Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999996685789 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032928)
  • known disease mutation: rs4200 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr8:75276240C>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.511C>T
cDNA.629C>T
g.42876C>T
AA changes L171F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 171
frameshift no
known variant Reference ID: rs104894080
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs4200 (pathogenic for GDAP1-Related Disorders|Sensory neuropathy|Polyneuropathy|Elevated serum creatine phosphokinase|Elevated alkaline phosphatase|Peripheral axonal neuropathy|Charcot-Marie-Tooth disease, type 4A|Charcot-Marie-Tooth disease type 2K|Charcot-Marie-Tooth disease, recessive intermediate A|Charcot-Marie-Tooth disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032928)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032928)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032928)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5391
5.5391
(flanking)4.5891
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      171EETPEEGQQPWLCGESFTLADVSL
mutated  not conserved    171EETPEEGQQPWFCGESFTLAD
Ptroglodytes  all identical  ENSPTRG00000020354  239EETPEEGQQPWLCGESFTLAD
Mmulatta  all identical  ENSMMUG00000022326  239EETPEEGQQPWLCGESFTLAD
Fcatus  all identical  ENSFCAG00000014031  239EETPEEGRQPWLCGESFTLADVS
Mmusculus  all identical  ENSMUSG00000025777  239EETPEEGNQPWLCGESFTLAD
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000058601  263EETPEEGSQQAWLCGDFFSIA
Dmelanogaster  all identical  FBgn0035587  238QELTAQAPRVEWLTGDELSVA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
153309DOMAINGST C-terminal.lost
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 511
cDNA position
(for ins/del: last normal base / first normal base)		 629
gDNA position
(for ins/del: last normal base / first normal base)		 42876
chromosomal position
(for ins/del: last normal base / first normal base)		 75276240
original gDNA sequence snippet AAGAGGGCCAGCAACCTTGGCTCTGCGGTGAATCCTTCACC
altered gDNA sequence snippet AAGAGGGCCAGCAACCTTGGTTCTGCGGTGAATCCTTCACC
original cDNA sequence snippet AAGAGGGCCAGCAACCTTGGCTCTGCGGTGAATCCTTCACC
altered cDNA sequence snippet AAGAGGGCCAGCAACCTTGGTTCTGCGGTGAATCCTTCACC
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 ETPEEGQQPW FCGESFTLAD
VSLAVTLHRL KFLGFARRNW GNGKRPNLET YYERVLKRKT FNKVLGHVNN ILISAVLPTA
FRVAKKRAPK VLGTTLVVGL LAGVGYFAFM LFRKRLGSMI LAFRPRPNYF *
speed 1.30 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