Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:75884216C>TN/A show variant in all transcripts   IGV
HGNC symbol TBC1D4
Ensembl transcript ID ENST00000377636
Genbank transcript ID NM_014832
UniProt peptide O60343
alteration type single base exchange
alteration region CDS
DNA changes c.2455G>A
cDNA.2802G>A
g.172035G>A
AA changes V819I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 819
frameshift no
known variant Reference ID: rs1062087
databasehomozygous (T/T)heterozygousallele carriers
1000G13847972181
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5620.016
-0.1610
(flanking)-0.2120
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased172046wt: 0.9719 / mu: 0.9722 (marginal change - not scored)wt: CCGCTGGTTGTATTCCTGTCTGGGGAGGATGACCCAGAAAA
mu: CCGCTGGTTATATTCCTGTCTGGGGAGGATGACCCAGAAAA		 gtct|GGGG
distance from splice site 72
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      819LSPTMEEEPLVVFLSGEDDPEKIE
mutated  all conserved    819LSPTMEEEPLVIFLSGEDDPEKI
Ptroglodytes  all conserved  ENSPTRG00000005932  819LSPTMEEEPLVIFLSGEDDPEKI
Mmulatta  all conserved  ENSMMUG00000021197  822LSPTMEEEPLVIFLSGEDDPEKI
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000033083  826LSPTMEEEPLIIFLSGDEDTEKV
Ggallus  not conserved  ENSGALG00000016925  794--------------TGE-----
Trubripes  not conserved  ENSTRUG00000011039  756HSRRSVMDPSRHLLPPGEKP---
Drerio  not conserved  ENSDARG00000075156  769RALTQDQGDQ----TGPQSPEQS
Dmelanogaster  not conserved  FBgn0261261  839VTPSKGLDSEVPTEFLSPMRKPAK-
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3897 / 3897
position (AA) of stopcodon in wt / mu AA sequence 1299 / 1299
position of stopcodon in wt / mu cDNA 4244 / 4244
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 348 / 348
chromosome 13
strand -1
last intron/exon boundary 4011
theoretical NMD boundary in CDS 3613
length of CDS 3897
coding sequence (CDS) position 2455
cDNA position
(for ins/del: last normal base / first normal base)		 2802
gDNA position
(for ins/del: last normal base / first normal base)		 172035
chromosomal position
(for ins/del: last normal base / first normal base)		 75884216
original gDNA sequence snippet TGGAGGAGGAACCGCTGGTTGTATTCCTGTCTGGGGAGGAT
altered gDNA sequence snippet TGGAGGAGGAACCGCTGGTTATATTCCTGTCTGGGGAGGAT
original cDNA sequence snippet TGGAGGAGGAACCGCTGGTTGTATTCCTGTCTGGGGAGGAT
altered cDNA sequence snippet TGGAGGAGGAACCGCTGGTTATATTCCTGTCTGGGGAGGAT
wildtype AA sequence MEPPSCIQDE PFPHPLEPEP GVSAQPGPGK PSDKRFRLWY VGGSCLDHRT TLPMLPWLMA
EIRRRSQKPE AGGCGAPAAR EVILVLSAPF LRCVPAPGAG ASGGTSPSAT QPNPAVFIFE
HKAQHISRFI HNSHDLTYFA YLIKAQPDDP ESQMACHVFR ATDPSQVPDV ISSIRQLSKA
AMKEDAKPSK DNEDAFYNSQ KFEVLYCGKV TVTHKKAPSS LIDDCMEKFS LHEQQRLKIQ
GEQRGPDPGE DLADLEVVVP GSPGDCLPEE ADGTDTHLGL PAGASQPALT SSRVCFPERI
LEDSGFDEQQ EFRSRCSSVT GVQRRVHEGS QKSQPRRRHA SAPSHVQPSD SEKNRTMLFQ
VGRFEINLIS PDTKSVVLEK NFKDISSCSQ GIKHVDHFGF ICRESPEPGL SQYICYVFQC
ASESLVDEVM LTLKQAFSTA AALQSAKTQI KLCEACPMHS LHKLCERIEG LYPPRAKLVI
QRHLSSLTDN EQADIFERVQ KMKPVSDQEE NELVILHLRQ LCEAKQKTHV HIGEGPSTIS
NSTIPENATS SGRFKLDILK NKAKRSLTSS LENIFSRGAN RMRGRLGSVD SFERSNSLAS
EKDYSPGDSP PGTPPASPPS SAWQTFPEED SDSPQFRRRA HTFSHPPSST KRKLNLQDGR
AQGVRSPLLR QSSSEQCSNL SSVRRMYKES NSSSSLPSLH TSFSAPSFTA PSFLKSFYQN
SGRLSPQYEN EIRQDTASES SDGEGRKRTS STCSNESLSV GGTSVTPRRI SWRQRIFLRV
ASPMNKSPSA MQQQDGLDRN ELLPLSPLSP TMEEEPLVVF LSGEDDPEKI EERKKSKELR
SLWRKAIHQQ ILLLRMEKEN QKLEASRDEL QSRKVKLDYE EVGACQKEVL ITWDKKLLNC
RAKIRCDMED IHTLLKEGVP KSRRGEIWQF LALQYRLRHR LPNKQQPPDI SYKELLKQLT
AQQHAILVDL GRTFPTHPYF SVQLGPGQLS LFNLLKAYSL LDKEVGYCQG ISFVAGVLLL
HMSEEQAFEM LKFLMYDLGF RKQYRPDMMS LQIQMYQLSR LLHDYHRDLY NHLEENEISP
SLYAAPWFLT LFASQFSLGF VARVFDIIFL QGTEVIFKVA LSLLSSQETL IMECESFENI
VEFLKNTLPD MNTSEMEKII TQVFEMDISK QLHAYEVEYH VLQDELQESS YSCEDSETLE
KLERANSQLK RQNMDLLEKL QVAHTKIQAL ESNLENLLTR ETKMKSLIRT LEQEKMAYQK
TVEQLRKLLP ADALVNCDLL LRDLNCNPNN KAKIGNKP*
mutated AA sequence MEPPSCIQDE PFPHPLEPEP GVSAQPGPGK PSDKRFRLWY VGGSCLDHRT TLPMLPWLMA
EIRRRSQKPE AGGCGAPAAR EVILVLSAPF LRCVPAPGAG ASGGTSPSAT QPNPAVFIFE
HKAQHISRFI HNSHDLTYFA YLIKAQPDDP ESQMACHVFR ATDPSQVPDV ISSIRQLSKA
AMKEDAKPSK DNEDAFYNSQ KFEVLYCGKV TVTHKKAPSS LIDDCMEKFS LHEQQRLKIQ
GEQRGPDPGE DLADLEVVVP GSPGDCLPEE ADGTDTHLGL PAGASQPALT SSRVCFPERI
LEDSGFDEQQ EFRSRCSSVT GVQRRVHEGS QKSQPRRRHA SAPSHVQPSD SEKNRTMLFQ
VGRFEINLIS PDTKSVVLEK NFKDISSCSQ GIKHVDHFGF ICRESPEPGL SQYICYVFQC
ASESLVDEVM LTLKQAFSTA AALQSAKTQI KLCEACPMHS LHKLCERIEG LYPPRAKLVI
QRHLSSLTDN EQADIFERVQ KMKPVSDQEE NELVILHLRQ LCEAKQKTHV HIGEGPSTIS
NSTIPENATS SGRFKLDILK NKAKRSLTSS LENIFSRGAN RMRGRLGSVD SFERSNSLAS
EKDYSPGDSP PGTPPASPPS SAWQTFPEED SDSPQFRRRA HTFSHPPSST KRKLNLQDGR
AQGVRSPLLR QSSSEQCSNL SSVRRMYKES NSSSSLPSLH TSFSAPSFTA PSFLKSFYQN
SGRLSPQYEN EIRQDTASES SDGEGRKRTS STCSNESLSV GGTSVTPRRI SWRQRIFLRV
ASPMNKSPSA MQQQDGLDRN ELLPLSPLSP TMEEEPLVIF LSGEDDPEKI EERKKSKELR
SLWRKAIHQQ ILLLRMEKEN QKLEASRDEL QSRKVKLDYE EVGACQKEVL ITWDKKLLNC
RAKIRCDMED IHTLLKEGVP KSRRGEIWQF LALQYRLRHR LPNKQQPPDI SYKELLKQLT
AQQHAILVDL GRTFPTHPYF SVQLGPGQLS LFNLLKAYSL LDKEVGYCQG ISFVAGVLLL
HMSEEQAFEM LKFLMYDLGF RKQYRPDMMS LQIQMYQLSR LLHDYHRDLY NHLEENEISP
SLYAAPWFLT LFASQFSLGF VARVFDIIFL QGTEVIFKVA LSLLSSQETL IMECESFENI
VEFLKNTLPD MNTSEMEKII TQVFEMDISK QLHAYEVEYH VLQDELQESS YSCEDSETLE
KLERANSQLK RQNMDLLEKL QVAHTKIQAL ESNLENLLTR ETKMKSLIRT LEQEKMAYQK
TVEQLRKLLP ADALVNCDLL LRDLNCNPNN KAKIGNKP*
speed 0.56 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