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mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999996157 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:36556823G>TN/A show variant in all transcripts   IGV
HGNC symbol APOL3
Ensembl transcript ID ENST00000349314
Genbank transcript ID NM_145640
UniProt peptide O95236
alteration type single base exchange
alteration region CDS
DNA changes c.117C>A
cDNA.155C>A
g.5403C>A
AA changes S39R Score: 110 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs132653
databasehomozygous (T/T)heterozygousallele carriers
1000G16526262278
ExAC---
regulatory features H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK12ac, Histone, Histone 2B Lysine 12 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1240
-0.9070
(flanking)0.2010
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased5407wt: 0.36 / mu: 0.58wt: GCCTGGAGAACGTGT
mu: GACTGGAGAACGTGT		 CTGG|agaa
Donor increased5406wt: 0.33 / mu: 0.43wt: AGCCTGGAGAACGTG
mu: AGACTGGAGAACGTG		 CCTG|gaga
Donor marginally increased5401wt: 0.6311 / mu: 0.6367 (marginal change - not scored)wt: CTCAGAGCCTGGAGA
mu: CTCAGAGACTGGAGA		 CAGA|gcct
Donor increased5403wt: 0.79 / mu: 0.95wt: CAGAGCCTGGAGAAC
mu: CAGAGACTGGAGAAC		 GAGC|ctgg
Donor gained53990.86mu: ATCTCAGAGACTGGA CTCA|gaga
distance from splice site 107
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39TFPFGFQGISQSLENVSGYYADAR
mutated  not conserved    39TFPFGFQGISQRLENVSGYYADA
Ptroglodytes  all identical  ENSPTRG00000014306  37TFPFGFQGISQSLEKVSGYYADA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000057346  202EALEQHMNALRLVRANP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
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 1209 / 1209
position (AA) of stopcodon in wt / mu AA sequence 403 / 403
position of stopcodon in wt / mu cDNA 1247 / 1247
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 39 / 39
chromosome 22
strand -1
last intron/exon boundary 389
theoretical NMD boundary in CDS 300
length of CDS 1209
coding sequence (CDS) position 117
cDNA position
(for ins/del: last normal base / first normal base)		 155
gDNA position
(for ins/del: last normal base / first normal base)		 5403
chromosomal position
(for ins/del: last normal base / first normal base)		 36556823
original gDNA sequence snippet TTCCAGGGTATATCTCAGAGCCTGGAGAACGTGTCTGGTTA
altered gDNA sequence snippet TTCCAGGGTATATCTCAGAGACTGGAGAACGTGTCTGGTTA
original cDNA sequence snippet TTCCAGGGTATATCTCAGAGCCTGGAGAACGTGTCTGGTTA
altered cDNA sequence snippet TTCCAGGGTATATCTCAGAGACTGGAGAACGTGTCTGGTTA
wildtype AA sequence MGLGQGWGWE ASCFACLIRS CCQVVTFTFP FGFQGISQSL ENVSGYYADA RLEVGSTQLR
TAGSCSHSFK RSFLEKKRFT EEATKYFRER VSPVHLQILL TNNEAWKRFV TAAELPRDEA
DALYEALKKL RTYAAIEDEY VQQKDEQFRE WFLKEFPQVK RKIQESIEKL RALANGIEEV
HRGCTISNVV SSSTGAASGI MSLAGLVLAP FTAGTSLALT AAGVGLGAAS AVTGITTSIV
EHSYTSSAEA EASRLTATSI DRLKVFKEVM RDITPNLLSL LNNYYEATQT IGSEIRAIRQ
ARARARLPVT TWRISAGSGG QAERTIAGTT RAVSRGARIL SATTSGIFLA LDVVNLVYES
KHLHEGAKSA SAEELRRQAQ ELEENLMELT QIYQRLNPCH TH*
mutated AA sequence MGLGQGWGWE ASCFACLIRS CCQVVTFTFP FGFQGISQRL ENVSGYYADA RLEVGSTQLR
TAGSCSHSFK RSFLEKKRFT EEATKYFRER VSPVHLQILL TNNEAWKRFV TAAELPRDEA
DALYEALKKL RTYAAIEDEY VQQKDEQFRE WFLKEFPQVK RKIQESIEKL RALANGIEEV
HRGCTISNVV SSSTGAASGI MSLAGLVLAP FTAGTSLALT AAGVGLGAAS AVTGITTSIV
EHSYTSSAEA EASRLTATSI DRLKVFKEVM RDITPNLLSL LNNYYEATQT IGSEIRAIRQ
ARARARLPVT TWRISAGSGG QAERTIAGTT RAVSRGARIL SATTSGIFLA LDVVNLVYES
KHLHEGAKSA SAEELRRQAQ ELEENLMELT QIYQRLNPCH TH*
speed 0.52 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