Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 3.25394570988505e-26 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr4:129043204C>GN/A show variant in all transcripts   IGV
HGNC symbol LARP1B
Ensembl transcript ID ENST00000354456
Genbank transcript ID N/A
UniProt peptide Q659C4
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.1516C>G
g.60782C>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs12508837
databasehomozygous (G/G)heterozygousallele carriers
1000G93810802018
ExAC26429-200916338
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3891
2.5431
(flanking)0.0360.993
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -121) | splice site change before start ATG (at aa -119) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor marginally increased60773wt: 0.5189 / mu: 0.5599 (marginal change - not scored)wt: TGTGAAAAAACATCC
mu: TGTGAAAAAACATCG		 TGAA|aaaa
Donor increased60781wt: 0.82 / mu: 0.99wt: AACATCCTGGAGGAG
mu: AACATCGTGGAGGAG		 CATC|ctgg
Donor gained607760.49mu: GAAAAAACATCGTGG AAAA|acat
distance from splice site 140
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
6060MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
114167COMPBIASArg-rich.might get lost (downstream of altered splice site)
209299DOMAINHTH La-type RNA-binding.might get lost (downstream of altered splice site)
272272CONFLICTA -> V (in Ref. 1; BAC03970).might get lost (downstream of altered splice site)
289289CONFLICTK -> E (in Ref. 1; BAA91576).might get lost (downstream of altered splice site)
291291CONFLICTE -> T (in Ref. 1; BAC05306).might get lost (downstream of altered splice site)
340340MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
343343MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
363363MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
432432MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
454454MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
473473CONFLICTR -> Q (in Ref. 1; BAC03970).might get lost (downstream of altered splice site)
639639CONFLICTT -> A (in Ref. 2; CAD97908).might get lost (downstream of altered splice site)
671671CONFLICTN -> S (in Ref. 4; AAH62606).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 1875 / 1875
chromosome 4
strand 1
last intron/exon boundary 2679
theoretical NMD boundary in CDS 754
length of CDS 846
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 1516
gDNA position
(for ins/del: last normal base / first normal base)		 60782
chromosomal position
(for ins/del: last normal base / first normal base)		 129043204
original gDNA sequence snippet ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA
altered gDNA sequence snippet ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA
original cDNA sequence snippet ACCTTATGTGAAAAAACATCCTGGAGGAGATCGAACAGGCA
altered cDNA sequence snippet ACCTTATGTGAAAAAACATCGTGGAGGAGATCGAACAGGCA
wildtype AA sequence MVHSLPTAVP ESPRIHPTRT PKTPRTPRLQ DPNKTPRFYP VVKEPKAIDV KSPRKRKTRH
STNPPLECHV GWVMDSRDRG PGTSSVSTSN ASPSEGAPLA GSYGCTPHSF PKFQHPSHEL
LKENGFTQQV YHKYRRRCLS ERKRLGIGQS QEMNTLFRFW SFFLRDHFNK KMYEEFRQLA
WEDAKENYRY GLECLFRFYS YGLEKKFRRE IFQDFQEETK KDYESGQLYG LEKFWAYLKY
SQSKTQSIDP KLQEYLCSFK RLEDFRVDNH HDRLLLLIIN I*
mutated AA sequence N/A
speed 0.96 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