Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1      (explain)
Summary
  • known as potential disease variant: rs18346 (probable pathogenic)
  • known disease mutation at this position (HGMD CM960299)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:4805305G>AN/A show variant in all transcripts   IGV
HGNC symbol C17orf107
Ensembl transcript ID ENST00000381365
Genbank transcript ID NM_001145536
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.2277G>A
g.2593G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121909512
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC033

known as potential disease variant: rs18346 (probable pathogenic for Myasthenic syndrome, congenital, 4a, slow-channel|Myasthenic syndrome, congenital, 4b, fast-channel) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960299)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960299)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960299)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.5550.595
5.2191
(flanking)5.2191
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 683) splice site change occurs after stopcodon (at aa 684)
effectgDNA positionscoredetection sequence  exon-intron border
Donor marginally increased2590wt: 0.5287 / mu: 0.5382 (marginal change - not scored)wt: AGATGGCCGGAGGCA
mu: AGATGGCCAGAGGCA		 ATGG|ccgg
Donor increased2595wt: 0.29 / mu: 0.57wt: GCCGGAGGCAGCCAC
mu: GCCAGAGGCAGCCAC		 CGGA|ggca
Donor gained25930.45mu: TGGCCAGAGGCAGCC GCCA|gagg
distance from splice site 923
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 signal is predicted to be ok
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 228 / 228
chromosome 17
strand 1
last intron/exon boundary 504
theoretical NMD boundary in CDS 226
length of CDS 573
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 2277
gDNA position
(for ins/del: last normal base / first normal base)		 2593
chromosomal position
(for ins/del: last normal base / first normal base)		 4805305
original gDNA sequence snippet AGACGCTGCGGTAGATGGCCGGAGGCAGCCACGTCACGGAG
altered gDNA sequence snippet AGACGCTGCGGTAGATGGCCAGAGGCAGCCACGTCACGGAG
original cDNA sequence snippet AGACGCTGCGGTAGATGGCCGGAGGCAGCCACGTCACGGAG
altered cDNA sequence snippet AGACGCTGCGGTAGATGGCCAGAGGCAGCCACGTCACGGAG
wildtype AA sequence MKGTPSSLDT LMWIYHFHSS TEVALQPPLL SSLELSVAAA HEYLEQRFRE LKSLEPPEPK
MQGMLPAPKP TLGLVLREAT ASLVSFGTTL LEISALWLQQ EARRLDGSAG PAPDGRDPGA
ALSRVAQAAG QGVRQAGAAV GASARLLVQG AWLCLCGRGL QGSASFLRQS QQQLGLGIPG
EPVSSGHGVS *
mutated AA sequence N/A
speed 0.84 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