Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999994969 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM011749)
  • known disease mutation: rs3598 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76215129C>TN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000543667
Genbank transcript ID N/A
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.167C>T
cDNA.485C>T
g.25094C>T
AA changes S56L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 56
frameshift no
known variant Reference ID: rs121434281
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs3598 (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 CM011749)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011749)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011749)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1021
6.181
(flanking)-0.1160.987
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      56GRKELNMGQRCSDTRGIVFEDVKV
mutated  not conserved    56GRKELNMGQRCLDTRG
Ptroglodytes  all identical  ENSPTRG00000000871  245GRKELNMGQRCSDTRG
Mmulatta  all identical  ENSMMUG00000007220  278GRKELNMGQRCSDTRG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  245GKKELNMGQRCSDTRG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  274GRKELNMGQRCSDTRG
Drerio  all identical  ENSDARG00000038900  250GRKELNMGQRCSDTRG
Dmelanogaster  all identical  FBgn0035811  241GRKELNMGQRASDTRG
Celegans  all identical  T08G2.3  235GKKEKNMGQRCSDTRVI
Xtropicalis  all identical  ENSXETG00000002983  250GRKEMNMGQRCSDTRG
protein features
start (aa)end (aa)featuredetails 
4359HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 699 / 699
position (AA) of stopcodon in wt / mu AA sequence 233 / 233
position of stopcodon in wt / mu cDNA 1017 / 1017
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 319 / 319
chromosome 1
strand 1
last intron/exon boundary 946
theoretical NMD boundary in CDS 577
length of CDS 699
coding sequence (CDS) position 167
cDNA position
(for ins/del: last normal base / first normal base)		 485
gDNA position
(for ins/del: last normal base / first normal base)		 25094
chromosomal position
(for ins/del: last normal base / first normal base)		 76215129
original gDNA sequence snippet AAACATGGGCCAGCGATGTTCAGATACTAGAGGAATTGTCT
altered gDNA sequence snippet AAACATGGGCCAGCGATGTTTAGATACTAGAGGAATTGTCT
original cDNA sequence snippet AAACATGGGCCAGCGATGTTCAGATACTAGAGGAATTGTCT
altered cDNA sequence snippet AAACATGGGCCAGCGATGTTTAGATACTAGAGGAATTGTCT
wildtype AA sequence MWITNGGKAN WYFLLARSDP DPKAPANKAF TGFIVEADTP GIQIGRKELN MGQRCSDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQILGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*
mutated AA sequence MWITNGGKAN WYFLLARSDP DPKAPANKAF TGFIVEADTP GIQIGRKELN MGQRCLDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQILGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*
speed 1.35 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