Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999918531 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012321)
  • known disease mutation: rs3599 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76199288C>TN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000420607
Genbank transcript ID NM_001127328
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.374C>T
cDNA.382C>T
g.9253C>T
AA changes T125I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 125
frameshift no
known variant Reference ID: rs121434283
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs3599 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012321)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012321)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012321)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0341
6.0971
(flanking)-0.2580.952
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      125EELAYGCTGVQTAIEGNSLGQMPI
mutated  not conserved    125TGVQIAIEGNSLGQMP
Ptroglodytes  all identical  ENSPTRG00000000871  121TGVQTAIEGNSLGQMP
Mmulatta  all identical  ENSMMUG00000007220  141EELAYGCTGVQTAIEGNSLGQMP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  121TGVQTAIEANSLGQMP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  150EELAYGCTGVQTAIEANSLGQMP
Drerio  all identical  ENSDARG00000038900  126EELAYGCTGVQTAIEANSLGQMP
Dmelanogaster  all identical  FBgn0035811  117EELAYGCTGIMTALEASG
Celegans  not conserved  T08G2.3  111EALSYGCTGIQLGIMGPSLAIAP
Xtropicalis  all identical  ENSXETG00000002983  126EEIAYGCTGVQTAIEANSLGQMP
protein features
start (aa)end (aa)featuredetails 
117129HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1278 / 1278
position (AA) of stopcodon in wt / mu AA sequence 426 / 426
position of stopcodon in wt / mu cDNA 1286 / 1286
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 9 / 9
chromosome 1
strand 1
last intron/exon boundary 1215
theoretical NMD boundary in CDS 1156
length of CDS 1278
coding sequence (CDS) position 374
cDNA position
(for ins/del: last normal base / first normal base)		 382
gDNA position
(for ins/del: last normal base / first normal base)		 9253
chromosomal position
(for ins/del: last normal base / first normal base)		 76199288
original gDNA sequence snippet TGGATGTACAGGGGTTCAGACTGCTATTGAAGGAAATTCTT
altered gDNA sequence snippet TGGATGTACAGGGGTTCAGATTGCTATTGAAGGAAATTCTT
original cDNA sequence snippet TGGATGTACAGGGGTTCAGACTGCTATTGAAGGAAATTCTT
altered cDNA sequence snippet TGGATGTACAGGGGTTCAGATTGCTATTGAAGGAAATTCTT
wildtype AA sequence MAAGFGRCCR CSLQVLRSIS RFHWRSQHTK ANRQREPGLG FSFEFTEQQK EFQATARKFA
REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG GLGLGTFDAC LISEELAYGC
TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC AYCVTEPGAG SDVAGIKTKA
EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN KAFTGFIVEA DTPGIQIGRK
ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN*
mutated AA sequence MAAGFGRCCR CSLQVLRSIS RFHWRSQHTK ANRQREPGLG FSFEFTEQQK EFQATARKFA
REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG GLGLGTFDAC LISEELAYGC
TGVQIAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC AYCVTEPGAG SDVAGIKTKA
EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN KAFTGFIVEA DTPGIQIGRK
ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN*
speed 1.17 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