Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999985644 (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) chr13:76397731G>AN/A show variant in all transcripts   IGV
HGNC symbol LMO7
Ensembl transcript ID ENST00000341547
Genbank transcript ID NM_005358
UniProt peptide Q8WWI1
alteration type single base exchange
alteration region CDS
DNA changes c.1825G>A
cDNA.3085G>A
g.203162G>A
AA changes V609I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 609
frameshift no
known variant Reference ID: rs4884021
databasehomozygous (A/A)heterozygousallele carriers
1000G2028961098
ExAC24461762520071
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0820.115
-0.2680.001
(flanking)0.3980.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased203162wt: 0.61 / mu: 0.92wt: GAGATGTTGAAGACA
mu: GAGATATTGAAGACA		 GATG|ttga
Donor marginally increased203167wt: 0.5194 / mu: 0.5671 (marginal change - not scored)wt: GTTGAAGACATTAAG
mu: ATTGAAGACATTAAG		 TGAA|gaca
Donor gained2031580.45mu: AATGGAGATATTGAA TGGA|gata
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      609TMDDAWKYNGDVEDIKRTPNNVVS
mutated  all conserved    609DAWKYNGDIEDIKRTPNNVV
Ptroglodytes  all identical  ENSPTRG00000005935  609DAWKYNGDVEDIKRTPNNVV
Mmulatta  all conserved  ENSMMUG00000001312  869TVKNVLSSFISISKIANASTNCK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000033060  938DGWKYNGDVEVVKREQLDLG
Ggallus  all identical  ENSGALG00000016920  852TMDDAQKYNGEVEKAKGT-QTLT
Trubripes  not conserved  ENSTRUG00000010628  898TVDDPQSRVNGDGSKKSAAPSRYQ
Drerio  not conserved  ENSDARG00000004930  1102TMDDSVKRTNGESNSLKKTAVQ
Dmelanogaster  no alignment  FBgn0051534  n/a
Celegans  not conserved  F28F5.3  302RVEATFKQPPPREGVKPFVSRAAQDIT
Xtropicalis  all conserved  ENSXETG00000004710  927TVDDSFKYNGDLGSTK---NNSA
protein features
start (aa)end (aa)featuredetails 
613613CONFLICTF -> L (in Ref. 5; AAF04521).might get lost (downstream of altered splice site)
704704MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
706706MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
709709MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
805805MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
867867MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
873873MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
891891CONFLICTR -> C (in Ref. 6; AAD33924).might get lost (downstream of altered splice site)
895895MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
913913MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
919919MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
926926MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
932932MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
943943CONFLICTV -> I (in Ref. 1; AAL37480 and 6; AAD33924).might get lost (downstream of altered splice site)
949949MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
955955MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
956956MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
960960MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
988988MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
991991MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
994994MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
995995MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10261026MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10381046STRANDmight get lost (downstream of altered splice site)
10421128DOMAINPDZ.might get lost (downstream of altered splice site)
10441044MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
10481048MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
10561062STRANDmight get lost (downstream of altered splice site)
10651071STRANDmight get lost (downstream of altered splice site)
10761079HELIXmight get lost (downstream of altered splice site)
10871091STRANDmight get lost (downstream of altered splice site)
11011114HELIXmight get lost (downstream of altered splice site)
11161124STRANDmight get lost (downstream of altered splice site)
11971197MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
14231423MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
14471447CONFLICTM -> T (in Ref. 6; AAD33924/AAB86592).might get lost (downstream of altered splice site)
14931493MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15101510MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15161516MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15631563MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15861586MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15881588MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
15931593MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15951595MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15971597MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
16011601MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
16121678DOMAINLIM zinc-binding.might get lost (downstream of altered splice site)
16721672MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4050 / 4050
position (AA) of stopcodon in wt / mu AA sequence 1350 / 1350
position of stopcodon in wt / mu cDNA 5310 / 5310
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 1261 / 1261
chromosome 13
strand 1
last intron/exon boundary 5288
theoretical NMD boundary in CDS 3977
length of CDS 4050
coding sequence (CDS) position 1825
cDNA position
(for ins/del: last normal base / first normal base)		 3085
gDNA position
(for ins/del: last normal base / first normal base)		 203162
chromosomal position
(for ins/del: last normal base / first normal base)		 76397731
original gDNA sequence snippet CTTGGAAGTATAATGGAGATGTTGAAGACATTAAGAGAACT
altered gDNA sequence snippet CTTGGAAGTATAATGGAGATATTGAAGACATTAAGAGAACT
original cDNA sequence snippet CTTGGAAGTATAATGGAGATGTTGAAGACATTAAGAGAACT
altered cDNA sequence snippet CTTGGAAGTATAATGGAGATATTGAAGACATTAAGAGAACT
wildtype AA sequence MKKIRICHIF TFYSWMSYDV LFQRTELGAL EIWRQLICAH VCICVGWLYL RDRVCSKKDI
ILRTEQNSGR TILIKAVTEK NFETKDFRAS LENGVLLCDL INKLKPGVIK KINRLSTPIA
GLDNINVFLK ACEQIGLKEA QLFHPGDLQD LSNRVTVKQE ETDRRVKNVL ITLYWLGRKA
QSNPYYNGPH LNLKAFENLL GQALTKALED SSFLKRSGRD SGYGDIWCPE RGEFLAPPRH
HKREDSFESL DSLGSRSLTS CSSDITLRGG REGFESDTDS EFTFKMQDYN KDDMSYRRIS
AVEPKTALPF NRFLPNKSRQ PSYVPAPLRK KKPDKHEDNR RSWASPVYTE ADGTFSRLFQ
KIYGENGSKS MSDVSAEDVQ NLRQLRYEEM QKIKSQLKEQ DQKWQDDLAK WKDRRKSYTS
DLQKKKEERE EIEKQALEKS KRSSKTFKEM LQDRESQNQK STVPSRRRMY SFDDVLEEGK
RPPTMTVSEA SYQSERVEEK GATYPSEIPK EDSTTFAKRE DRVTTEIQLP SQSPVEEQSP
ASLSSLRSRS TQMESTRVSA SLPRSYRKTD TVRLTSVVTP RPFGSQTRGI SSLPRSYTMD
DAWKYNGDVE DIKRTPNNVV STPAPSPDAS QLASSLSSQK EVAATEEDVT RLPSPTSPFS
SLSQDQAATS KATLSSTSGL DLMSESGEGE ISPQREVSRS QDQFSDMRIS INQTPGKSLD
FGFTIKWDIP GIFVASVEAG SPAEFSQLQV DDEIIAINNT KFSYNDSKEW EEAMAKAQET
GHLVMDVRRY GKAGSPETKW IDATSGIYNS EKSSNLSVTT DFSESLQSSN IESKEINGIH
DESNAFESKA SESISLKNLK RRSQFFEQGS SDSVVPDLPV PTISAPSRWV WDQEEERKRQ
ERWQKEQDRL LQEKYQREQE KLREEWQRAK QEAERENSKY LDEELMVLSS NSMSLTTREP
SLATWEATWS EGSKSSDREG TRAGEEERRQ PQEEVVHEDQ GKKPQDQLVI ERERKWEQQL
QEEQEQKRLQ AEAEEQKRPA EEQKRQAEIE RETSVRIYQY RRPVDSYDIP KTEEASSGFL
PGDRNKSRST TELDDYSTNK NGNNKYLDQI GNMTSSQRRS KKEQVPSGAE LERQQILQEM
RKRTPLHNDN SWIRQRSASV NKEPVSLPGI MRRGESLDNL DSPRSNSWRQ PPWLNQPTGF
YASSSVQDFS RPPPQLVSTS NRAYMRNPSS SVPPPSAGSV KTSTTGVATT QSPTPRSHSP
SASQSGSQLR NRSVSGKRIC SYCNNILGKG AAMIIESLGL CYHLHCFKCV ACECDLGGSS
SGAEVRIRNH QLYCNDCYLR FKSGRPTAM*
mutated AA sequence MKKIRICHIF TFYSWMSYDV LFQRTELGAL EIWRQLICAH VCICVGWLYL RDRVCSKKDI
ILRTEQNSGR TILIKAVTEK NFETKDFRAS LENGVLLCDL INKLKPGVIK KINRLSTPIA
GLDNINVFLK ACEQIGLKEA QLFHPGDLQD LSNRVTVKQE ETDRRVKNVL ITLYWLGRKA
QSNPYYNGPH LNLKAFENLL GQALTKALED SSFLKRSGRD SGYGDIWCPE RGEFLAPPRH
HKREDSFESL DSLGSRSLTS CSSDITLRGG REGFESDTDS EFTFKMQDYN KDDMSYRRIS
AVEPKTALPF NRFLPNKSRQ PSYVPAPLRK KKPDKHEDNR RSWASPVYTE ADGTFSRLFQ
KIYGENGSKS MSDVSAEDVQ NLRQLRYEEM QKIKSQLKEQ DQKWQDDLAK WKDRRKSYTS
DLQKKKEERE EIEKQALEKS KRSSKTFKEM LQDRESQNQK STVPSRRRMY SFDDVLEEGK
RPPTMTVSEA SYQSERVEEK GATYPSEIPK EDSTTFAKRE DRVTTEIQLP SQSPVEEQSP
ASLSSLRSRS TQMESTRVSA SLPRSYRKTD TVRLTSVVTP RPFGSQTRGI SSLPRSYTMD
DAWKYNGDIE DIKRTPNNVV STPAPSPDAS QLASSLSSQK EVAATEEDVT RLPSPTSPFS
SLSQDQAATS KATLSSTSGL DLMSESGEGE ISPQREVSRS QDQFSDMRIS INQTPGKSLD
FGFTIKWDIP GIFVASVEAG SPAEFSQLQV DDEIIAINNT KFSYNDSKEW EEAMAKAQET
GHLVMDVRRY GKAGSPETKW IDATSGIYNS EKSSNLSVTT DFSESLQSSN IESKEINGIH
DESNAFESKA SESISLKNLK RRSQFFEQGS SDSVVPDLPV PTISAPSRWV WDQEEERKRQ
ERWQKEQDRL LQEKYQREQE KLREEWQRAK QEAERENSKY LDEELMVLSS NSMSLTTREP
SLATWEATWS EGSKSSDREG TRAGEEERRQ PQEEVVHEDQ GKKPQDQLVI ERERKWEQQL
QEEQEQKRLQ AEAEEQKRPA EEQKRQAEIE RETSVRIYQY RRPVDSYDIP KTEEASSGFL
PGDRNKSRST TELDDYSTNK NGNNKYLDQI GNMTSSQRRS KKEQVPSGAE LERQQILQEM
RKRTPLHNDN SWIRQRSASV NKEPVSLPGI MRRGESLDNL DSPRSNSWRQ PPWLNQPTGF
YASSSVQDFS RPPPQLVSTS NRAYMRNPSS SVPPPSAGSV KTSTTGVATT QSPTPRSHSP
SASQSGSQLR NRSVSGKRIC SYCNNILGKG AAMIIESLGL CYHLHCFKCV ACECDLGGSS
SGAEVRIRNH QLYCNDCYLR FKSGRPTAM*
speed 0.33 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