mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known disease mutation at this position (HGMD CM002020)
known disease mutation at this position (HGMD CX163073)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:71687538C>TN/A show variant in all transcripts IGV

HGNC symbol

FXN

Ensembl transcript ID

ENST00000396366

Genbank transcript ID

NM_181425

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.501C>T
cDNA.522C>T
g.37364C>T

AA changes

no AA changes

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

known variant

Reference ID: rs138034837
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CX163073)

known disease mutation at this position, please check HGMD for details (HGMD ID CX163073)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002020)

known disease mutation at this position, please check HGMD for details (HGMD ID CX163073)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002020)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002020)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.293	1
	5.515	1
(flanking)	5.515	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	37354	wt: 0.7657 / mu: 0.7916 (marginal change - not scored)	wt: GCATTTGTTTTGTCTTCCAGTGGACCTAAGCGTTATGACTG mu: GCATTTGTTTTGTCTTCCAGTGGACCTAAGTGTTATGACTG	cagt\|GGAC
Donor marginally increased	37357	wt: 0.9864 / mu: 0.9958 (marginal change - not scored)	wt: AGTGGACCTAAGCGT mu: AGTGGACCTAAGTGT	TGGA\|ccta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

normal

AA sequence altered

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

strand

last intron/exon boundary

512

theoretical NMD boundary in CDS

440

length of CDS

591

coding sequence (CDS) position

501

cDNA position
(for ins/del: last normal base / first normal base)

522

gDNA position
(for ins/del: last normal base / first normal base)

37364

chromosomal position
(for ins/del: last normal base / first normal base)

71687538

original gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered gDNA sequence snippet

TGTCTTCCAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

original cDNA sequence snippet

AGGTATGTAGTGGACCTAAGCGTTATGACTGGACTGGGAAA

altered cDNA sequence snippet

AGGTATGTAGTGGACCTAAGTGTTATGACTGGACTGGGAAA

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

speed

1.11 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