Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999961446684326 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM081555)
  • known disease mutation: rs18365 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:233392148T>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.236T>A
cDNA.264T>A
g.1446T>A
AA changes I79K Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 79
frameshift no
known variant Reference ID: rs121909509
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs18365 (pathogenic for Congenital myasthenic syndrome 3B) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081555)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081555)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081555)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7161
4.0990.996
(flanking)-1.970.32
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 increased1436wt: 0.4414 / mu: 0.4757 (marginal change - not scored)wt: TTGAGGAGACCCTCACTACCAATGTGTGGATAGAGCACGTA
mu: TTGAGGAGACCCTCACTACCAATGTGTGGAAAGAGCACGTA		 acca|ATGT
Acc marginally increased1440wt: 0.8116 / mu: 0.8249 (marginal change - not scored)wt: GGAGACCCTCACTACCAATGTGTGGATAGAGCACGTAAGAA
mu: GGAGACCCTCACTACCAATGTGTGGAAAGAGCACGTAAGAA		 atgt|GTGG
Donor increased1442wt: 0.28 / mu: 0.99wt: ATGTGTGGATAGAGC
mu: ATGTGTGGAAAGAGC		 GTGT|ggat
Donor increased1448wt: 0.40 / mu: 0.65wt: GGATAGAGCACGTAA
mu: GGAAAGAGCACGTAA		 ATAG|agca
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      79EVEETLTTNVWIEHGWTDNRLKWN
mutated  not conserved    79EVEETLTTNVWKEHGWTDNRLKW
Ptroglodytes  all identical  ENSPTRG00000013040  79EVEETLTTNVWIEHGWTDNRLKW
Mmulatta  all identical  ENSMMUG00000022147  79EVEETLTTNVWIEHGWTDNRLKW
Fcatus  all conserved  ENSFCAG00000005679  78EVEETLTTNVWMEHGWTDPRLQW
Mmusculus  all identical  ENSMUSG00000026251  82EVEETLTTNVWIDHAWVDSRLQW
Ggallus  all conserved  ENSGALG00000007899  76EVDETLTTNVWVEQSWTDYRLQW
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000019342  79EVDETLLTNVWMEHGWKDHRLTW
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000027884  79DETLTTNVWVELGWYDKRLAW
protein features
start (aa)end (aa)featuredetails 
22245TOPO_DOMExtracellular (Potential).lost
9797CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
151151DISULFIDBy similarity.might get lost (downstream of altered splice site)
164164CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
165165DISULFIDBy similarity.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 yes
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 236
cDNA position
(for ins/del: last normal base / first normal base)		 264
gDNA position
(for ins/del: last normal base / first normal base)		 1446
chromosomal position
(for ins/del: last normal base / first normal base)		 233392148
original gDNA sequence snippet CCTCACTACCAATGTGTGGATAGAGCACGTAAGAATGCCCC
altered gDNA sequence snippet CCTCACTACCAATGTGTGGAAAGAGCACGTAAGAATGCCCC
original cDNA sequence snippet CCTCACTACCAATGTGTGGATAGAGCACGGCTGGACAGACA
altered cDNA sequence snippet CCTCACTACCAATGTGTGGAAAGAGCACGGCTGGACAGACA
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 ETLTTNVWKE HGWTDNRLKW NAEEFGNISV LRLPPDMVWL PEIVLENNND
GSFQISYSCN VLVYHYGFVY WLPPAIFRSS CPISVTYFPF DWQNCSLKFR ERGVGDSPPA
GQGQRGPQSP SGQPQPPGHH LLPHHPPQAP LLHHQHPGAL RAHLLHGQPG LLPTG*
speed 0.25 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