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 CM940124)
  • known disease mutation: rs2607 (pathogenic)
  • protein features (might be) affected
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:3402354C>AN/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.14793G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28940574
databasehomozygous (A/A)heterozygousallele carriers
1000G022
ExAC02727

known disease mutation: rs2607 (pathogenic for Spongy degeneration of central nervous system|Canavan Disease, Familial Form|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940124)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3390.998
5.3390.998
(flanking)0.3490.486
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 marginally increased14794wt: 0.6617 / mu: 0.6802 (marginal change - not scored)wt: ACAGCAGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTTG
mu: ACAGCAGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTTG		 ttgc|ATTG
Acc increased14798wt: 0.47 / mu: 0.93wt: CAGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTTGTCTT
mu: CAGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTTGTCTT		 attg|AGCG
Acc increased14801wt: 0.51 / mu: 0.87wt: CGAATACTTTTTGCATTGAGCGTTAGTTTAGTTGTCTTTGC
mu: CGAATACTTTTTTCATTGAGCGTTAGTTTAGTTGTCTTTGC		 gagc|GTTA
Acc increased14799wt: 0.56 / mu: 0.95wt: AGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTTGTCTTT
mu: AGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTTGTCTTT		 ttga|GCGT
distance from splice site 14352
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)		 14793
chromosomal position
(for ins/del: last normal base / first normal base)		 3402354
original gDNA sequence snippet AACAGCAGCGAATACTTTTTGCATTGAGCGTTAGTTTAGTT
altered gDNA sequence snippet AACAGCAGCGAATACTTTTTTCATTGAGCGTTAGTTTAGTT
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 0.07 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