Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.00360171793758352 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:79954544T>AN/A show variant in all transcripts   IGV
HGNC symbol ASPSCR1
Ensembl transcript ID ENST00000580534
Genbank transcript ID N/A
UniProt peptide Q9BZE9
alteration type single base exchange
alteration region CDS
DNA changes c.524T>A
cDNA.712T>A
g.19862T>A
AA changes L175Q Score: 113 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 175
frameshift no
known variant Reference ID: rs8074498
databasehomozygous (A/A)heterozygousallele carriers
1000G41310911504
ExAC15662144317105
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)3.4840.994
2.9231
(flanking)0.2940.999
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 increased19856wt: 0.8748 / mu: 0.9058 (marginal change - not scored)wt: GGGACAGAGACTGGG
mu: GGGACAGAGACAGGG		 GACA|gaga
Donor increased19858wt: 0.53 / mu: 0.97wt: GACAGAGACTGGGGG
mu: GACAGAGACAGGGGG		 CAGA|gact
Donor gained198620.87mu: GAGACAGGGGGGCCC GACA|gggg
distance from splice site 179
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      175PFVPFSGGGQRLGGPPGPTRPLTS
mutated  not conserved    175PFVPFSGGGQRQGGPPG
Ptroglodytes  all identical  ENSPTRG00000009782  248PFVPFSGGGQRLGGPPG
Mmulatta  all identical  ENSMMUG00000010887  174PFVPFSGGGQRLGGPPG
Fcatus  all identical  ENSFCAG00000011662  257PFVPFSGGGQRLGGSSGSARSLM
Mmusculus  all identical  ENSMUSG00000025142  267VPFSGGGQRLGGPSASLRPLT
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000089727  160PSSGQQGAVEEHCDPHTAADRPNR
Dmelanogaster  not conserved  FBgn0064126  221G----SGGG---GGFALTSNMIK
Celegans  not conserved  B0024.10  269VPEQNPNSWSFDGPAFSRQVP
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
257257CONFLICTG -> E (in Ref. 2; BAB71595).might get lost (downstream of altered splice site)
263263MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
264264MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
311312SITEBreakpoint for translocation to form ASPSCR1-TFE3.might get lost (downstream of altered splice site)
317380REGIONInteraction with GLUT4 (By similarity).might get lost (downstream of altered splice site)
386462DOMAINUBX.might get lost (downstream of altered splice site)
444444CONFLICTD -> G (in Ref. 2; BAB71595).might get lost (downstream of altered splice site)
500500MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
502502MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1506 / 1506
position (AA) of stopcodon in wt / mu AA sequence 502 / 502
position of stopcodon in wt / mu cDNA 1694 / 1694
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 189 / 189
chromosome 17
strand 1
last intron/exon boundary 1681
theoretical NMD boundary in CDS 1442
length of CDS 1506
coding sequence (CDS) position 524
cDNA position
(for ins/del: last normal base / first normal base)		 712
gDNA position
(for ins/del: last normal base / first normal base)		 19862
chromosomal position
(for ins/del: last normal base / first normal base)		 79954544
original gDNA sequence snippet CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA
altered gDNA sequence snippet CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA
original cDNA sequence snippet CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA
altered cDNA sequence snippet CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA
wildtype AA sequence MVPASRSREG PENMVRIALQ LDDGSRLQDS FCSGQTLWEL LSHFPQIREC LQHPGGATPV
CVYTRDEVTG EAALRGTTLQ SLGLTGGSAT IRFVMKCYDP VGKTPGSLGS SASAGQAAAS
APLPLESGEL SRGDLSRPED ADTSGPCCEH TQEKQSTRAP AAAPFVPFSG GGQRLGGPPG
PTRPLTSSSA KLPKSLSSPG GPSKPKKSKS GQDPQQEQEQ ERERDPQQEQ ERERPVDREP
VDREPVVCHP DLEERLQAWP AELPDEFFEL TVDDVRRRLA QLKSERKRLE EAPLVTKAFR
EAQIKEKLER YPKVALRVLF PDRYVLQGFF RPSETVGDLR DFVRSHLGNP ELSFYLCLSS
FGRMDGRGPR CFLTRRCLLS SVITPPKTVL DDHTQTLFQA NLFPAALVHL GAEEPAGVYL
EPGLLEHAIS PSAADVLVAR YMSRAAGSPS PLPAPDPAPK SEPAAEEGAL VPPEPIPGTA
QPVKRSLGKV PKWLKLPASK R*
mutated AA sequence MVPASRSREG PENMVRIALQ LDDGSRLQDS FCSGQTLWEL LSHFPQIREC LQHPGGATPV
CVYTRDEVTG EAALRGTTLQ SLGLTGGSAT IRFVMKCYDP VGKTPGSLGS SASAGQAAAS
APLPLESGEL SRGDLSRPED ADTSGPCCEH TQEKQSTRAP AAAPFVPFSG GGQRQGGPPG
PTRPLTSSSA KLPKSLSSPG GPSKPKKSKS GQDPQQEQEQ ERERDPQQEQ ERERPVDREP
VDREPVVCHP DLEERLQAWP AELPDEFFEL TVDDVRRRLA QLKSERKRLE EAPLVTKAFR
EAQIKEKLER YPKVALRVLF PDRYVLQGFF RPSETVGDLR DFVRSHLGNP ELSFYLCLSS
FGRMDGRGPR CFLTRRCLLS SVITPPKTVL DDHTQTLFQA NLFPAALVHL GAEEPAGVYL
EPGLLEHAIS PSAADVLVAR YMSRAAGSPS PLPAPDPAPK SEPAAEEGAL VPPEPIPGTA
QPVKRSLGKV PKWLKLPASK R*
speed 0.98 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