Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999960076291 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM020375)
  • known disease mutation: rs4192 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:75272543G>AN/A show variant in all transcripts   IGV
HGNC symbol GDAP1
Ensembl transcript ID ENST00000220822
Genbank transcript ID NM_018972
UniProt peptide Q8TB36
alteration type single base exchange
alteration region CDS
DNA changes c.482G>A
cDNA.562G>A
g.39179G>A
AA changes R161H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 161
frameshift no
known variant Reference ID: rs104894076
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4192 (pathogenic for Charcot-Marie-Tooth disease, type 4A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM020375)

known disease mutation at this position, please check HGMD for details (HGMD ID CM020375)
known disease mutation at this position, please check HGMD for details (HGMD ID CM020375)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.731
5.731
(flanking)0.5341
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 lost39180sequence motif lost- wt: CGTA|gtat
 mu: CATA.gtat
Donor increased39176wt: 0.35 / mu: 0.49wt: AAGGATTCGTAGTAT
mu: AAGGATTCATAGTAT		 GGAT|tcgt
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      161SMIPAYATTRIRSQIGNTESELKK
mutated  not conserved    161SMIPAYATTRIHSQIGNTESELK
Ptroglodytes  all identical  ENSPTRG00000020354  161SMIPAYATTRIRSQIGNTESELK
Mmulatta  all identical  ENSMMUG00000022326  161SMIPAYATTRIRSQIGNTESELK
Fcatus  all identical  ENSFCAG00000014031  161SMIPAYATTRIRSQI
Mmusculus  all identical  ENSMUSG00000025777  161SMIPAYATTRIRSQIGNTESELK
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000058601  185SHIPAYATTHIRTQIGNTESELK
Dmelanogaster  all conserved  FBgn0035587  161PKAPFIGPVR-QSCLKNNEKVLD
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 1077 / 1077
position (AA) of stopcodon in wt / mu AA sequence 359 / 359
position of stopcodon in wt / mu cDNA 1157 / 1157
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 81 / 81
chromosome 8
strand 1
last intron/exon boundary 775
theoretical NMD boundary in CDS 644
length of CDS 1077
coding sequence (CDS) position 482
cDNA position
(for ins/del: last normal base / first normal base)		 562
gDNA position
(for ins/del: last normal base / first normal base)		 39179
chromosomal position
(for ins/del: last normal base / first normal base)		 75272543
original gDNA sequence snippet TTATGCAACTACAAGGATTCGTAGTATGTAAACATTTTAAA
altered gDNA sequence snippet TTATGCAACTACAAGGATTCATAGTATGTAAACATTTTAAA
original cDNA sequence snippet TTATGCAACTACAAGGATTCGTAGCCAAATTGGAAACACAG
altered cDNA sequence snippet TTATGCAACTACAAGGATTCATAGCCAAATTGGAAACACAG
wildtype AA sequence MAERQEEQRG SPPLRAEGKA DAEVKLILYH WTHSFSSQKV RLVIAEKALK CEEHDVSLPL
SEHNEPWFMR LNSTGEVPVL IHGENIICEA TQIIDYLEQT FLDERTPRLM PDKESMYYPR
VQHYRELLDS LPMDAYTHGC ILHPELTVDS MIPAYATTRI RSQIGNTESE LKKLAEENPD
LQEAYIAKQK RLKSKLLDHD NVKYLKKILD ELEKVLDQVE TELQRRNEET PEEGQQPWLC
GESFTLADVS LAVTLHRLKF LGFARRNWGN GKRPNLETYY ERVLKRKTFN KVLGHVNNIL
ISAVLPTAFR VAKKRAPKVL GTTLVVGLLA GVGYFAFMLF RKRLGSMILA FRPRPNYF*
mutated AA sequence MAERQEEQRG SPPLRAEGKA DAEVKLILYH WTHSFSSQKV RLVIAEKALK CEEHDVSLPL
SEHNEPWFMR LNSTGEVPVL IHGENIICEA TQIIDYLEQT FLDERTPRLM PDKESMYYPR
VQHYRELLDS LPMDAYTHGC ILHPELTVDS MIPAYATTRI HSQIGNTESE LKKLAEENPD
LQEAYIAKQK RLKSKLLDHD NVKYLKKILD ELEKVLDQVE TELQRRNEET PEEGQQPWLC
GESFTLADVS LAVTLHRLKF LGFARRNWGN GKRPNLETYY ERVLKRKTFN KVLGHVNNIL
ISAVLPTAFR VAKKRAPKVL GTTLVVGLLA GVGYFAFMLF RKRLGSMILA FRPRPNYF*
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