Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999992252944 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910001)
  • known disease mutation: rs3591 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76200535G>AN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000541113
Genbank transcript ID N/A
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.339G>A
cDNA.392G>A
g.10500G>A
AA changes M113I Score: 10 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 113
frameshift no
known variant Reference ID: rs121434277
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs3591 (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 CM910001)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910001)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910001)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0061
6.0641
(flanking)2.4681
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 increased10503wt: 0.9901 / mu: 0.9948 (marginal change - not scored)wt: ATGACTGAGGAGCCA
mu: ATAACTGAGGAGCCA		 GACT|gagg
Donor increased10492wt: 0.45 / mu: 0.69wt: ATTTGGGGAGAATGA
mu: ATTTGGGGAGAATAA		 TTGG|ggag
Donor increased10501wt: 0.62 / mu: 0.85wt: GAATGACTGAGGAGC
mu: GAATAACTGAGGAGC		 ATGA|ctga
Donor increased10500wt: 0.29 / mu: 0.67wt: AGAATGACTGAGGAG
mu: AGAATAACTGAGGAG		 AATG|actg
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      113NDQQKKKYLGRMTEEPLMCAYCVT
mutated  all conserved    113NDQQKKKYLGRITEEPLMC
Ptroglodytes  all identical  ENSPTRG00000000871  149NDQQKKKYLGRMTEEPLMCAYC
Mmulatta  all identical  ENSMMUG00000007220  182NEQQKKKYLGRMTEEPLMCAYCV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  149NDQQKKKYLGRMTEQPMMCAYC
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000007137  178NDAQKRKYLGRLIEEPLMCAYCV
Drerio  all identical  ENSDARG00000038900  154NDAQRKKYLGRMTEEPLMCAYC
Dmelanogaster  all conserved  FBgn0035811  145NKEQKKKYLGRLLEEPLVAAYCV
Celegans  all conserved  T08G2.3  139NEEQKKKYLGALAAEPIIASYC
Xtropicalis  all identical  ENSXETG00000002983  154NEAQKKKYLGRMMEEPLMCAY
protein features
start (aa)end (aa)featuredetails 
102115HELIXlost
117129HELIXmight get lost (downstream of altered splice site)
131136HELIXmight get lost (downstream of altered splice site)
139151HELIXmight get lost (downstream of altered splice site)
156159STRANDmight get lost (downstream of altered splice site)
158167NP_BINDFAD.might get lost (downstream of altered splice site)
165168STRANDmight get lost (downstream of altered splice site)
167167BINDINGSubstrate; via carbonyl oxygen.might get lost (downstream of altered splice site)
169171HELIXmight get lost (downstream of altered splice site)
175178STRANDmight get lost (downstream of altered splice site)
180193STRANDmight get lost (downstream of altered splice site)
191191MUTAGENW->A: Loss of electron transfer to ETF.might get lost (downstream of altered splice site)
191191MUTAGENW->F: Reduces rate of electron transfer to ETF about six-fold.might get lost (downstream of altered splice site)
191193NP_BINDFAD.might get lost (downstream of altered splice site)
194197TURNmight get lost (downstream of altered splice site)
199206STRANDmight get lost (downstream of altered splice site)
212212MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
215217HELIXmight get lost (downstream of altered splice site)
216216BINDINGSubstrate.might get lost (downstream of altered splice site)
219225STRANDmight get lost (downstream of altered splice site)
231233STRANDmight get lost (downstream of altered splice site)
237237MUTAGENE->A: Strongly reduced rate of electron transfer to ETF.might get lost (downstream of altered splice site)
239241STRANDmight get lost (downstream of altered splice site)
247258STRANDmight get lost (downstream of altered splice site)
259261HELIXmight get lost (downstream of altered splice site)
262265STRANDmight get lost (downstream of altered splice site)
266268TURNmight get lost (downstream of altered splice site)
269303HELIXmight get lost (downstream of altered splice site)
278281REGIONSubstrate binding.might get lost (downstream of altered splice site)
279279MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
301301MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
306308NP_BINDFAD.might get lost (downstream of altered splice site)
309312STRANDmight get lost (downstream of altered splice site)
313315HELIXmight get lost (downstream of altered splice site)
316317NP_BINDFAD.might get lost (downstream of altered splice site)
317345HELIXmight get lost (downstream of altered splice site)
351376HELIXmight get lost (downstream of altered splice site)
356356CONFLICTI -> T (in Ref. 3; AAF63626).might get lost (downstream of altered splice site)
374378NP_BINDFAD.might get lost (downstream of altered splice site)
377379HELIXmight get lost (downstream of altered splice site)
384384MUTAGENE->A: Reduces rate of electron transfer to ETF three-fold.might get lost (downstream of altered splice site)
384384MUTAGENE->Q: Reduces rate of electron transfer to ETF two-fold.might get lost (downstream of altered splice site)
387394HELIXmight get lost (downstream of altered splice site)
395398HELIXmight get lost (downstream of altered splice site)
399401TURNmight get lost (downstream of altered splice site)
401401ACT_SITEProton acceptor.might get lost (downstream of altered splice site)
402402BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
403405NP_BINDFAD.might get lost (downstream of altered splice site)
404417HELIXmight get lost (downstream of altered splice site)
413413BINDINGSubstrate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1158 / 1158
position (AA) of stopcodon in wt / mu AA sequence 386 / 386
position of stopcodon in wt / mu cDNA 1211 / 1211
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 54 / 54
chromosome 1
strand 1
last intron/exon boundary 1140
theoretical NMD boundary in CDS 1036
length of CDS 1158
coding sequence (CDS) position 339
cDNA position
(for ins/del: last normal base / first normal base)		 392
gDNA position
(for ins/del: last normal base / first normal base)		 10500
chromosomal position
(for ins/del: last normal base / first normal base)		 76200535
original gDNA sequence snippet AAGAAGTATTTGGGGAGAATGACTGAGGAGCCATTGATGTG
altered gDNA sequence snippet AAGAAGTATTTGGGGAGAATAACTGAGGAGCCATTGATGTG
original cDNA sequence snippet AAGAAGTATTTGGGGAGAATGACTGAGGAGCCATTGATGTG
altered cDNA sequence snippet AAGAAGTATTTGGGGAGAATAACTGAGGAGCCATTGATGTG
wildtype AA sequence MLQEFTEQQK 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 MLQEFTEQQK EFQATARKFA REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG
GLGLGTFDAC LISEELAYGC TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRITEEPLMC
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 0.15 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