Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999986834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061636)
  • known disease mutation: rs4415 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:202626247C>TN/A show variant in all transcripts   IGV
HGNC symbol ALS2
Ensembl transcript ID ENST00000467448
Genbank transcript ID NM_001135745
UniProt peptide Q96Q42
alteration type single base exchange
alteration region CDS
DNA changes c.470G>A
cDNA.610G>A
g.19666G>A
AA changes C157Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 157
frameshift no
known variant Reference ID: rs121908138
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs4415 (pathogenic for Infantile-onset ascending hereditary spastic paralysis|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM061636)

known disease mutation at this position, please check HGMD for details (HGMD ID CM061636)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061636)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7961
61
(flanking)4.9691
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 increased19670wt: 0.9582 / mu: 0.9810 (marginal change - not scored)wt: TGTGGCGAGGAGCAC
mu: TATGGCGAGGAGCAC		 TGGC|gagg
Donor increased19667wt: 0.49 / mu: 0.74wt: GCGTGTGGCGAGGAG
mu: GCGTATGGCGAGGAG		 GTGT|ggcg
Donor increased19668wt: 0.41 / mu: 0.85wt: CGTGTGGCGAGGAGC
mu: CGTATGGCGAGGAGC		 TGTG|gcga
distance from splice site 295
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157PLLAVRILQLACGEEHTLALSISR
mutated  not conserved    157PLLAVRILQLAYGEEHTLALSIS
Ptroglodytes  all identical  ENSPTRG00000012811  157PLLAVRILQLACGEEHTLALSIS
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000004007  157SLLAVRILQLACGEEHTLALSIS
Mmusculus  all identical  ENSMUSG00000026024  157PSLAVRILQLACGEEHTLALSLS
Ggallus  all identical  ENSGALG00000008415  157PLLSVRVLQLACGEEHTLALSLS
Trubripes  all identical  ENSTRUG00000009974  150LPQTVQVLELACGEQHTLALSAQ
Drerio  all identical  ENSDARG00000076924  152PPQTVKILEVACGDQHTLALSAK
Dmelanogaster  all identical  FBgn0037116  353ALEATCGDYHTLLLNAS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000012406  155PPRWVRTIQLSCGEEHTLALSVS
protein features
start (aa)end (aa)featuredetails 
109167REPEATRCC1 2.lost
169218REPEATRCC1 3.might get lost (downstream of altered splice site)
483483MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
492492MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
525576REPEATRCC1 4.might get lost (downstream of altered splice site)
533533MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
578627REPEATRCC1 5.might get lost (downstream of altered splice site)
690885DOMAINDH.might get lost (downstream of altered splice site)
9011007DOMAINPH.might get lost (downstream of altered splice site)
10491071REPEATMORN 1.might get lost (downstream of altered splice site)
10721094REPEATMORN 2.might get lost (downstream of altered splice site)
11001122REPEATMORN 3.might get lost (downstream of altered splice site)
11231145REPEATMORN 4.might get lost (downstream of altered splice site)
11511173REPEATMORN 5.might get lost (downstream of altered splice site)
11751197REPEATMORN 6.might get lost (downstream of altered splice site)
11981220REPEATMORN 7.might get lost (downstream of altered splice site)
12211244REPEATMORN 8.might get lost (downstream of altered splice site)
13441344MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
14641464MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15131657DOMAINVPS9.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1191 / 1191
position (AA) of stopcodon in wt / mu AA sequence 397 / 397
position of stopcodon in wt / mu cDNA 1331 / 1331
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 141 / 141
chromosome 2
strand -1
last intron/exon boundary 316
theoretical NMD boundary in CDS 125
length of CDS 1191
coding sequence (CDS) position 470
cDNA position
(for ins/del: last normal base / first normal base)		 610
gDNA position
(for ins/del: last normal base / first normal base)		 19666
chromosomal position
(for ins/del: last normal base / first normal base)		 202626247
original gDNA sequence snippet CAGGATTTTACAGTTGGCGTGTGGCGAGGAGCACACTCTGG
altered gDNA sequence snippet CAGGATTTTACAGTTGGCGTATGGCGAGGAGCACACTCTGG
original cDNA sequence snippet CAGGATTTTACAGTTGGCGTGTGGCGAGGAGCACACTCTGG
altered cDNA sequence snippet CAGGATTTTACAGTTGGCGTATGGCGAGGAGCACACTCTGG
wildtype AA sequence MDSKKRSSTE AEGSKERGLV HIWQAGSFPI TPERLPGWGG KTVLQAALGV KHGVLLTEDG
EVYSFGTLPW RSGPVEICPS SPILENALVG QYVITVATGS FHSGAVTDNG VAYMWGENSA
GQCAVANQQY VPEPNPVSIA DSEASPLLAV RILQLACGEE HTLALSISRE IWAWGTGCQL
GLITTAFPVT KPQKVEHLAG RVVLQVACGA FHSLALVQCL PSQDLKPVPE RCNQCSQLLI
TMTDKEDHVI ISDSHCCPLG VTLTESQAEN HASTALSPST ETLDRQEEVF ENTLVANDQS
VATELNAVSA QITSSDAMSS QQNVMGTTEI SSARNIPSYP DTQAVNEYLR KLSDHSVRED
SEHGEKPVPS QVPAQFYKIK VCLELNCMGF SLETLK*
mutated AA sequence MDSKKRSSTE AEGSKERGLV HIWQAGSFPI TPERLPGWGG KTVLQAALGV KHGVLLTEDG
EVYSFGTLPW RSGPVEICPS SPILENALVG QYVITVATGS FHSGAVTDNG VAYMWGENSA
GQCAVANQQY VPEPNPVSIA DSEASPLLAV RILQLAYGEE HTLALSISRE IWAWGTGCQL
GLITTAFPVT KPQKVEHLAG RVVLQVACGA FHSLALVQCL PSQDLKPVPE RCNQCSQLLI
TMTDKEDHVI ISDSHCCPLG VTLTESQAEN HASTALSPST ETLDRQEEVF ENTLVANDQS
VATELNAVSA QITSSDAMSS QQNVMGTTEI SSARNIPSYP DTQAVNEYLR KLSDHSVRED
SEHGEKPVPS QVPAQFYKIK VCLELNCMGF SLETLK*
speed 1.12 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