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 ENST00000441387
Genbank transcript ID N/A
UniProt peptide Q659C4
alteration type single base exchange
alteration region CDS
DNA changes c.1385C>G
cDNA.1516C>G
g.60782C>G
AA changes P462R Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 462
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      462VTQTPPYVKKHPGGDRTGTHMSRA
mutated  not conserved    462VTQTPPYVKKHRGGDRTGTHMSR
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000021347  462VTQTPPYVKKHPGGDRTGNHMSR
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000037814  n/a
Ggallus  all identical  ENSGALG00000010207  426VTQTPPYMRKHPGEDRAGNHVCH
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0261618  1150VAQVGR-APKHEGYDRTADFTSR
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000022512  556VTQTPPHLKKHPGGDRTGNHIS
protein features
start (aa)end (aa)featuredetails 
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 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 1385
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 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 HRGGDRTGTH 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*
speed 0.57 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