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 ENST00000350303
Genbank transcript ID NM_001033859
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1283G>A
cDNA.1405G>A
g.6860G>A
AA changes R428H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 428
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      428GMGFMKEPGVERVLRDLRIFRIFE
mutated  not conserved    428MKEPGVEHVLRDLRIFRIF
Ptroglodytes  all identical  ENSPTRG00000008664  473MKEPGVERVLRDLRVFRIF
Mmulatta  all identical  ENSMMUG00000010538  470RMARTREEPGVERVLRDLRIF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  451GMGFMKEPGVERVLRDIRIFRIF
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  452GMGFMKDSGVERVMRDLRIFRIF
Drerio  all identical  ENSDARG00000016687  455GMGFMKDAGVERVLRDLRIFRIF
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
412437HELIXlost
435439NP_BINDFAD (By similarity).might get lost (downstream of altered splice site)
439442HELIXmight get lost (downstream of altered splice site)
448455HELIXmight get lost (downstream of altered splice site)
456459HELIXmight get lost (downstream of altered splice site)
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.might get lost (downstream of altered splice site)
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 1902 / 1902
position (AA) of stopcodon in wt / mu AA sequence 634 / 634
position of stopcodon in wt / mu cDNA 2024 / 2024
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 123 / 123
chromosome 17
strand 1
last intron/exon boundary 1884
theoretical NMD boundary in CDS 1711
length of CDS 1902
coding sequence (CDS) position 1283
cDNA position
(for ins/del: last normal base / first normal base)		 1405
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 MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQESKS FAVGMFKGQL
TTDQVFPYPS VLNEEQTQFL KELVEPVSRF FEEVNDPAKN DALEMVEETT WQGLKELGAF
GLQVPSELGG VGLCNTQYAR LVEIVGMHDL GVGITLGAHQ SIGFKGILLF GTKAQKEKYL
PKLASGETVA AFCLTEPSSG SDAASIRTSA VPSPCGKYYT LNGSKLWISN GGLADIFTVF
AKTPVTDPAT GAVKEKITAF VVERGFGGIT HGPPEKKMGI KASNTAEVFF DGVRVPSENV
LGEVGSGFKV AMHILNNGRF GMAAALAGTM RGIIAKAVDH ATNRTQFGEK IHNFGLIQEK
LARMVMLQYV TESMAYMVSA NMDQGATDFQ IEAAISKIFG SEAAWKVTDE CIQIMGGMGF
MKEPGVERVL RDLRIFRIFE GTNDILRLFV ALQGCMDKGK ELSGLGSALK NPFGNAGLLL
GEAGKQLRRR AGLGSGLSLS GLVHPELSRS GELAVRALEQ FATVVEAKLI KHKKGIVNEQ
FLLQRLADGA IDLYAMVVVL SRASRSLSEG HPTAQHEKML CDTWCIEAAA RIREGMAALQ
SDPWQQELYR NFKSISKALV ERGGVVTSNP LGF*
mutated AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQESKS FAVGMFKGQL
TTDQVFPYPS VLNEEQTQFL KELVEPVSRF FEEVNDPAKN DALEMVEETT WQGLKELGAF
GLQVPSELGG VGLCNTQYAR LVEIVGMHDL GVGITLGAHQ SIGFKGILLF GTKAQKEKYL
PKLASGETVA AFCLTEPSSG SDAASIRTSA VPSPCGKYYT LNGSKLWISN GGLADIFTVF
AKTPVTDPAT GAVKEKITAF VVERGFGGIT HGPPEKKMGI KASNTAEVFF DGVRVPSENV
LGEVGSGFKV AMHILNNGRF GMAAALAGTM RGIIAKAVDH ATNRTQFGEK IHNFGLIQEK
LARMVMLQYV TESMAYMVSA NMDQGATDFQ IEAAISKIFG SEAAWKVTDE CIQIMGGMGF
MKEPGVEHVL RDLRIFRIFE GTNDILRLFV ALQGCMDKGK ELSGLGSALK NPFGNAGLLL
GEAGKQLRRR AGLGSGLSLS GLVHPELSRS GELAVRALEQ FATVVEAKLI KHKKGIVNEQ
FLLQRLADGA IDLYAMVVVL SRASRSLSEG HPTAQHEKML CDTWCIEAAA RIREGMAALQ
SDPWQQELYR NFKSISKALV ERGGVVTSNP LGF*
speed 0.78 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