Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 9.21994670376815e-12 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:140793007A>GN/A show variant in all transcripts   IGV
HGNC symbol PCDHGB3
Ensembl transcript ID ENST00000576222
Genbank transcript ID NM_018924
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.43177A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs4912751
databasehomozygous (G/G)heterozygousallele carriers
1000G9199471866
ExAC14948287117819
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2AZ, Histone, Histone 2A variant Z
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3420.998
0.2430.986
(flanking)2.960.987
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc gained431860.30mu: GCGGCAGCTTGGTCACCGCGGGCAGGATAGACCGGGAGGAG gcgg|GCAG
Donor gained431710.49mu: GCGGCAGCTTGGTCA GGCA|gctt
distance from splice site 40631
Kozak consensus sequence altered? N/A
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 132 / 132
chromosome 5
strand 1
last intron/exon boundary 2695
theoretical NMD boundary in CDS 2513
length of CDS 2790
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 43177
chromosomal position
(for ins/del: last normal base / first normal base)		 140793007
original gDNA sequence snippet ACCCGCGCAGCGGCAGCTTGATCACCGCGGGCAGGATAGAC
altered gDNA sequence snippet ACCCGCGCAGCGGCAGCTTGGTCACCGCGGGCAGGATAGAC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGNSSGWRGP AGQRRMLFLF LLSLLDQVLS EPIRYAIPEE LDRGSLVGNL AKDLGFGVGD
LPTRNLRVIA EKKFFTVSPE NGNLLVSDRI DREEICGKKS TCVLEFEMVA EKPLNFFHVT
VLIQDINDNP PTFSQNITEL EISELALTGA TFALESAQDP DVGVNSLQQY YLSPDPHFSL
IQKENLDGSR YPELVLKAPL DREEQPHHHL VLTAVDGGEP SRSCTTQIRV IVADANDNPP
VFTQDMYRVN VAENLPAGSS VLKVMAIDMD EGINAEIIYA FINIGKEVRQ LFKLDSKTGE
LTTIGELDFE ERDSYTIGVE AKDGGHHTAY CKVQIDISDE NDNAPEITLA SESQHIQEDA
ELGTAVALIK THDLDSGFNG EILCQLKGNF PFKIVQDTKN TYRLVTDGAL DREQIPEYNV
TITATDKGNP PLSSSKTITL HILDVNDNVP VFHQASYTVH VAENNPPGAS IAHVRASDPD
LGPNGLVSYY IVASDLEPRE LSSYVSVSAR SGVVFAQRAF DHEQLRAFEL TLQARDQGSP
TLSANVSLRV LVDDRNDNAP LVLYPALGPE GSALFDMVPR SAEPGYLVTK VVAVDADSGY
NAWLSYHIVQ ASEPGLFSLG LRTGEVRTAR TLGDREAARQ RLLVTVRDGG QQPLSATVML
HLIFADSLQE IQPDLSDRPT PSDPQAELQF HLVVALALIS VLFLLAVILA ISLRLRCSSR
PATEGYFQPG VCFKTVPGVL PTYSERTLPY SYNPCAASHS SNTEFKFLNI KAENAAPQDL
LCDEASWFES NDNPEMPSNS GNLQKQAPPN TDWRFSQAQR PGTSGSQNGD DTGTWPNNQF
DTEMLQAMIL ASASEAADGS STLGGGAGTM GLSARYGPQF TLQHVPDYRQ NVYIPGSNAT
LTNAAGKRDG KAPAGGNGNK KKSGKKEKK*
mutated AA sequence N/A
speed 0.85 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