Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.998673825316061 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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 ENST00000541146
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.401G>C
g.36880G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
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? no
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 671 / 671
chromosome 16
strand 1
last intron/exon boundary 1132
theoretical NMD boundary in CDS 411
length of CDS 681
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 401
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 MEGQYPCQPE SKAWFPRCYR QRVTWVVCTV WLETTVPPSL PEPPMWPLSS DSSWSLWIST
GMAPAPSSST RSFSESLKQK LVRVLEENLI LSEKIQQLEE GAAISIVSGQ QSHTYDDLLH
KNQQLTMQVA CLNQELAQLK KLEKTVAILH ESQRSLVVTN EYLLQQLNKE PKGYSGKALL
PPEKGHHLGR SSPFGKSTLS SSSPVAHETG QYLIQSVLDA APEPGL*
mutated AA sequence N/A
speed 0.32 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