Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM030015)
  • known disease mutation: rs18364 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:233394841C>AN/A show variant in all transcripts   IGV
HGNC symbol CHRND
Ensembl transcript ID ENST00000536614
Genbank transcript ID N/A
UniProt peptide Q07001
alteration type single base exchange
alteration region CDS
DNA changes c.702C>A
cDNA.730C>A
g.4139C>A
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift no
known variant Reference ID: rs121909503
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18364 (pathogenic for Congenital myasthenic syndrome 3B) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.021
4.360.999
(flanking)-2.4090.009
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased4139wt: 0.3633 / mu: 0.3942 (marginal change - not scored)wt: CAACCTGGTCTTCTACCTACCGGCTGACAGTGAGCCTCCAG
mu: CAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCAG		 tacc|GGCT
Acc gained41380.33mu: TCAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCA ctac|AGGC
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
22245TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
246270TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
278299TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
312333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334471TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
390390MOD_RESPhosphotyrosine; by Tyr-kinases (By similarity).might get lost (downstream of altered splice site)
472490TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered no
position of stopcodon in wt / mu CDS 708 / 708
position (AA) of stopcodon in wt / mu AA sequence 236 / 236
position of stopcodon in wt / mu cDNA 736 / 736
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 29 / 29
chromosome 2
strand 1
last intron/exon boundary 851
theoretical NMD boundary in CDS 772
length of CDS 708
coding sequence (CDS) position 702
cDNA position
(for ins/del: last normal base / first normal base)		 730
gDNA position
(for ins/del: last normal base / first normal base)		 4139
chromosomal position
(for ins/del: last normal base / first normal base)		 233394841
original gDNA sequence snippet CAACCTGGTCTTCTACCTACCGGCTGACAGTGAGCCTCCAG
altered gDNA sequence snippet CAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCAG
original cDNA sequence snippet CAACCTGGTCTTCTACCTACCGGCTGACAGTGGTGAGAAGA
altered cDNA sequence snippet CAACCTGGTCTTCTACCTACAGGCTGACAGTGGTGAGAAGA
wildtype AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLKEVE ETLTTNVWIE HGWTDNRLKW NAEEFGNISV LRLPPDMVWL PEIVLENNND
GSFQISYSCN VLVYHYGFVY WLPPAIFRSS CPISVTYFPF DWQNCSLKFR ERGVGDSPPA
GQGQRGPQSP SGQPQPPGHH LLPHHPPQAP LLHHQHPGAL RAHLLHGQPG LLPTG*
mutated AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLKEVE ETLTTNVWIE HGWTDNRLKW NAEEFGNISV LRLPPDMVWL PEIVLENNND
GSFQISYSCN VLVYHYGFVY WLPPAIFRSS CPISVTYFPF DWQNCSLKFR ERGVGDSPPA
GQGQRGPQSP SGQPQPPGHH LLPHHPPQAP LLHHQHPGAL RAHLLHGQPG LLPTG*
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