Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999973440784289 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM081280)
  • known disease mutation: rs4201 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:75275246C>GN/A show variant in all transcripts   IGV
HGNC symbol GDAP1
Ensembl transcript ID ENST00000434412
Genbank transcript ID NM_001040875
UniProt peptide Q8TB36
alteration type single base exchange
alteration region CDS
DNA changes c.448C>G
cDNA.566C>G
g.41882C>G
AA changes Q150E Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 150
frameshift no
known variant Reference ID: rs121908113
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4201 (pathogenic for Charcot-Marie-Tooth disease type 2K) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081280)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081280)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081280)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.2571
5.2741
(flanking)4.3711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained418780.49mu: GTCTTGGATGAGGTT CTTG|gatg
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      150KILDELEKVLDQVETELQRRNEET
mutated  all conserved    150KILDELEKVLDEVETELQRRNEE
Ptroglodytes  all identical  ENSPTRG00000020354  218KILDELEKVLDQVETELQRRNEE
Mmulatta  all identical  ENSMMUG00000022326  218KILDELEKVLDQVETELQRRNEE
Fcatus  all identical  ENSFCAG00000014031  218KILDELEKVLDQVETELQ
Mmusculus  all identical  ENSMUSG00000025777  218KILDELEKVLDQVETELQRRNEE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000058601  242KLLDELENVLDQVETELQRRSEE
Dmelanogaster  not conserved  FBgn0035587  217SSREEFQKVLDAVRHFLLYVEQEL
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
153309DOMAINGST C-terminal.might get lost (downstream of altered splice site)
157157MUTAGENT->P: No effect on mitochondrial localization.might get lost (downstream of altered splice site)
203203MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
292312TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320340TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
320358REGIONRequired for mitochondrial localization.might get lost (downstream of altered splice site)
351351CONFLICTF -> L (in Ref. 1; CAA76892).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 873 / 873
position (AA) of stopcodon in wt / mu AA sequence 291 / 291
position of stopcodon in wt / mu cDNA 991 / 991
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 119 / 119
chromosome 8
strand 1
last intron/exon boundary 609
theoretical NMD boundary in CDS 440
length of CDS 873
coding sequence (CDS) position 448
cDNA position
(for ins/del: last normal base / first normal base)		 566
gDNA position
(for ins/del: last normal base / first normal base)		 41882
chromosomal position
(for ins/del: last normal base / first normal base)		 75275246
original gDNA sequence snippet AGTTGGAGAAAGTCTTGGATCAGGTTGAAACTGAATTGCAA
altered gDNA sequence snippet AGTTGGAGAAAGTCTTGGATGAGGTTGAAACTGAATTGCAA
original cDNA sequence snippet AGTTGGAGAAAGTCTTGGATCAGGTTGAAACTGAATTGCAA
altered cDNA sequence snippet AGTTGGAGAAAGTCTTGGATGAGGTTGAAACTGAATTGCAA
wildtype AA sequence MRLNSTGEVP VLIHGENIIC EATQIIDYLE QTFLDERTPR LMPDKESMYY PRVQHYRELL
DSLPMDAYTH GCILHPELTV DSMIPAYATT RIRSQIGNTE SELKKLAEEN PDLQEAYIAK
QKRLKSKLLD HDNVKYLKKI LDELEKVLDQ VETELQRRNE ETPEEGQQPW LCGESFTLAD
VSLAVTLHRL KFLGFARRNW GNGKRPNLET YYERVLKRKT FNKVLGHVNN ILISAVLPTA
FRVAKKRAPK VLGTTLVVGL LAGVGYFAFM LFRKRLGSMI LAFRPRPNYF *
mutated AA sequence MRLNSTGEVP VLIHGENIIC EATQIIDYLE QTFLDERTPR LMPDKESMYY PRVQHYRELL
DSLPMDAYTH GCILHPELTV DSMIPAYATT RIRSQIGNTE SELKKLAEEN PDLQEAYIAK
QKRLKSKLLD HDNVKYLKKI LDELEKVLDE VETELQRRNE ETPEEGQQPW LCGESFTLAD
VSLAVTLHRL KFLGFARRNW GNGKRPNLET YYERVLKRKT FNKVLGHVNN ILISAVLPTA
FRVAKKRAPK VLGTTLVVGL LAGVGYFAFM LFRKRLGSMI LAFRPRPNYF *
speed 0.90 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