Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: complex_aae, prob: 1 (classification due to NMD, real probability is shown anyway)      (explain)
Summary
  • NMD
  • amino acid sequence changed
  • frameshift
  • known disease mutation at this position (HGMD CM107568)
  • protein features (might be) affected
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:32341236_32341237insA show variant in all transcripts   IGV
HGNC symbol SPAST
Ensembl transcript ID ENST00000315285
Genbank transcript ID NM_014946
UniProt peptide Q9UBP0
alteration type insertion
alteration region CDS
DNA changes c.1053_1054insA
cDNA.1178_1179insA
g.52557_52558insA
AA changes Q352Tfs*15
position(s) of altered AA
if AA alteration in CDS		 352 (frameshift or PTC - further changes downstream)
frameshift yes
known variant Variant was neither found in ExAC nor 1000G.
Search ExAC.

known disease mutation at this position, please check HGMD for details (HGMD ID CM107568)

known disease mutation at this position, please check HGMD for details (HGMD ID CM107568)
known disease mutation at this position, please check HGMD for details (HGMD ID CM107568)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2191
(flanking)4.6821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased52555wt: 0.9914 / mu: 0.9943 (marginal change - not scored)wt: TGGCAAAACAAGCAT
mu: GGCAAAAACAAGCAT		 GCAA|aaca
Donor increased52550wt: 0.63 / mu: 0.91wt: AGACTTGGCAAAACA
mu: AGACTTGGCAAAAAC		 ACTT|ggca
distance from splice site 46
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      352FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDEVDSLLCERREGEHDASRRLKTE
mutated  partly conserved    352FDDIAGQDLAKTSI
Ptroglodytes  all identical  ENSPTRG00000011812  352FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGE
Mmulatta  all identical  ENSMMUG00000021691  321FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGE
Fcatus  all conserved  ENSFCAG00000006681  345FDDIAGQELAKQALQEIVILPSLRPE
Mmusculus  all identical  ENSMUSG00000024068  350FDDIAGQELAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGE
Ggallus  all identical  ENSGALG00000010620  336FDDIAGQELAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSK
Trubripes  no homologue    
Drerio  partly conserved  ENSDARG00000024933  305FDDIAGQDLAKQALQEIVILPALRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAMESNATFFNISAATLTSKYVGEGEKLVRALFAVARELQPSIIFIDEIDSLLCE
Dmelanogaster  partly conserved  FBgn0039141  492WTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSKYVGDGEKLVRALFAVARHMQP
Celegans  partly conserved  C24B5.2  250MDDVAGCHSAKAALEEAVILPALNPNLFKGLRQPVKGILLFGPPGNGKTLLAKAVAGESKQMFFNISASSLTSKWVGDSEKTIRGLFQIARNAQPSIIFIDEIDSILCERSEK
Xtropicalis  all conserved  ENSXETG00000011392  340FADIAGQDLAKQALQEIVILPSIRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYV
protein features
start (aa)end (aa)featuredetails 
228616REGIONSufficient for microtubule severing.lost
348357HELIXlost
359363HELIXlost
365367TURNlost
370372HELIXlost
376383STRANDlost
382389NP_BINDATP (Probable).lost
388388MUTAGENK->A: Abrogates ATPase activity and abolishes microtubule severing.lost
388398HELIXlost
402406STRANDlost
415415MUTAGENY->A: Abrogates binding to the tail of alpha-tubulin and beta-3-tubulin, impairs ATPase activity and abolishes microtubule severing.lost
420432HELIXlost
433441STRANDlost
442442MUTAGENE->Q: Abrogates ATP hydrolysis, abolishes microtubule severing, stabilizes the homohexameric form, and promotes microtubule binding and redistribution from the endosome to microtubules.lost
443446HELIXlost
451451MUTAGENR->G: Abrogates binding to the tail of alpha-tubulin and beta-3-tubulin, impairs ATPase activity and abolishes microtubule severing.lost
457457MUTAGENA->E: Abrogates binding to the tail of alpha-tubulin and beta-3-tubulin and abolishes microtubule severing.lost
458472HELIXlost
480487STRANDlost
489491HELIXlost
494497HELIXlost
502505STRANDlost
511522HELIXlost
531540HELIXlost
541543TURNlost
546556HELIXlost
559562HELIXlost
573575STRANDlost
582591HELIXlost
598610HELIXlost
length of protein NMD
AA sequence altered yes
position of stopcodon in wt / mu CDS 1851 / 1098
position (AA) of stopcodon in wt / mu AA sequence 617 / 366
position of stopcodon in wt / mu cDNA 1976 / 1223
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 126 / 126
chromosome 2
strand 1
last intron/exon boundary 1854
theoretical NMD boundary in CDS 1678
length of CDS 1851
coding sequence (CDS) position 1053 / 1054
cDNA position
(for ins/del: last normal base / first normal base)		 1178 / 1179
gDNA position
(for ins/del: last normal base / first normal base)		 52557 / 52558
chromosomal position
(for ins/del: last normal base / first normal base)		 32341236 / 32341237
original gDNA sequence snippet CTGGTCAAGACTTGGCAAAACAAGCATTGCAAGAAATTGT
altered gDNA sequence snippet CTGGTCAAGACTTGGCAAAAACAAGCATTGCAAGAAATTGT
original cDNA sequence snippet CTGGTCAAGACTTGGCAAAACAAGCATTGCAAGAAATTGT
altered cDNA sequence snippet CTGGTCAAGACTTGGCAAAAACAAGCATTGCAAGAAATTGT
wildtype AA sequence MNSPGGRGKK KGSGGASNPV PPRPPPPCLA PAPPAAGPAP PPESPHKRNL YYFSYPLFVG
FALLRLVAFH LGLLFVWLCQ RFSRALMAAK RSSGAAPAPA SASAPAPVPG GEAERVRVFH
KQAFEYISIA LRIDEDEKAG QKEQAVEWYK KGIEELEKGI AVIVTGQGEQ CERARRLQAK
MMTNLVMAKD RLQLLEKMQP VLPFSKSQTD VYNDSTNLAC RNGHLQSESG AVPKRKDPLT
HTSNSLPRSK TVMKTGSAGL SGHHRAPSYS GLSMVSGVKQ GSGPAPTTHK GTPKTNRTNK
PSTPTTATRK KKDLKNFRNV DSNLANLIMN EIVDNGTAVK FDDIAGQDLA KQALQEIVIL
PSLRPELFTG LRAPARGLLL FGPPGNGKTM LAKAVAAESN ATFFNISAAS LTSKYVGEGE
KLVRALFAVA RELQPSIIFI DEVDSLLCER REGEHDASRR LKTEFLIEFD GVQSAGDDRV
LVMGATNRPQ ELDEAVLRRF IKRVYVSLPN EETRLLLLKN LLCKQGSPLT QKELAQLARM
TDGYSGSDLT ALAKDAALGP IRELKPEQVK NMSASEMRNI RLSDFTESLK KIKRSVSPQT
LEAYIRWNKD FGDTTV*
mutated AA sequence MNSPGGRGKK KGSGGASNPV PPRPPPPCLA PAPPAAGPAP PPESPHKRNL YYFSYPLFVG
FALLRLVAFH LGLLFVWLCQ RFSRALMAAK RSSGAAPAPA SASAPAPVPG GEAERVRVFH
KQAFEYISIA LRIDEDEKAG QKEQAVEWYK KGIEELEKGI AVIVTGQGEQ CERARRLQAK
MMTNLVMAKD RLQLLEKMQP VLPFSKSQTD VYNDSTNLAC RNGHLQSESG AVPKRKDPLT
HTSNSLPRSK TVMKTGSAGL SGHHRAPSYS GLSMVSGVKQ GSGPAPTTHK GTPKTNRTNK
PSTPTTATRK KKDLKNFRNV DSNLANLIMN EIVDNGTAVK FDDIAGQDLA KTSIARNCYS
SFSEA*
speed 1.71 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