Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999947677 (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) chr16:67397580G>CN/A show variant in all transcripts   IGV
HGNC symbol LRRC36
Ensembl transcript ID ENST00000329956
Genbank transcript ID NM_018296
UniProt peptide Q1X8D7
alteration type single base exchange
alteration region CDS
DNA changes c.665G>C
cDNA.684G>C
g.36880G>C
AA changes R222P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 222
frameshift no
known variant Reference ID: rs9922085
databasehomozygous (C/C)heterozygousallele carriers
1000G286460746
ExAC162876499277
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOXA2, Transcription Factor, FOXA2 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
USF1, Transcription Factor, USF1 Transcription Factor Binding (-1)
USF1, Transcription Factor, USF1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding (1)
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1160.012
0.7210.189
(flanking)0.0460.295
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 increased36884wt: 0.2758 / mu: 0.3062 (marginal change - not scored)wt: CGTGATCAGAAATTA
mu: CCTGATCAGAAATTA		 TGAT|caga
distance from splice site 38
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      222LSTSATQGNGTRDQKLDTFPLGTQ
mutated  not conserved    222LSTSATQGNGTPDQKLDTFPLGT
Ptroglodytes  not conserved  ENSPTRG00000008227  222LSTSATQGNGTPDQKLDTFPLGT
Mmulatta  not conserved  ENSMMUG00000009821  222LSTSATQGNGTPDQKLDTFPLGT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000054320  222LTSICAAQGSGTPAQKLDVFPLGT
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000057934  n/a
Dmelanogaster  no homologue    
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 2265 / 2265
position (AA) of stopcodon in wt / mu AA sequence 755 / 755
position of stopcodon in wt / mu cDNA 2284 / 2284
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 20 / 20
chromosome 16
strand 1
last intron/exon boundary 2065
theoretical NMD boundary in CDS 1995
length of CDS 2265
coding sequence (CDS) position 665
cDNA position
(for ins/del: last normal base / first normal base)		 684
gDNA position
(for ins/del: last normal base / first normal base)		 36880
chromosomal position
(for ins/del: last normal base / first normal base)		 67397580
original gDNA sequence snippet AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT
altered gDNA sequence snippet AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT
original cDNA sequence snippet AACTCAGGGCAATGGTACACGTGATCAGAAATTAGACACCT
altered cDNA sequence snippet AACTCAGGGCAATGGTACACCTGATCAGAAATTAGACACCT
wildtype AA sequence MAEQWELDEE GIRRLGALTL EQPELVESLS LQGSYAGKIH SIGDAFRNFK NLRSLDLSRN
LITSLKGIQY LCSLQDLNLY YNNIPSLVEV SRLQPLPFLK ELDLRLNPVV RKDTDYRLFA
VYTLQTLEKL DDRTVREGER KAAKLHFSQL GNSENFLLEV EKSSREKTMK NCVTGESSAS
KVSANVDSRI EMDSNKGLFI PFPNREIKDS LSTSATQGNG TRDQKLDTFP LGTQTQEVAR
REMPSDNHQE DEFRHYSPRQ STVRSPEKMT REGYQVSFLD NKSSGSSPEK ELIPKPDTFH
LTHDASLSKC LDVGDSSQIH PYQLPSDVGL ENYDSCYSQT LSLHGSLGKR PQRSKNYQEY
SIKPSNDIKT TASHSCGDLL TSLSNPDSST GRLLKLSSDL YATTHFNSDP AVLVNVEQQL
STSLDDLTPA HGSVPNNAVL GNRTTPLRTL LLSPGTSEHR KIFTKRSLSP SKRGFKWKDN
ILANLNLKHG FQDATGSEPL SSDLGSLHGL AGNHSPPISA RTPHVATVLR QLLELVDKHW
NGSGSLLLNK KFLGPARDLL LSLVVPAPSQ PRCCSHPEDT MKAFCRRELE LKEAAQLVPN
DMESLKQKLV RVLEENLILS EKIQQLEEGA AISIVSGQQS HTYDDLLHKN QQLTMQVACL
NQELAQLKKL EKTVAILHES QRSLVVTNEY LLQQLNKEPK GYSGKALLPP EKGHHLGRSS
PFGKSTLSSS SPVAHETGQY LIQSVLDAAP EPGL*
mutated AA sequence MAEQWELDEE GIRRLGALTL EQPELVESLS LQGSYAGKIH SIGDAFRNFK NLRSLDLSRN
LITSLKGIQY LCSLQDLNLY YNNIPSLVEV SRLQPLPFLK ELDLRLNPVV RKDTDYRLFA
VYTLQTLEKL DDRTVREGER KAAKLHFSQL GNSENFLLEV EKSSREKTMK NCVTGESSAS
KVSANVDSRI EMDSNKGLFI PFPNREIKDS LSTSATQGNG TPDQKLDTFP LGTQTQEVAR
REMPSDNHQE DEFRHYSPRQ STVRSPEKMT REGYQVSFLD NKSSGSSPEK ELIPKPDTFH
LTHDASLSKC LDVGDSSQIH PYQLPSDVGL ENYDSCYSQT LSLHGSLGKR PQRSKNYQEY
SIKPSNDIKT TASHSCGDLL TSLSNPDSST GRLLKLSSDL YATTHFNSDP AVLVNVEQQL
STSLDDLTPA HGSVPNNAVL GNRTTPLRTL LLSPGTSEHR KIFTKRSLSP SKRGFKWKDN
ILANLNLKHG FQDATGSEPL SSDLGSLHGL AGNHSPPISA RTPHVATVLR QLLELVDKHW
NGSGSLLLNK KFLGPARDLL LSLVVPAPSQ PRCCSHPEDT MKAFCRRELE LKEAAQLVPN
DMESLKQKLV RVLEENLILS EKIQQLEEGA AISIVSGQQS HTYDDLLHKN QQLTMQVACL
NQELAQLKKL EKTVAILHES QRSLVVTNEY LLQQLNKEPK GYSGKALLPP EKGHHLGRSS
PFGKSTLSSS SPVAHETGQY LIQSVLDAAP EPGL*
speed 0.80 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