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mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999944136957386      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993647)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:71668156G>TN/A show variant in all transcripts   IGV
HGNC symbol FXN
Ensembl transcript ID ENST00000498653
Genbank transcript ID N/A
UniProt peptide Q16595
alteration type single base exchange
alteration region CDS
DNA changes c.139G>T
cDNA.244G>T
g.17982G>T
AA changes D47Y Score: 160 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 47
frameshift no
known variant Reference ID: rs142157346
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM993647)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993647)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993647)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3210.968
3.9531
(flanking)3.2971
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased17975wt: 0.57 / mu: 0.96wt: TACACGTTTGAGGAC
mu: TACACGTTTGAGTAC		 CACG|tttg
Donor increased17985wt: 0.85 / mu: 0.94wt: AGGACTATGATGTCT
mu: AGTACTATGATGTCT		 GACT|atga
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      47EDLADKPYTFEDYDVSFGSGVLTV
mutated  not conserved    47EDLADKPYTFEYYDVSFGSGVLT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000000357  122EDLADKPYTFEDYDVSFGSGVLT
Fcatus  all identical  ENSFCAG00000008813  120EDLADKPYTLKDYDVSFGSGVLT
Mmusculus  all identical  ENSMUSG00000059363  119EDLADKPYTLEDYDVSFGDGVLT
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074356  116EDLTDENFTGLDYDVVFSNGVLT
Dmelanogaster  not conserved  FBgn0030092  100EELTENASELQGTDVAYSDGVLT
Celegans  not conserved  F59G1.7  52DQIADSFPVSEQFDVSHAMGVLT
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
5354MUTAGENRR->GG: No effect on processing of wild- type FXN.might get lost (downstream of altered splice site)
7879MUTAGENLR->GG: Abolishes cleavage to yield frataxin mature form and allows accumulation of frataxin(56-210) and frataxin(78-210).might get lost (downstream of altered splice site)
7980MUTAGENRK->GG: Abolishes cleavage to yield frataxin mature form and allows the accumulation of frataxin(56-210).might get lost (downstream of altered splice site)
92114HELIXmight get lost (downstream of altered splice site)
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 408 / 408
position (AA) of stopcodon in wt / mu AA sequence 136 / 136
position of stopcodon in wt / mu cDNA 513 / 513
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 106 / 106
chromosome 9
strand 1
last intron/exon boundary 363
theoretical NMD boundary in CDS 207
length of CDS 408
coding sequence (CDS) position 139
cDNA position
(for ins/del: last normal base / first normal base)		 244
gDNA position
(for ins/del: last normal base / first normal base)		 17982
chromosomal position
(for ins/del: last normal base / first normal base)		 71668156
original gDNA sequence snippet ACAAGCCATACACGTTTGAGGACTATGATGTCTCCTTTGGG
altered gDNA sequence snippet ACAAGCCATACACGTTTGAGTACTATGATGTCTCCTTTGGG
original cDNA sequence snippet ACAAGCCATACACGTTTGAGGACTATGATGTCTCCTTTGGG
altered cDNA sequence snippet ACAAGCCATACACGTTTGAGTACTATGATGTCTCCTTTGGG
wildtype AA sequence MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEDYDV SFGSGVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKR YDWTGKNWVY SHDGVSLHEL LAAELTKALK
TKLDLSSLAY SGKDA*
mutated AA sequence MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEYYDV SFGSGVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKR YDWTGKNWVY SHDGVSLHEL LAAELTKALK
TKLDLSSLAY SGKDA*
speed 0.56 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