Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999875747 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960010)
  • known disease mutation: rs21016 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7127184G>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.1391G>A
cDNA.1412G>A
g.6741G>A
AA changes G464D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 464
frameshift no
known variant Reference ID: rs2309689
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs21016 (pathogenic for 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 CM960010)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960010)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960010)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2631
5.2631
(flanking)0.7331
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 increased6746wt: 0.9548 / mu: 0.9649 (marginal change - not scored)wt: GCTTCATGAAGGTAC
mu: ACTTCATGAAGGTAC		 TTCA|tgaa
Donor marginally increased6745wt: 0.5509 / mu: 0.5717 (marginal change - not scored)wt: GGCTTCATGAAGGTA
mu: GACTTCATGAAGGTA		 CTTC|atga
Donor increased6733wt: 0.21 / mu: 0.39wt: ATGGGGGGTATGGGC
mu: ATGGGGGGTATGGAC		 GGGG|ggta
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      464TDECIQIMGGMGFMKEPGVERVLR
mutated  not conserved    464TDECIQIMGGMDFMKEPGVERVL
Ptroglodytes  all identical  ENSPTRG00000008664  464TDECIQIMGGMGFMKEPGVERVL
Mmulatta  not conserved  ENSMMUG00000010538  462SGACQQYQKRMARTREEPGVERVL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  442MGFMKEPGVERVL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  443GFMKDSGVERVM
Drerio  all identical  ENSDARG00000016687  446TDECIQVMGGMGFMKDAGVERVL
Dmelanogaster  all identical  FBgn0034432  414CDEAIQILGGMGYMVDNGLERVL
Celegans  all identical  E04F6.5  409CDDAIQVHGGMGFMRETGLERVL
Xtropicalis  all identical  ENSXETG00000031271  238TDECIQILGGTGFMTVS--NRCI
protein features
start (aa)end (aa)featuredetails 
41482REGIONCatalytic.lost
461463STRANDmight get lost (downstream of altered splice site)
462462ACT_SITEProton acceptor.might get lost (downstream of altered splice site)
462463REGIONSubstrate binding.might get lost (downstream of altered splice site)
463463BINDINGSubstrate; via amide nitrogen (By similarity).might get lost (downstream of altered splice site)
464466NP_BINDFAD.lost
465485HELIXmight get lost (downstream of altered splice site)
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 1391
cDNA position
(for ins/del: last normal base / first normal base)		 1412
gDNA position
(for ins/del: last normal base / first normal base)		 6741
chromosomal position
(for ins/del: last normal base / first normal base)		 7127184
original gDNA sequence snippet CCAAATCATGGGGGGTATGGGCTTCATGAAGGTACAGGACG
altered gDNA sequence snippet CCAAATCATGGGGGGTATGGACTTCATGAAGGTACAGGACG
original cDNA sequence snippet CCAAATCATGGGGGGTATGGGCTTCATGAAGGAACCTGGAG
altered cDNA sequence snippet CCAAATCATGGGGGGTATGGACTTCATGAAGGAACCTGGAG
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 GGMDFMKEPG VERVLRDLRI
FRIFEGTNDI LRLFVALQGC MDKGKELSGL GSALKNPFGN AGLLLGEAGK QLRRRAGLGS
GLSLSGLVHP ELSRSGELAV RALEQFATVV EAKLIKHKKG IVNEQFLLQR LADGAIDLYA
MVVVLSRASR SLSEGHPTAQ HEKMLCDTWC IEAAARIREG MAALQSDPWQ QELYRNFKSI
SKALVERGGV VTSNPLGF*
speed 0.39 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