGEVG SGFKVAMHIL
NNGRFGMAAA LAGTMRGIIA KAVDHATNRT QFGEKIHNFG LIQEKLARMV MLQYVTESMA
YMVSANMDQG ATDFQIEAAI SKIFGSEAAW KVTDECIQIM GGMGFMKEPG VERVLRDLRI
FRIFEGTNDI LRLFVALQGC MDKGKELSGL GSALKNPFGN AGLLLGEAGK QLRRRAGLGS
GLSLSGLVHP ELSRSGELAV RALEQFATVV EAKLIKHKKG IVNEQFLLQR LADGAIDLYA
MVVVLSRASR SLSEGHPTAQ HEKMLCDTWC IEAAARIREG MAALQSDPWQ QELYRNFKSI
SKALVERGGV VTSNPLGF*
mutated AA sequence MLGGLAAAAG TRIMGKEIEA EAQRPLRQTW RPGQPPAMTA KTMSSRLTAL LGQPRPGPAR
RPYAGGAAQL ALDKSDSHPS DALTRKKPAK AESKSFAVGM FKGQLTTDQV FPYPSVLNEE
QTQFLKELVE PVSRFFEEVN DPAKNDALEM VEETTWQGLK ELGAFGLQVP SELGGVGLCN
TQYARLVEIV GMHDLGVGIT LGAHQSIGFK GILLFGTKAQ KEKYLPKLAS GETVAAFCLT
EPSSGSDAAS IRTSAVPSPC GKYYTLNGSK LWISNGGLAD IFTVFAKTPV TDPATGAVKE
KITAFVVERG FGGITHGPPE KKMGIKASNT AEVFFDGVRV PSENVLGEVG SGFKVAMHIL
NNGRFGMAAA LAGTMRGIIA KAVDHATNRT QFGEKIHNFG LIQEKLARMV MLQYVTESMA
YMVSANMDQG ATDFQIEAAI SKIFGSEAAW KVTDECIQIM GGMGFMKEPG VERVLRDLRI
FRIFEGTNDI LWLFVALQGC MDKGKELSGL GSALKNPFGN AGLLLGEAGK QLRRRAGLGS
GLSLSGLVHP ELSRSGELAV RALEQFATVV EAKLIKHKKG IVNEQFLLQR LADGAIDLYA
MVVVLSRASR SLSEGHPTAQ HEKMLCDTWC IEAAARIREG MAALQSDPWQ QELYRNFKSI
SKALVERGGV VTSNPLGF*
speed 1.00 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