Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.00694424079836709 (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) chr4:129043204C>GN/A show variant in all transcripts   IGV
HGNC symbol LARP1B
Ensembl transcript ID ENST00000264584
Genbank transcript ID N/A
UniProt peptide Q659C4
alteration type single base exchange
alteration region CDS
DNA changes c.1244C>G
cDNA.1375C>G
g.60782C>G
AA changes P415R Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 415
frameshift no
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
effectgDNA positionscorewt detection 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? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      415VTQTPPYVKKHPGGDRTGTHMSRA
mutated  not conserved    415VTQTPPYVKKHRGGDRT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000021347  462VTQTPPYVKKHPGGDRTGNHMSR
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000037814  n/a
Ggallus  all identical  ENSGALG00000010207  426VTQTPPYMRKHPGE
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0261618  1150VAQVGR-APKHEGYDRTADFTSR
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000022512  556VTQTPPHLKKHPGGDRTGNHISR
protein features
start (aa)end (aa)featuredetails 
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2568 / 2568
position (AA) of stopcodon in wt / mu AA sequence 856 / 856
position of stopcodon in wt / mu cDNA 2699 / 2699
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 132 / 132
chromosome 4
strand 1
last intron/exon boundary 2502
theoretical NMD boundary in CDS 2320
length of CDS 2568
coding sequence (CDS) position 1244
cDNA position
(for ins/del: last normal base / first normal base)		 1375
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 MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRGWKRDREK RDDQDDVSSV RSEGGNIRGS FRGRGRGRGR GRGRGRGNPR
LNFDYSYGYQ EHGERTDQPF QTELNTSMMY YYDDGTGVQV YPVEEALLKE YIKRQIEYYF
SVENLERDFF LRGKMDEQGF LPISLIAGFQ RVQALTTNLN LILEALKDST EVEIVDEKMR
KKIEPEKWPI PGPPPRSVPP TDFSQLIDCP EFVPGQAFCS HTESAPNSPR IGSPLSPKKN
SETSILQAMS RGLSTSLPDL DSEPWIEVKK RHQPAPVKLR ESVSVPEGSL NQLCSSEEPE
QEELDFLFDE EIEQIGRKNT FTDWSDNDSD YEIDDQDLNK ILIVTQTPPY VKKHPGGDRT
GTHMSRAKIT SELAKVINDG LYYYEQDLWM EEDENKHTAI KQEVENFKKL NLISKEQFEN
LTPELPFEPN QEVPVAPSQS RQDLTDELAQ KLFDVSEITS AAMVHSLPTA VPESPRIHPT
RTPKTPRTPR LQDPNKTPRF YPVVKEPKAI DVKSPRKRKT RHSTNPPLEC HVGWVMDSRD
RGPGTSSVST SNASPSEGAP LAGSYGCTPH SFPKFQHPSH ELLKENGFTQ QVYHKYRRRC
LSERKRLGIG QSQEMNTLFR FWSFFLRDHF NKKMYEEFRQ LAWEDAKENY RYGLECLFRF
YSYGLEKKFR REIFQDFQEE TKKDYESGQL YGLEKFWAYL KYSQSKTQSI DPKLQEYLCS
FKRLEDFRVD PPISDEFGRK RHSSTSGEES NRHRLPPNSS TKPPNAAKPT STSELQVPIN
SPRRNISPES SDNSH*
mutated AA sequence MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRGWKRDREK RDDQDDVSSV RSEGGNIRGS FRGRGRGRGR GRGRGRGNPR
LNFDYSYGYQ EHGERTDQPF QTELNTSMMY YYDDGTGVQV YPVEEALLKE YIKRQIEYYF
SVENLERDFF LRGKMDEQGF LPISLIAGFQ RVQALTTNLN LILEALKDST EVEIVDEKMR
KKIEPEKWPI PGPPPRSVPP TDFSQLIDCP EFVPGQAFCS HTESAPNSPR IGSPLSPKKN
SETSILQAMS RGLSTSLPDL DSEPWIEVKK RHQPAPVKLR ESVSVPEGSL NQLCSSEEPE
QEELDFLFDE EIEQIGRKNT FTDWSDNDSD YEIDDQDLNK ILIVTQTPPY VKKHRGGDRT
GTHMSRAKIT SELAKVINDG LYYYEQDLWM EEDENKHTAI KQEVENFKKL NLISKEQFEN
LTPELPFEPN QEVPVAPSQS RQDLTDELAQ KLFDVSEITS AAMVHSLPTA VPESPRIHPT
RTPKTPRTPR LQDPNKTPRF YPVVKEPKAI DVKSPRKRKT RHSTNPPLEC HVGWVMDSRD
RGPGTSSVST SNASPSEGAP LAGSYGCTPH SFPKFQHPSH ELLKENGFTQ QVYHKYRRRC
LSERKRLGIG QSQEMNTLFR FWSFFLRDHF NKKMYEEFRQ LAWEDAKENY RYGLECLFRF
YSYGLEKKFR REIFQDFQEE TKKDYESGQL YGLEKFWAYL KYSQSKTQSI DPKLQEYLCS
FKRLEDFRVD PPISDEFGRK RHSSTSGEES NRHRLPPNSS TKPPNAAKPT STSELQVPIN
SPRRNISPES SDNSH*
speed 0.93 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