Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910002)
  • known disease mutation: rs3590 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76215125T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000370834
Genbank transcript ID N/A
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.829T>C
cDNA.908T>C
g.25090T>C
AA changes C277R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 277
frameshift no
known variant Reference ID: rs121434276
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3590 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3830.907
5.1021
(flanking)6.181
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 increased25085wt: 0.9982 / mu: 0.9986 (marginal change - not scored)wt: GGGCCAGCGATGTTC
mu: GGGCCAGCGACGTTC		 GCCA|gcga
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      277IGRKELNMGQRCSDTRGIVFEDVK
mutated  not conserved    277IGRKELNMGQRRSDTRGIVFEDV
Ptroglodytes  all identical  ENSPTRG00000000871  244IGRKELNMGQRCSDTRGIVFEDV
Mmulatta  all identical  ENSMMUG00000007220  277IGRKELNMGQRCSDTRGIVFEDV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  244IGKKELNMGQRCSDTRGIAFEDV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  273IGRKELNMGQRCSDTRGITFEDV
Drerio  all identical  ENSDARG00000038900  249RCSDTRGITFEDV
Dmelanogaster  not conserved  FBgn0035811  240PGRKELNMGQRASDTRGITFEDV
Celegans  all identical  T08G2.3  234RGKKEKNMGQRCSDTRVITFEDV
Xtropicalis  all identical  ENSXETG00000002983  249IGRKEMNMGQRCSDTRGIVFEDV
protein features
start (aa)end (aa)featuredetails 
269303HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1365 / 1365
position (AA) of stopcodon in wt / mu AA sequence 455 / 455
position of stopcodon in wt / mu cDNA 1444 / 1444
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 80 / 80
chromosome 1
strand 1
last intron/exon boundary 1373
theoretical NMD boundary in CDS 1243
length of CDS 1365
coding sequence (CDS) position 829
cDNA position
(for ins/del: last normal base / first normal base)		 908
gDNA position
(for ins/del: last normal base / first normal base)		 25090
chromosomal position
(for ins/del: last normal base / first normal base)		 76215125
original gDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered gDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
original cDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered cDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
wildtype AA sequence MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI
IPVAAEYDKT GEYPVPLIRR AWELGLMNTH IPENCDYSVC PLLEACTLYL DAFFLLLTGS
NLNLHLNLGG LGLGTFDACL ISEELAYGCT GVQTAIEGNS LGQMPIIIAG NDQQKKKYLG
RMTEEPLMCA YCVTEPGAGS DVAGIKTKAE KKGDEYIING QKMWITNGGK ANWYFLLARS
DPDPKAPANK AFTGFIVEAD TPGIQIGRKE LNMGQRCSDT RGIVFEDVKV PKENVLIGDG
AGFKVAMGAF DKTRPVVAAG AVGLAQRALD EATKYALERK TFGKLLVEHQ AISFMLAEMA
MKVELARMSY QRAAWEVDSG RRNTYYASIA KAFAGDIANQ LATDAVQILG GNGFNTEYPV
EKLMRDAKIY QIYEGTSQIQ RLIVAREHID KYKN*
mutated AA sequence MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI
IPVAAEYDKT GEYPVPLIRR AWELGLMNTH IPENCDYSVC PLLEACTLYL DAFFLLLTGS
NLNLHLNLGG LGLGTFDACL ISEELAYGCT GVQTAIEGNS LGQMPIIIAG NDQQKKKYLG
RMTEEPLMCA YCVTEPGAGS DVAGIKTKAE KKGDEYIING QKMWITNGGK ANWYFLLARS
DPDPKAPANK AFTGFIVEAD TPGIQIGRKE LNMGQRRSDT RGIVFEDVKV PKENVLIGDG
AGFKVAMGAF DKTRPVVAAG AVGLAQRALD EATKYALERK TFGKLLVEHQ AISFMLAEMA
MKVELARMSY QRAAWEVDSG RRNTYYASIA KAFAGDIANQ LATDAVQILG GNGFNTEYPV
EKLMRDAKIY QIYEGTSQIQ RLIVAREHID KYKN*
speed 0.48 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