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 ENST00000441387
Genbank transcript ID N/A
UniProt peptide Q659C4
alteration type single base exchange
alteration region CDS
DNA changes c.1979G>A
cDNA.2110G>A
g.118221G>A
AA changes R660H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 660
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      660CHVGWVMDSRDRGPGTSSVSTSNA
mutated  not conserved    660CHVGWVMDSRDHGPGTSSVSTSN
Ptroglodytes  no homologue    
Mmulatta  not conserved  ENSMMUG00000021347  659CHVGWVMDSRDHGPRTSSVSTSN
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000037814  n/a
Ggallus  not conserved  ENSGALG00000010207  594RDHRPRTSSVSSSN
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0261618  1314AHVGWLLDTVEHRPRTTSMG-SS
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000022512  734WVMDSKEHRPRTSSVSSSN
protein features
start (aa)end (aa)featuredetails 
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 2364 / 2364
position (AA) of stopcodon in wt / mu AA sequence 788 / 788
position of stopcodon in wt / mu cDNA 2495 / 2495
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 2569
theoretical NMD boundary in CDS 2387
length of CDS 2364
coding sequence (CDS) position 1979
cDNA position
(for ins/del: last normal base / first normal base)		 2110
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 KRANKHKWVP LHLDVVRSES QERPGSRNSS RCQPEANKPT HNNRRNDTRS
WKRDREKRDD QDDVSSVRSE GGNIRGSFRG RGRGRGRGRG RGRGNPRLNF DYSYGYQEHG
ERTDQPFQTE LNTSMMYYYD DGTGVQVYPV EEALLKEYIK RQIEYYFSVE NLERDFFLRG
KMDEQGFLPI SLIAGFQRVQ ALTTNLNLIL EALKDSTEVE IVDEKMRKKI EPEKWPIPGP
PPRSVPPTDF SQLIDCPEFV PGQAFCSHTE SAPNSPRIGS PLSPKKNSET SILQAMSRGL
STSLPDLDSE PWIEVKKRHQ PAPVKLRESV SVPEGSLNQL CSSEEPEQEE LDFLFDEEIE
QIGRKNTFTD WSDNDSDYEI DDQDLNKILI VTQTPPYVKK HPGGDRTGTH MSRAKITSEL
AKVINDGLYY YEQDLWMEED ENKHTAIKQE VENFKKLNLI SKEQFENLTP ELPFEPNQEV
PVAPSQSRQG GVQGVLHIPK KDLTDELAQK LFDVSEITSA AMVHSLPTAV PESPRIHPTR
TPKTPRTPRL QDPNKTPRFY PVVKEPKAID VKSPRKRKTR HSTNPPLECH VGWVMDSRDR
GPGTSSVSTS NASPSEGAPL AGSYGCTPHS FPKFQHPSHE LLKENGFTQQ VYHKYRRRCL
SERKRLGIGQ SQEMNTLFRF WSFFLRDHFN KKMYEEFRQL AWEDAKENYR SAVWTRKVLG
LFEIFSI*
mutated AA sequence MENWPTPSEL VNTGFQSVLS QGNKKPQNRK EKEEKVEKRS NSDSKENRET KLNGPGENVS
EDEAQSSNQR KRANKHKWVP LHLDVVRSES QERPGSRNSS RCQPEANKPT HNNRRNDTRS
WKRDREKRDD QDDVSSVRSE GGNIRGSFRG RGRGRGRGRG RGRGNPRLNF DYSYGYQEHG
ERTDQPFQTE LNTSMMYYYD DGTGVQVYPV EEALLKEYIK RQIEYYFSVE NLERDFFLRG
KMDEQGFLPI SLIAGFQRVQ ALTTNLNLIL EALKDSTEVE IVDEKMRKKI EPEKWPIPGP
PPRSVPPTDF SQLIDCPEFV PGQAFCSHTE SAPNSPRIGS PLSPKKNSET SILQAMSRGL
STSLPDLDSE PWIEVKKRHQ PAPVKLRESV SVPEGSLNQL CSSEEPEQEE LDFLFDEEIE
QIGRKNTFTD WSDNDSDYEI DDQDLNKILI VTQTPPYVKK HPGGDRTGTH MSRAKITSEL
AKVINDGLYY YEQDLWMEED ENKHTAIKQE VENFKKLNLI SKEQFENLTP ELPFEPNQEV
PVAPSQSRQG GVQGVLHIPK KDLTDELAQK LFDVSEITSA AMVHSLPTAV PESPRIHPTR
TPKTPRTPRL QDPNKTPRFY PVVKEPKAID VKSPRKRKTR HSTNPPLECH VGWVMDSRDH
GPGTSSVSTS NASPSEGAPL AGSYGCTPHS FPKFQHPSHE LLKENGFTQQ VYHKYRRRCL
SERKRLGIGQ SQEMNTLFRF WSFFLRDHFN KKMYEEFRQL AWEDAKENYR SAVWTRKVLG
LFEIFSI*
speed 0.78 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