Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999911347528 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002425)
  • known disease mutation: rs5126 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:8757823T>CN/A show variant in all transcripts   IGV
HGNC symbol AICDA
Ensembl transcript ID ENST00000229335
Genbank transcript ID NM_020661
UniProt peptide Q9GZX7
alteration type single base exchange
alteration region CDS
DNA changes c.415A>G
cDNA.519A>G
g.7645A>G
AA changes M139V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 139
frameshift no
known variant Reference ID: rs104894322
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5126 (pathogenic for Hyper-IgM syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002425)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002425)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002425)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4541
4.4541
(flanking)2.7441
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 increased7638wt: 0.5849 / mu: 0.5938 (marginal change - not scored)wt: CAAATAGCCATCATG
mu: CAAATAGCCATCGTG		 AATA|gcca
Donor gained76440.69mu: GCCATCGTGACCTTC CATC|gtga
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      139RLHRAGVQIAIMTFKDYFYCWNTF
mutated  all conserved    139RLHRAGVQIAIVTFKDYFYCWNT
Ptroglodytes  all identical  ENSPTRG00000004640  139RLHRAGVQIAIMTFKDYFYCWNT
Mmulatta  all identical  ENSMMUG00000019134  138RLHRAGVQIAIMTFKDYFYCWNT
Fcatus  all identical  ENSFCAG00000006052  87RLHRAGVQIAIMTFKXXXXXXXX
Mmusculus  all identical  ENSMUSG00000040627  139RLHRAGVQIGIMTFKDYFYCWNT
Ggallus  all identical  ENSGALG00000014280  139RLHRAGAQIAIMTFKDFFYCWNT
Trubripes  all identical  ENSTRUG00000007079  152MLTKAGVRISVMSYKDYFYCWQK
Drerio  all identical  ENSDARG00000015734  151HLKRAGVQISVMTYKDFFYCWQT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023905  142KLQKAGVRLAVMSYKDYFYCWNT
protein features
start (aa)end (aa)featuredetails 
183198REGIONNuclear export signal.might get lost (downstream of altered splice site)
193193MUTAGENF->A: Completely abolishes nuclear import; when associated with W-24 or D- 112. Little affect on nuclear import; when associated with A-10. Greatly impaired nuclear import; when associated with K-20 or G-50. Almost completely abolishes nuclear import; when associated with S-18 and V-19.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 701 / 701
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 105 / 105
chromosome 12
strand -1
last intron/exon boundary 648
theoretical NMD boundary in CDS 493
length of CDS 597
coding sequence (CDS) position 415
cDNA position
(for ins/del: last normal base / first normal base)		 519
gDNA position
(for ins/del: last normal base / first normal base)		 7645
chromosomal position
(for ins/del: last normal base / first normal base)		 8757823
original gDNA sequence snippet CCGGGGTGCAAATAGCCATCATGACCTTCAAAGGTGCGAAA
altered gDNA sequence snippet CCGGGGTGCAAATAGCCATCGTGACCTTCAAAGGTGCGAAA
original cDNA sequence snippet CCGGGGTGCAAATAGCCATCATGACCTTCAAAGATTATTTT
altered cDNA sequence snippet CCGGGGTGCAAATAGCCATCGTGACCTTCAAAGATTATTTT
wildtype AA sequence MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL
LPLYEVDDLR DAFRTLGL*
mutated AA sequence MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIVT FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL
LPLYEVDDLR DAFRTLGL*
speed 1.48 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