Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.982449390232502 (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) chr4:129100643G>AN/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.1802G>A
cDNA.1933G>A
g.118221G>A
AA changes R601H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 601
frameshift no
known variant Reference ID: rs12645577
databasehomozygous (A/A)heterozygousallele carriers
1000G88510821967
ExAC26108-194496659
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8841
2.5910.998
(flanking)-0.4470.897
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 increased118214wt: 0.7969 / mu: 0.7970 (marginal change - not scored)wt: ATTCCAGAGACCGTG
mu: ATTCCAGAGACCATG		 TCCA|gaga
Donor increased118224wt: 0.81 / mu: 0.93wt: CCGTGGGCCAGGAAC
mu: CCATGGGCCAGGAAC		 GTGG|gcca
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      601CHVGWVMDSRDRGPGTSSVSTSNA
mutated  not conserved    601HGPGTSSVSTSN
Ptroglodytes  no homologue    
Mmulatta  not conserved  ENSMMUG00000021347  659CHVGWVMDSRDHGPRTSSVSTSN
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000037814  n/a
Ggallus  not conserved  ENSGALG00000010207  594SRDHRPRTSSVSSSN
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0261618  1295AHVGWLLDTVEHRPRTTSMG-SS
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000022512  734YHVGWVMDSKEHRPRTSSVSS
protein features
start (aa)end (aa)featuredetails 
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 1802
cDNA position
(for ins/del: last normal base / first normal base)		 1933
gDNA position
(for ins/del: last normal base / first normal base)		 118221
chromosomal position
(for ins/del: last normal base / first normal base)		 129100643
original gDNA sequence snippet GGTAATGGATTCCAGAGACCGTGGGCCAGGAACATCCTCTG
altered gDNA sequence snippet GGTAATGGATTCCAGAGACCATGGGCCAGGAACATCCTCTG
original cDNA sequence snippet GGTAATGGATTCCAGAGACCGTGGGCCAGGAACATCCTCTG
altered cDNA sequence snippet GGTAATGGATTCCAGAGACCATGGGCCAGGAACATCCTCTG
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 VKKHPGGDRT
GTHMSRAKIT SELAKVINDG LYYYEQDLWM EEDENKHTAI KQEVENFKKL NLISKEQFEN
LTPELPFEPN QEVPVAPSQS RQDLTDELAQ KLFDVSEITS AAMVHSLPTA VPESPRIHPT
RTPKTPRTPR LQDPNKTPRF YPVVKEPKAI DVKSPRKRKT RHSTNPPLEC HVGWVMDSRD
HGPGTSSVST 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 0.70 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