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 CM081556)
  • known disease mutation: rs18371 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:233391374T>CN/A show variant in all transcripts   IGV
HGNC symbol CHRND
Ensembl transcript ID ENST00000457943
Genbank transcript ID N/A
UniProt peptide Q07001
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.216T>C
g.672T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121909508
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs18371 (pathogenic for Congenital myasthenic syndrome 3B) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081556)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081556)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081556)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)4.1011
4.7431
(flanking)1.0091
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -28) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally decreased681wt: 0.9492 / mu: 0.9213 (marginal change - not scored)wt: ACTCTCCAACCTCATCTCCCTGGTGAGAGGCCCTCCGGTGC
mu: ACTCTCCAACCCCATCTCCCTGGTGAGAGGCCCTCCGGTGC		 ccct|GGTG
Acc increased669wt: 0.33 / mu: 0.41wt: CCTGGCCCTCACACTCTCCAACCTCATCTCCCTGGTGAGAG
mu: CCTGGCCCTCACACTCTCCAACCCCATCTCCCTGGTGAGAG		 ccaa|CCTC
Acc marginally increased679wt: 0.3647 / mu: 0.3686 (marginal change - not scored)wt: ACACTCTCCAACCTCATCTCCCTGGTGAGAGGCCCTCCGGT
mu: ACACTCTCCAACCCCATCTCCCTGGTGAGAGGCCCTCCGGT		 ctcc|CTGG
Acc marginally increased672wt: 0.2346 / mu: 0.2380 (marginal change - not scored)wt: GGCCCTCACACTCTCCAACCTCATCTCCCTGGTGAGAGGCC
mu: GGCCCTCACACTCTCCAACCCCATCTCCCTGGTGAGAGGCC		 acct|CATC
distance from splice site 11
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
121SIGNALBy similarity.might get lost (downstream of altered splice site)
22245TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 300 / 300
chromosome 2
strand 1
last intron/exon boundary 1089
theoretical NMD boundary in CDS 739
length of CDS 972
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 216
gDNA position
(for ins/del: last normal base / first normal base)		 672
chromosomal position
(for ins/del: last normal base / first normal base)		 233391374
original gDNA sequence snippet GGCCCTCACACTCTCCAACCTCATCTCCCTGGTGAGAGGCC
altered gDNA sequence snippet GGCCCTCACACTCTCCAACCCCATCTCCCTGGTGAGAGGCC
original cDNA sequence snippet GGCCCTCACACTCTCCAACCTCATCTCCCTGAAAGAAGTTG
altered cDNA sequence snippet GGCCCTCACACTCTCCAACCCCATCTCCCTGAAAGAAGTTG
wildtype AA sequence MLKNLETSVS CASPRTWCGS QRLCWRTTMT APSRSPTPAT CLSTTTASCT GCHLPSSAPP
APSLSPISPS TGRTAPSSSG GEKTSVAISV LLAQSVFLLL ISKRLPATSM AIPLIGKFLL
FGMVLVTMVV VICVIVLNIH FRTPSTHVLS EGVKKLFLET LPELLHMSRP AEDGPSPGAL
VRRSSSLGYI SKAEEYFLLK SRSDLMFEKQ SERHGLARRL TTARRPPASS EQAQQELFNE
LKPAVDGANF IVNHMRDQNN YNEEKDSWNR VARTVDRLCL FVVTPVMVVG TAWIFLQGVY
NQPPPQPFPG DPYSYNVQDK RFI*
mutated AA sequence N/A
speed 0.63 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