Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999980732 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM000501)
  • known disease mutation: rs5524 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:34005932A>GN/A show variant in all transcripts   IGV
HGNC symbol AMACR
Ensembl transcript ID ENST00000382072
Genbank transcript ID NM_203382
UniProt peptide Q9UHK6
alteration type single base exchange
alteration region CDS
DNA changes c.320T>C
cDNA.332T>C
g.2289T>C
AA changes L107P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 107
frameshift no
known variant Reference ID: rs121917816
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs5524 (pathogenic for Congenital bile acid synthesis defect 4) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000501)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000501)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000501)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2860.98
3.4740.978
(flanking)0.10.364
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2286wt: 0.23 / mu: 0.29wt: TCCAAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGT
mu: TCCAAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGT		 ccag|GCTG
Donor marginally increased2291wt: 0.6556 / mu: 0.7170 (marginal change - not scored)wt: GGCTGAGTGGATTTG
mu: GGCCGAGTGGATTTG		 CTGA|gtgg
Donor marginally increased2286wt: 0.9779 / mu: 0.9794 (marginal change - not scored)wt: TGCCAGGCTGAGTGG
mu: TGCCAGGCCGAGTGG		 CCAG|gctg
Donor increased2281wt: 0.88 / mu: 0.97wt: ATTTATGCCAGGCTG
mu: ATTTATGCCAGGCCG		 TTAT|gcca
distance from splice site 72
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      107QRENPRLIYARLSGFGQSGSFCRL
mutated  not conserved    107QRENPRLIYARPSGFGQSGSFCR
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000013467  107QRDNPRLIYARLTGFGQSGSFSR
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022244  106LQDNPKLIYARLSGFGQSGIFSK
Ggallus  all identical  ENSGALG00000003326  108LHENPRLIYARLTGFGQTGKYAK
Trubripes  all identical  ENSTRUG00000014396  107LRENPCLIYARLTGYGQSGSYAT
Drerio  all identical  ENSDARG00000057435  107IKENPRLIYARLTGYGQSGSYAK
Dmelanogaster  all identical  FBgn0032881  106CTANPRLIYARLTGFGQHGRLAQ
Celegans  all conserved  C24A3.4  108WNDNKGLIICRISGYGQTGRMSQ
Xtropicalis  all identical  ENSXETG00000002559  107LKENPQLIYARLTGFGQSGKYAK
protein features
start (aa)end (aa)featuredetails 
128128CONFLICTA -> T (in Ref. 6; ABQ59031).might get lost (downstream of altered splice site)
150150CONFLICTL -> V (in Ref. 1; CAB44062).might get lost (downstream of altered splice site)
152152ACT_SITENucleophile (By similarity).might get lost (downstream of altered splice site)
183183CONFLICTN -> D (in Ref. 3; AAD10205).might get lost (downstream of altered splice site)
257257CONFLICTN -> S (in Ref. 3; AAD10205).might get lost (downstream of altered splice site)
327327CONFLICTP -> L (in Ref. 1; CAB44062).might get lost (downstream of altered splice site)
340342CONFLICTFKR -> SKG (in Ref. 1; CAB44062).might get lost (downstream of altered splice site)
380382MOTIFMicrobody targeting signal.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 597 / 597
position (AA) of stopcodon in wt / mu AA sequence 199 / 199
position of stopcodon in wt / mu cDNA 609 / 609
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 13 / 13
chromosome 5
strand -1
last intron/exon boundary 591
theoretical NMD boundary in CDS 528
length of CDS 597
coding sequence (CDS) position 320
cDNA position
(for ins/del: last normal base / first normal base)		 332
gDNA position
(for ins/del: last normal base / first normal base)		 2289
chromosomal position
(for ins/del: last normal base / first normal base)		 34005932
original gDNA sequence snippet AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG
altered gDNA sequence snippet AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG
original cDNA sequence snippet AAGGCTTATTTATGCCAGGCTGAGTGGATTTGGCCAGTCAG
altered cDNA sequence snippet AAGGCTTATTTATGCCAGGCCGAGTGGATTTGGCCAGTCAG
wildtype AA sequence MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARLSGF GQSGSFCRLA
GHDINYLALS GGRNSIFKFF SVENSEIESV GSTSRTEHVG WWSTFLYDLQ DSRWGIHGCW
SNRTPVLRAA DQRTWTKV*
mutated AA sequence MALQGISVVE LSGLAPGPFC AMVLADFGAR VVRVDRPGSR YDVSRLGRGK RSLVLDLKQP
RGAAVLRRLC KRSDVLLEPF RRGVMEKLQL GPEILQRENP RLIYARPSGF GQSGSFCRLA
GHDINYLALS GGRNSIFKFF SVENSEIESV GSTSRTEHVG WWSTFLYDLQ DSRWGIHGCW
SNRTPVLRAA DQRTWTKV*
speed 1.24 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