Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999996356028 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950004)
  • known disease mutation: rs1623 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7128285C>TN/A show variant in all transcripts   IGV
HGNC symbol ACADVL
Ensembl transcript ID ENST00000356839
Genbank transcript ID NM_000018
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1837C>T
cDNA.2016C>T
g.7842C>T
AA changes R613W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 613
frameshift no
known variant Reference ID: rs118204014
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01010

known disease mutation: rs1623 (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 CM950004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950004)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6531
3.7941
(flanking)4.8881
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 increased7833wt: 0.4749 / mu: 0.4976 (marginal change - not scored)wt: CCCTCCTTCCCTCTCCCCAGGCTGCAGCTCGGATCCGAGAG
mu: CCCTCCTTCCCTCTCCCCAGGCTGCAGCTTGGATCCGAGAG		 cagg|CTGC
Acc marginally increased7842wt: 0.4210 / mu: 0.4224 (marginal change - not scored)wt: CCTCTCCCCAGGCTGCAGCTCGGATCCGAGAGGGCATGGCC
mu: CCTCTCCCCAGGCTGCAGCTTGGATCCGAGAGGGCATGGCC		 gctc|GGAT
Donor increased7838wt: 0.24 / mu: 0.42wt: GCTGCAGCTCGGATC
mu: GCTGCAGCTTGGATC		 TGCA|gctc
Donor marginally increased7845wt: 0.2015 / mu: 0.2182 (marginal change - not scored)wt: CTCGGATCCGAGAGG
mu: CTTGGATCCGAGAGG		 CGGA|tccg
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      613LCDTWCIEAAARIREGMAALQSDP
mutated  not conserved    613LCDTWCIEAAAWIREGMAALQSD
Ptroglodytes  all identical  ENSPTRG00000008664  635LCDTWCIEAAARIREGMAALQSD
Mmulatta  all identical  ENSMMUG00000010538  635LCDTWCIEAAARIREGMAALQSD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  614LCDSWCIEAATRIRENMASLQSS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  617LCDTWCKEAYGRITRDV
Drerio  all identical  ENSDARG00000016687  618LCETWCTEAHERVMQDIKFLRSG
Dmelanogaster  all identical  FBgn0034432  585MTKALTIQASDRVIKNLQAATSS
Celegans  not conserved  E04F6.5  571ATYYVDKAMKSSNRFLKDAGSG
Xtropicalis  all identical  ENSXETG00000031271  404LCDIWCSEAQSRIHRNLQSL
protein features
start (aa)end (aa)featuredetails 
596622HELIXlost
627644HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1968 / 1968
position (AA) of stopcodon in wt / mu AA sequence 656 / 656
position of stopcodon in wt / mu cDNA 2147 / 2147
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 180 / 180
chromosome 17
strand 1
last intron/exon boundary 2007
theoretical NMD boundary in CDS 1777
length of CDS 1968
coding sequence (CDS) position 1837
cDNA position
(for ins/del: last normal base / first normal base)		 2016
gDNA position
(for ins/del: last normal base / first normal base)		 7842
chromosomal position
(for ins/del: last normal base / first normal base)		 7128285
original gDNA sequence snippet CCTCTCCCCAGGCTGCAGCTCGGATCCGAGAGGGCATGGCC
altered gDNA sequence snippet CCTCTCCCCAGGCTGCAGCTTGGATCCGAGAGGGCATGGCC
original cDNA sequence snippet GGTGTATCGAGGCTGCAGCTCGGATCCGAGAGGGCATGGCC
altered cDNA sequence snippet GGTGTATCGAGGCTGCAGCTTGGATCCGAGAGGGCATGGCC
wildtype AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFT VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRIFRI FEGTNDILRL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AARIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*
mutated AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFT VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRIFRI FEGTNDILRL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AAWIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*
speed 0.57 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