Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999622466194479 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • heterozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM960004)
  • known disease mutation: rs21025 (pathogenic)
  • protein features (might be) affected
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7125591T>CN/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.917T>C
cDNA.938T>C
g.5148T>C
AA changes V306A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 306
frameshift no
known variant Reference ID: rs113994167
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC0173173

known disease mutation: rs21025 (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 CM960004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960004)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5711
4.4691
(flanking)0.1320.997
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 increased5148wt: 0.3048 / mu: 0.3185 (marginal change - not scored)wt: GGAGAAGATCACAGCTTTTGTGGTGGAGAGGGGCTTCGGGG
mu: GGAGAAGATCACAGCTTTTGCGGTGGAGAGGGGCTTCGGGG		 ttgt|GGTG
Donor marginally increased5149wt: 0.8899 / mu: 0.9681 (marginal change - not scored)wt: TTTGTGGTGGAGAGG
mu: TTTGCGGTGGAGAGG		 TGTG|gtgg
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      306TGAVKEKITAFVVERGFGGITHGP
mutated  not conserved    306KITAFAVERGFGGITHG
Ptroglodytes  all identical  ENSPTRG00000008664  306FVVERGFGGITHG
Mmulatta  all identical  ENSMMUG00000010538  293TGAVKEKITAFVVERGFGGVTHG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  284TGAVKEKITAFVVERSFGGVTHG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  285TGEMKDKITAFVVERSFGSVTHG
Drerio  all conserved  ENSDARG00000016687  288EMKDKITAFIVERSFGGVSSG
Dmelanogaster  all conserved  FBgn0034432  256TGEKKDKVTAFIVERSFGGVTNG
Celegans  all conserved  E04F6.5  252DGSTKDKMSAFIVERAFGGVTSG
Xtropicalis  all conserved  ENSXETG00000031271  81TGETREKVTAFIVERG-EGVTHG
protein features
start (aa)end (aa)featuredetails 
41482REGIONCatalytic.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 917
cDNA position
(for ins/del: last normal base / first normal base)		 938
gDNA position
(for ins/del: last normal base / first normal base)		 5148
chromosomal position
(for ins/del: last normal base / first normal base)		 7125591
original gDNA sequence snippet GGAGAAGATCACAGCTTTTGTGGTGGAGAGGGGCTTCGGGG
altered gDNA sequence snippet GGAGAAGATCACAGCTTTTGCGGTGGAGAGGGGCTTCGGGG
original cDNA sequence snippet GGAGAAGATCACAGCTTTTGTGGTGGAGAGGGGCTTCGGGG
altered cDNA sequence snippet GGAGAAGATCACAGCTTTTGCGGTGGAGAGGGGCTTCGGGG
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
KITAFAVERG 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*
speed 0.98 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