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 CM950102)
  • known disease mutation: rs2606 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3386814T>CN/A show variant in all transcripts   IGV
HGNC symbol SPATA22
Ensembl transcript ID ENST00000541913
Genbank transcript ID N/A
UniProt peptide Q8NHS9
alteration type single base exchange
alteration region intron
DNA changes g.30333A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894548
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2606 (pathogenic for Spongy degeneration of central nervous system) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950102)
regulatory features H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9931
2.5781
(flanking)3.3731
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -23) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor marginally increased30330wt: 0.9717 / mu: 0.9752 (marginal change - not scored)wt: AACGTAGCAGGGTAG
mu: AACGTAGCGGGGTAG		 CGTA|gcag
Donor marginally increased30325wt: 0.8548 / mu: 0.8559 (marginal change - not scored)wt: AGATAAACGTAGCAG
mu: AGATAAACGTAGCGG		 ATAA|acgt
Donor gained303270.98mu: ATAAACGTAGCGGGG AAAC|gtag
distance from splice site 14122
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
66CONFLICTN -> S (in Ref. 1; AAK51120/AAK53408/ AAK61373/AAK61374).might get lost (downstream of altered splice site)
8484CONFLICTV -> A (in Ref. 1; AAK53408/AAK61373/ AAK61374).might get lost (downstream of altered splice site)
279279MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
280280MOD_RESPhosphotyrosine.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 515 / 515
chromosome 17
strand -1
last intron/exon boundary 1367
theoretical NMD boundary in CDS 802
length of CDS 1044
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 30333
chromosomal position
(for ins/del: last normal base / first normal base)		 3386814
original gDNA sequence snippet CTCAATCAGATAAACGTAGCAGGGTAGTGGAGCCAGAGAAG
altered gDNA sequence snippet CTCAATCAGATAAACGTAGCGGGGTAGTGGAGCCAGAGAAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MKRSLNENSA RSTAGCLPVP LFNQKKRNRQ PLTSNPLKDD SDWAWEAVNP ELAPVMKTVD
TGQIPHSVSR PLRSQDSVFN SIQSNTGRSQ GGWSYRDGNK NTSLKTWNKN DFKPQCKRTN
LVANDGKNSC PVSSGAQQQK QLRIPEPPNL SRNKETELLR QTHSSKISGC TMRGLDKNSA
LQTLKPNFQQ NQYKKQMLDD IPEDNTLKET SLYQLQFKEK ASSLRIISAV IESMKYWREH
AQKTVLLFEV LAVLDSAVTP GPYYSKTFLM RDGKNTLPCV FYEIDRELPR LIRGRVHRCV
GNYDQKKNIF QCVSVRPASV SEQKTFQAFV KIADVEMQYY INVMNET*
mutated AA sequence N/A
speed 0.77 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