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 CM023015)
  • known disease mutation: rs2615 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402186A>TN/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.14961T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894552
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC01515

known disease mutation: rs2615 (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 CM023015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023015)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.6511
4.6821
(flanking)2.171
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
Acc increased14960wt: 0.37 / mu: 0.57wt: TGCAGTGGTTTCCAGTCTTGATCCTCTCAGGAAACAATCAA
mu: TGCAGTGGTTTCCAGTCTTGAACCTCTCAGGAAACAATCAA		 ttga|TCCT
Donor increased14953wt: 0.62 / mu: 0.86wt: TTTCCAGTCTTGATC
mu: TTTCCAGTCTTGAAC		 TCCA|gtct
distance from splice site 14520
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)		 14961
chromosomal position
(for ins/del: last normal base / first normal base)		 3402186
original gDNA sequence snippet GCAGTGGTTTCCAGTCTTGATCCTCTCAGGAAACAATCAAA
altered gDNA sequence snippet GCAGTGGTTTCCAGTCTTGAACCTCTCAGGAAACAATCAAA
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 1.07 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