Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999839470843 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990097)
  • known disease mutation: rs1634 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7127303G>AN/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.1418G>A
cDNA.1439G>A
g.6860G>A
AA changes R473H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 473
frameshift no
known variant Reference ID: rs118204016
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC055

known disease mutation: rs1634 (pathogenic for Rhabdomyolysis|Abnormality of circulating enzyme level|Very long chain acyl-CoA dehydrogenase deficiency|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990097)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990097)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990097)
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)0.5820.969
3.1530.965
(flanking)-1.8150.314
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 increased6852wt: 0.9948 / mu: 0.9964 (marginal change - not scored)wt: CCTGGAGTAGAGCGT
mu: CCTGGAGTAGAGCAT		 TGGA|gtag
Donor gained68560.69mu: GAGTAGAGCATGTGC GTAG|agca
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      473GMGFMKEPGVERVLRDLRIFRIFE
mutated  not conserved    473GMGFMKEPGVEHVLRDLRI
Ptroglodytes  all identical  ENSPTRG00000008664  473GMGFMKEPGVERVLRDLRVFRIF
Mmulatta  all identical  ENSMMUG00000010538  471RMARTREEPGVERVLRDLRIFRIF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  451MGFMKEPGVERVLRDIRIFRIF
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  452GFMKDSGVERVMRDLRIFRIF
Drerio  all identical  ENSDARG00000016687  455GMGFMKDAGVERVLR
Dmelanogaster  all identical  FBgn0034432  423GMGYMVDNGLERVLRDLRIFRIF
Celegans  all identical  E04F6.5  418GMGFMRETGLERVLRDLRIFRIF
Xtropicalis  all identical  ENSXETG00000031271  247MTVS--NRCICSLHCCGLI
protein features
start (aa)end (aa)featuredetails 
41482REGIONCatalytic.lost
465485HELIXlost
483516REGIONMembrane-anchoring (Probable).might get lost (downstream of altered splice site)
486488HELIXmight get lost (downstream of altered splice site)
522524TURNmight get lost (downstream of altered splice site)
527529HELIXmight get lost (downstream of altered splice site)
530554HELIXmight get lost (downstream of altered splice site)
555560HELIXmight get lost (downstream of altered splice site)
562591HELIXmight get lost (downstream of altered splice site)
596622HELIXmight get lost (downstream of altered splice site)
627644HELIXmight get lost (downstream of altered splice site)
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 1418
cDNA position
(for ins/del: last normal base / first normal base)		 1439
gDNA position
(for ins/del: last normal base / first normal base)		 6860
chromosomal position
(for ins/del: last normal base / first normal base)		 7127303
original gDNA sequence snippet CTAGGAACCTGGAGTAGAGCGTGTGCTCCGAGATCTTCGCA
altered gDNA sequence snippet CTAGGAACCTGGAGTAGAGCATGTGCTCCGAGATCTTCGCA
original cDNA sequence snippet GAAGGAACCTGGAGTAGAGCGTGTGCTCCGAGATCTTCGCA
altered cDNA sequence snippet GAAGGAACCTGGAGTAGAGCATGTGCTCCGAGATCTTCGCA
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 VEHVLRDLRI
FRIFEGTNDI LRLFVALQGC MDKGKELSGL GSALKNPFGN AGLLLGEAGK QLRRRAGLGS
GLSLSGLVHP ELSRSGELAV RALEQFATVV EAKLIKHKKG IVNEQFLLQR LADGAIDLYA
MVVVLSRASR SLSEGHPTAQ HEKMLCDTWC IEAAARIREG MAALQSDPWQ QELYRNFKSI
SKALVERGGV VTSNPLGF*
speed 0.89 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