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 ENST00000350303
Genbank transcript ID NM_001033859
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1771C>T
cDNA.1893C>T
g.7842C>T
AA changes R591W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 591
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      591LCDTWCIEAAARIREGMAALQSDP
mutated  not conserved    591LCDTWCIEAAAWIREGMAALQ
Ptroglodytes  all identical  ENSPTRG00000008664  635LCDTWCIEAAARIREGMAALQ
Mmulatta  all identical  ENSMMUG00000010538  635LCDTWCIEAAARIREGMAALQSD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  614LCDSWCIEAATRIRENMASLQSS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  617CKEAYGRITRDVQELRSS
Drerio  all identical  ENSDARG00000016687  618EAHERVMQDIKFLRSG
Dmelanogaster  all identical  FBgn0034432  585TIQASDRVIKNLQAATSS
Celegans  not conserved  E04F6.5  571YVDKAMKSSNRFLKDAGSG
Xtropicalis  all identical  ENSXETG00000031271  404LCDIWCSEAQSRIHRNLQSL
protein features
start (aa)end (aa)featuredetails 
562591HELIXlost
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 1771
cDNA position
(for ins/del: last normal base / first normal base)		 1893
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 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
MKEPGVERVL RDLRIFRIFE GTNDILRLFV ALQGCMDKGK ELSGLGSALK NPFGNAGLLL
GEAGKQLRRR AGLGSGLSLS GLVHPELSRS GELAVRALEQ FATVVEAKLI KHKKGIVNEQ
FLLQRLADGA IDLYAMVVVL SRASRSLSEG HPTAQHEKML CDTWCIEAAA WIREGMAALQ
SDPWQQELYR NFKSISKALV ERGGVVTSNP LGF*
speed 0.56 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