Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1      (explain)
Summary
  • known disease mutation at this position (HGMD CM920599)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:94884084G>AN/A show variant in all transcripts   IGV
HGNC symbol ABCD3
Ensembl transcript ID ENST00000536817
Genbank transcript ID N/A
UniProt peptide P28288
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.114G>A
g.152G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121917999
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM920599)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920599)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920599)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8331
2.8331
(flanking)0.2831
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -43) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased153wt: 0.73 / mu: 0.93wt: GCTGGTGCCGCGTTC
mu: GCTGATGCCGCGTTC		 TGGT|gccg
distance from splice site 61
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
1124REGIONTargeting to peroxisomes.might get lost (downstream of altered splice site)
1199REGIONInteraction with PEX19.might get lost (downstream of altered splice site)
1212CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
84104TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
85372DOMAINABC transmembrane type-1.might get lost (downstream of altered splice site)
106106CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
126146TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
145145MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
175175CONFLICTM -> K (in Ref. 2; CAA41416).might get lost (downstream of altered splice site)
191192CONFLICTQD -> LV (in Ref. 3; CAA58470).might get lost (downstream of altered splice site)
206206CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
224244TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
260260MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
313333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
336336CONFLICTP -> L (in Ref. 3; CAA58470).might get lost (downstream of altered splice site)
399399MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
440659DOMAINABC transporter.might get lost (downstream of altered splice site)
473480NP_BINDATP (Potential).might get lost (downstream of altered splice site)
478478MUTAGENG->R: Decreased ATP-binding affinity.might get lost (downstream of altered splice site)
503503CONFLICTG -> R (in Ref. 2; CAA41416).might get lost (downstream of altered splice site)
542542CONFLICTL -> Q (in Ref. 2; CAA41416).might get lost (downstream of altered splice site)
572572MUTAGENS->I: Decreased ATPase activity.might get lost (downstream of altered splice site)
616634CONFLICTVGITLFTVSHRKSLWKHHE -> GWHHSLHLCLIGNLFGNI MR (in Ref. 3; CAA58470).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 247 / 247
chromosome 1
strand 1
last intron/exon boundary 1930
theoretical NMD boundary in CDS 1633
length of CDS 1761
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 114
gDNA position
(for ins/del: last normal base / first normal base)		 152
chromosomal position
(for ins/del: last normal base / first normal base)		 94884084
original gDNA sequence snippet GCGAAACTCCTCGCTGGCTGGTGCCGCGTTCCTGCTGCTCT
altered gDNA sequence snippet GCGAAACTCCTCGCTGGCTGATGCCGCGTTCCTGCTGCTCT
original cDNA sequence snippet GCGAAACTCCTCGCTGGCTGGTGCCGCGTTCCTGCTGCTCT
altered cDNA sequence snippet GCGAAACTCCTCGCTGGCTGATGCCGCGTTCCTGCTGCTCT
wildtype AA sequence MVPRTFCKET GYLVLIAVML VSRTYCDVWM IQNGTLIESG IIGRSRKDFK RYLLNFIAAM
PLISLVNNFL KYGLNELKLC FRVRLTKYLY EEYLQAFTYY KMGNLDNRIA NPDQLLTQDV
EKFCNSVVDL YSNLSKPFLD IVLYIFKLTS AIGAQGPASM MAYLVVSGLF LTRLRRPIGK
MTITEQKYEG EYRYVNSRLI TNSEEIAFYN GNKREKQTVH SVFRKLVEHL HNFILFRFSM
GFIDSIIAKY LATVVGYLVV SRPFLDLSHP RHLKSTHSEL LEDYYQSGRM LLRMSQALGR
IVLAGREMTR LAGFTARITE LMQVLKDLNH GKYERTMVSQ QEKGIEGVQV IPLIPGAGEI
IIADNIIKFD HVPLATPNGD VLIRDLNFEV RSGANVLICG PNGCGKSSLF RVLGELWPLF
GGRLTKPERG KLFYVPQRPY MTLGTLRDQV IYPDGREDQK RKGISDLVLK EYLDNVQLGH
ILEREGGWDS VQDWMDVLSG GEKQRMAMAR LFYHKPQFAI LDECTSAVSV DVEGYIYSHC
RKVGITLFTV SHRKSLWKHH EYYLHMDGRG NYEFKQITED TVEFGS*
mutated AA sequence N/A
speed 0.19 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