Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.997558424554628      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000315713
Genbank transcript ID NM_001122674
UniProt peptide P28288
alteration type single base exchange
alteration region CDS
DNA changes c.50G>A
cDNA.50G>A
g.152G>A
AA changes G17D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 17
frameshift no
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
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased153wt: 0.73 / mu: 0.93wt: GCTGGTGCCGCGTTC
mu: GCTGATGCCGCGTTC		 TGGT|gccg
distance from splice site 50
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      17KYLTARNSSLAGAAFLLLCLLHKR
mutated  not conserved    17KYLTARNSSLADAAFLLLCLLHK
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000014013  17KYLTARNSSLAGAAFLLLCLLHK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028127  17KYLTARNTSLAGAAFLLLCLLHK
Ggallus  not conserved  ENSGALG00000005647  17KYLTVRHSAIVGGTAAACALLCLLNK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000015167  17KYLTAKNSAVAGGVLLVLYILKQ
Dmelanogaster  no alignment  FBgn0031069  n/a
Celegans  no alignment  C44B7.9  n/a
Xtropicalis  all identical  ENSXETG00000008218  18KYLTARNSSVAGAALFLLYLINK
protein features
start (aa)end (aa)featuredetails 
1124REGIONTargeting to peroxisomes.lost
1199REGIONInteraction with PEX19.lost
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 711 / 711
position (AA) of stopcodon in wt / mu AA sequence 237 / 237
position of stopcodon in wt / mu cDNA 711 / 711
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 1 / 1
chromosome 1
strand 1
last intron/exon boundary 685
theoretical NMD boundary in CDS 634
length of CDS 711
coding sequence (CDS) position 50
cDNA position
(for ins/del: last normal base / first normal base)		 50
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 MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD
KVFFSRLIQI LKIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIIGRSRK
DFKRYLLNFI AAMPLISLVN NFLKYGLNEL KLCFRVRLTK YLYEEYLQAF TYYKMGNLDN
RIANPDQLLT QDVEKFCNSV VDLYSNLSKP FLDIVLYIFK LTSAIGAQVL GKILWH*
mutated AA sequence MAAFSKYLTA RNSSLADAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD
KVFFSRLIQI LKIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIIGRSRK
DFKRYLLNFI AAMPLISLVN NFLKYGLNEL KLCFRVRLTK YLYEEYLQAF TYYKMGNLDN
RIANPDQLLT QDVEKFCNSV VDLYSNLSKP FLDIVLYIFK LTSAIGAQVL GKILWH*
speed 1.23 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