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 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 ENST00000457943
Genbank transcript ID N/A
UniProt peptide Q07001
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.264T>A
g.1446T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
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 splice site change before start ATG (at aa -13) | splice site change before start ATG (at aa -11) |
effectgDNA positionscoredetection 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? 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)		 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 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 0.47 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