Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.290410848655202 (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) chr20:43547677T>GN/A show variant in all transcripts   IGV
HGNC symbol PABPC1L
Ensembl transcript ID ENST00000537323
Genbank transcript ID N/A
UniProt peptide Q4VXU2
alteration type single base exchange
alteration region CDS
DNA changes c.634T>G
cDNA.654T>G
g.8975T>G
AA changes S212A Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 212
frameshift no
known variant Reference ID: rs2075960
databasehomozygous (G/G)heterozygousallele carriers
1000G1448711015
ExAC37692169325462
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5371
0.4610.997
(flanking)1.6470.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc decreased8983wt: 0.96 / mu: 0.82wt: CAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTCCCCAAGGG
mu: CAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTCCCCAAGGG		 gttt|GGTG
Donor increased8979wt: 0.36 / mu: 0.46wt: CTCCCAGTTTGGTGG
mu: CGCCCAGTTTGGTGG		 CCCA|gttt
Donor gained89740.96mu: CTCTTCGCCCAGTTT CTTC|gccc
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      212DVDEQGLQDLFSQFGKMLSVKVMR
mutated  all conserved    212DVDEQGLQDLFAQFGKMLSVKVM
Ptroglodytes  all identical  ENSPTRG00000013531  212DVDEQGLQELFSQFGKMLSVKVM
Mmulatta  all identical  ENSMMUG00000013209  212DVDEQGLQDLFSQFGKMLSVKVM
Fcatus  not conserved  ENSFCAG00000011692  212XXXXXXXXXXXXXXXKMLSVKVM
Mmusculus  all identical  ENSMUSG00000054582  212NVDEQRLQDLFSQFGNMQSVKVM
Ggallus  all identical  ENSGALG00000004123  212DMDDNRLREIFSRFGKTLSVKVM
Trubripes  all conserved  ENSTRUG00000011085  212DYNDEKLKEVFAAFGRTLSVRVM
Drerio  all conserved  ENSDARG00000002597  212DIDSEKLKNIFTEFGKTLSVCVM
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000022831  212DMDDKRLREIFSAFGNTLSVKVM
protein features
start (aa)end (aa)featuredetails 
191268DOMAINRRM 3.lost
294370DOMAINRRM 4.might get lost (downstream of altered splice site)
409458COMPBIASPro-rich.might get lost (downstream of altered splice site)
528605DOMAINPABC.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 993 / 993
position (AA) of stopcodon in wt / mu AA sequence 331 / 331
position of stopcodon in wt / mu cDNA 1013 / 1013
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 21 / 21
chromosome 20
strand 1
last intron/exon boundary 1723
theoretical NMD boundary in CDS 1652
length of CDS 993
coding sequence (CDS) position 634
cDNA position
(for ins/del: last normal base / first normal base)		 654
gDNA position
(for ins/del: last normal base / first normal base)		 8975
chromosomal position
(for ins/del: last normal base / first normal base)		 43547677
original gDNA sequence snippet AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGTGGGTGTGTC
altered gDNA sequence snippet AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGTGGGTGTGTC
original cDNA sequence snippet AAGGCCTGCAGGACCTCTTCTCCCAGTTTGGGAAAATGCTG
altered cDNA sequence snippet AAGGCCTGCAGGACCTCTTCGCCCAGTTTGGGAAAATGCTG
wildtype AA sequence MNASGSGYPL ASLYVGDLHP DVTEAMLYEK FSPAGPILSI RVCRDVATRR SLGYAYINFQ
QPADAERALD TMNFEMLKGQ PIRIMWSQRD PGLRKSGVGN IFIKNLEDSI DNKALYDTFS
TFGNILSCKV ACDEHGSRGF GFVHFETHEA AQQAINTMNG MLLNDRKVFV GHFKSRRERE
AELGARALEF TNIYVKNLPV DVDEQGLQDL FSQFGKMLSV KVMRDNSGHS RCFGFVNFEK
HEEAQKAVVH MNGKEVSGRL LYAGRAQKRV ERQNELKRRF EQMKQDRLRR YQGVNLYVKN
LDDSIDDDKL RKEFSPYGVI TSAKKRRQRP *
mutated AA sequence MNASGSGYPL ASLYVGDLHP DVTEAMLYEK FSPAGPILSI RVCRDVATRR SLGYAYINFQ
QPADAERALD TMNFEMLKGQ PIRIMWSQRD PGLRKSGVGN IFIKNLEDSI DNKALYDTFS
TFGNILSCKV ACDEHGSRGF GFVHFETHEA AQQAINTMNG MLLNDRKVFV GHFKSRRERE
AELGARALEF TNIYVKNLPV DVDEQGLQDL FAQFGKMLSV KVMRDNSGHS RCFGFVNFEK
HEEAQKAVVH MNGKEVSGRL LYAGRAQKRV ERQNELKRRF EQMKQDRLRR YQGVNLYVKN
LDDSIDDDKL RKEFSPYGVI TSAKKRRQRP *
speed 1.11 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