Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999961023372 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM083517)
  • known disease mutation: rs4202 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:75275286C>TN/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.488C>T
cDNA.606C>T
g.41922C>T
AA changes P163L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 163
frameshift no
known variant Reference ID: rs121908114
databasehomozygous (T/T)heterozygousallele carriers
1000G044
ExAC033

known disease mutation: rs4202 (pathogenic for Charcot-Marie-Tooth disease, type 4A|Charcot-Marie-Tooth disease type 2K|Charcot-Marie-Tooth disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM083517)

known disease mutation at this position, please check HGMD for details (HGMD ID CM083517)
known disease mutation at this position, please check HGMD for details (HGMD ID CM083517)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4291
3.4081
(flanking)1.4661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost41923sequence motif lost- wt: CCAG|gtag
 mu: CTAG.gtag
Donor marginally decreased41923wt: 0.9879 / mu: 0.9858 (marginal change - not scored)wt: ACCCCAGGTAGGTTC
mu: ACCCTAGGTAGGTTC		 CCCA|ggta
Donor gained419180.40mu: AAGAAACCCTAGGTA GAAA|ccct
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      163ETELQRRNEETPEEGQQPWLCGES
mutated  not conserved    163ETELQRRNEETLEEGQQPWLCGE
Ptroglodytes  all identical  ENSPTRG00000020354  231ETELQRRNEETPEEGQQPWLCGE
Mmulatta  all identical  ENSMMUG00000022326  231ETELQRRNEETPEEGQQPWLCGE
Fcatus  all identical  ENSFCAG00000014031  231RRNEETPEEGRQPWLCGE
Mmusculus  all identical  ENSMUSG00000025777  231ETELQRRNEETPEEGNQPWLCGE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000058601  255ETELQRRSEETPEEGSQQAWLCGD
Dmelanogaster  not conserved  FBgn0035587  230RHFLLYVEQELTAQAPRVEWLTGD
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
153309DOMAINGST C-terminal.lost
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 488
cDNA position
(for ins/del: last normal base / first normal base)		 606
gDNA position
(for ins/del: last normal base / first normal base)		 41922
chromosomal position
(for ins/del: last normal base / first normal base)		 75275286
original gDNA sequence snippet AAGAAGAAATGAAGAAACCCCAGGTAGGTTCTCATTTATAT
altered gDNA sequence snippet AAGAAGAAATGAAGAAACCCTAGGTAGGTTCTCATTTATAT
original cDNA sequence snippet AAGAAGAAATGAAGAAACCCCAGAAGAGGGCCAGCAACCTT
altered cDNA sequence snippet AAGAAGAAATGAAGAAACCCTAGAAGAGGGCCAGCAACCTT
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 LDELEKVLDQ VETELQRRNE ETLEEGQQPW LCGESFTLAD
VSLAVTLHRL KFLGFARRNW GNGKRPNLET YYERVLKRKT FNKVLGHVNN ILISAVLPTA
FRVAKKRAPK VLGTTLVVGL LAGVGYFAFM LFRKRLGSMI LAFRPRPNYF *
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