Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970534)
  • known disease mutation: rs3982 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:71679858G>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.389G>T
cDNA.410G>T
g.29684G>T
AA changes G130V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 130
frameshift no
known variant Reference ID: rs104894107
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs3982 (pathogenic for Friedreich's ataxia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970534)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970534)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970534)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7061
5.7061
(flanking)-0.4580.964
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased29674wt: 0.5958 / mu: 0.6065 (marginal change - not scored)wt: TGCTTTTTTTCCACCTAATCCCCTAGAGTGGTGTCTTAACT
mu: TGCTTTTTTTCCACCTAATCCCCTAGAGTGTTGTCTTAACT		 atcc|CCTA
Acc decreased29679wt: 0.30 / mu: 0.21wt: TTTTTCCACCTAATCCCCTAGAGTGGTGTCTTAACTGTCAA
mu: TTTTTCCACCTAATCCCCTAGAGTGTTGTCTTAACTGTCAA		 ctag|AGTG
Acc marginally increased29675wt: 0.2590 / mu: 0.2848 (marginal change - not scored)wt: GCTTTTTTTCCACCTAATCCCCTAGAGTGGTGTCTTAACTG
mu: GCTTTTTTTCCACCTAATCCCCTAGAGTGTTGTCTTAACTG		 tccc|CTAG
Donor increased29675wt: 0.85 / mu: 0.97wt: AATCCCCTAGAGTGG
mu: AATCCCCTAGAGTGT		 TCCC|ctag
Acc gained296940.51mu: CCCTAGAGTGTTGTCTTAACTGTCAAACTGGGTGGAGATCT aact|GTCA
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      130TFEDYDVSFGSGVLTVKLGGDLGT
mutated  not conserved    130EDYDVSFGSVVLTVKLGGDLG
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000000357  130EDYDVSFGSGVLTVKLGGDLG
Fcatus  all identical  ENSFCAG00000008813  128YDVSFGSGVLTVKLGGDLG
Mmusculus  all identical  ENSMUSG00000059363  127EDYDVSFGDGVLTIKLGGDLG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074356  124TGLDYDVVFSNGVLTVKVGSDHG
Dmelanogaster  all identical  FBgn0030092  108ELQGTDVAYSDGVLTVNLGGQHG
Celegans  all identical  F59G1.7  60VSEQFDVSHAMGVLTVNVSKSVG
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
124128STRANDmight get lost (downstream of altered splice site)
131135STRANDmight get lost (downstream of altered splice site)
138140TURNmight get lost (downstream of altered splice site)
142148STRANDmight get lost (downstream of altered splice site)
149152TURNmight get lost (downstream of altered splice site)
153157STRANDmight get lost (downstream of altered splice site)
159161STRANDmight get lost (downstream of altered splice site)
164168STRANDmight get lost (downstream of altered splice site)
170175STRANDmight get lost (downstream of altered splice site)
175175CONFLICTY -> F (in Ref. 1; AAA98508/AAA98510).might get lost (downstream of altered splice site)
176178TURNmight get lost (downstream of altered splice site)
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 yes
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 389
cDNA position
(for ins/del: last normal base / first normal base)		 410
gDNA position
(for ins/del: last normal base / first normal base)		 29684
chromosomal position
(for ins/del: last normal base / first normal base)		 71679858
original gDNA sequence snippet CCACCTAATCCCCTAGAGTGGTGTCTTAACTGTCAAACTGG
altered gDNA sequence snippet CCACCTAATCCCCTAGAGTGTTGTCTTAACTGTCAAACTGG
original cDNA sequence snippet TGATGTCTCCTTTGGGAGTGGTGTCTTAACTGTCAAACTGG
altered cDNA sequence snippet TGATGTCTCCTTTGGGAGTGTTGTCTTAACTGTCAAACTGG
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
EDYDVSFGSV VLTVKLGGDL GTYVINKQTP NKQIWLSSPS RYVVDLSVMT GLGKTGCTPT
TACPSMSCWP QSSLKP*
speed 0.68 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