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mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1      (explain)
Summary
  • known disease mutation at this position (HGMD CM983507)
  • protein features (might be) affected
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:71687589C>TN/A show variant in all transcripts   IGV
HGNC symbol FXN
Ensembl transcript ID ENST00000396366
Genbank transcript ID NM_181425
UniProt peptide Q16595
alteration type single base exchange
alteration region CDS
DNA changes c.552C>T
cDNA.573C>T
g.37415C>T
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift no
known variant Reference ID: rs139616452
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983507)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2230.904
3.7681
(flanking)4.4721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased37420wt: 0.53 / mu: 0.65wt: CACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGCT
mu: CACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGCT		 ccat|GAGC
Acc increased37418wt: 0.22 / mu: 0.43wt: CCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAG
mu: CCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAG		 ctcc|ATGA
Acc increased37419wt: 0.27 / mu: 0.50wt: CCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCAGAGC
mu: CCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCAGAGC		 tcca|TGAG
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
182194HELIXmight get lost (downstream of altered splice site)
202202CONFLICTS -> W (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
206208STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered no
position of stopcodon in wt / mu CDS 591 / 591
position (AA) of stopcodon in wt / mu AA sequence 197 / 197
position of stopcodon in wt / mu cDNA 612 / 612
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 22 / 22
chromosome 9
strand 1
last intron/exon boundary 512
theoretical NMD boundary in CDS 440
length of CDS 591
coding sequence (CDS) position 552
cDNA position
(for ins/del: last normal base / first normal base)		 573
gDNA position
(for ins/del: last normal base / first normal base)		 37415
chromosomal position
(for ins/del: last normal base / first normal base)		 71687589
original gDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered gDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
original cDNA sequence snippet ACTCCCACGACGGCGTGTCCCTCCATGAGCTGCTGGCCGCA
altered cDNA sequence snippet ACTCCCACGACGGCGTGTCCTTCCATGAGCTGCTGGCCGCA
wildtype AA sequence MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS RYVVDLSVMT GLGKTGCTPT
TACPSMSCWP QSSLKP*
mutated AA sequence MWTLGRRAVA GLLASPSPAQ AQTLTRVPRP AELAPLCGRR GLRTDIDATC TPRRASSNQR
GLNQIWNVKK QSVYLMNLRK SGTLGHPGSL DETTYERLAE ETLDSLAEFF EDLADKPYTF
EDYDVSFGSG VLTVKLGGDL GTYVINKQTP NKQIWLSSPS RYVVDLSVMT GLGKTGCTPT
TACPSMSCWP QSSLKP*
speed 0.95 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