Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999996 (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) chr19:51728641A>GN/A show variant in all transcripts   IGV
HGNC symbol CD33
Ensembl transcript ID ENST00000262262
Genbank transcript ID NM_001772
UniProt peptide P20138
alteration type single base exchange
alteration region CDS
DNA changes c.205A>G
cDNA.245A>G
g.322A>G
AA changes R69G Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 69
frameshift no
known variant Reference ID: rs2455069
databasehomozygous (G/G)heterozygousallele carriers
1000G33110161347
ExAC86591544924108
regulatory features Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.1040
-2.1680
(flanking)-4.2820
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained3210.82mu: ATATCCGGGGACTCT ATCC|gggg
distance from splice site 168
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      69GYWFREGAIISRDSPVATNKLDQE
mutated  not conserved    69FREGAIISGDSPVATNKLDQ
Ptroglodytes  not conserved  ENSPTRG00000011375  69FREGPIVSGDSPVATNKPDQ
Mmulatta  not conserved  ENSMMUG00000009486  68GAIVSLDSPVATNKLDQ
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000039013  64NIFSGSPVATNDPQR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
18259TOPO_DOMExtracellular (Potential).lost
19135DOMAINIg-like V-type.lost
100100CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
101101DISULFIDBy similarity.might get lost (downstream of altered splice site)
113113CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
119119BINDINGSialic acid (By similarity).might get lost (downstream of altered splice site)
145228DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
160160CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
163163DISULFIDPotential.might get lost (downstream of altered splice site)
169169DISULFIDBy similarity.might get lost (downstream of altered splice site)
209209CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
212212DISULFIDPotential.might get lost (downstream of altered splice site)
230230CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
260282TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
283364TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
338343MOTIFITIM motif 1.might get lost (downstream of altered splice site)
340340MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
340340MUTAGENY->A: Abolishes binding to PTPN6 and PTPN11. Increases binding of red blood cells.might get lost (downstream of altered splice site)
356361MOTIFITIM motif 2.might get lost (downstream of altered splice site)
358358MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
358358MUTAGENY->A,F: Reduces binding to PTPN6.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1095 / 1095
position (AA) of stopcodon in wt / mu AA sequence 365 / 365
position of stopcodon in wt / mu cDNA 1135 / 1135
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 41 / 41
chromosome 19
strand 1
last intron/exon boundary 965
theoretical NMD boundary in CDS 874
length of CDS 1095
coding sequence (CDS) position 205
cDNA position
(for ins/del: last normal base / first normal base)		 245
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 51728641
original gDNA sequence snippet GGGAAGGAGCCATTATATCCAGGGACTCTCCAGTGGCCACA
altered gDNA sequence snippet GGGAAGGAGCCATTATATCCGGGGACTCTCCAGTGGCCACA
original cDNA sequence snippet GGGAAGGAGCCATTATATCCAGGGACTCTCCAGTGGCCACA
altered cDNA sequence snippet GGGAAGGAGCCATTATATCCGGGGACTCTCCAGTGGCCACA
wildtype AA sequence MPLLLLLPLL WAGALAMDPN FWLQVQESVT VQEGLCVLVP CTFFHPIPYY DKNSPVHGYW
FREGAIISRD SPVATNKLDQ EVQEETQGRF RLLGDPSRNN CSLSIVDARR RDNGSYFFRM
ERGSTKYSYK SPQLSVHVTD LTHRPKILIP GTLEPGHSKN LTCSVSWACE QGTPPIFSWL
SAAPTSLGPR TTHSSVLIIT PRPQDHGTNL TCQVKFAGAG VTTERTIQLN VTYVPQNPTT
GIFPGDGSGK QETRAGVVHG AIGGAGVTAL LALCLCLIFF IVKTHRRKAA RTAVGRNDTH
PTTGSASPKH QKKSKLHGPT ETSSCSGAAP TVEMDEELHY ASLNFHGMNP SKDTSTEYSE
VRTQ*
mutated AA sequence MPLLLLLPLL WAGALAMDPN FWLQVQESVT VQEGLCVLVP CTFFHPIPYY DKNSPVHGYW
FREGAIISGD SPVATNKLDQ EVQEETQGRF RLLGDPSRNN CSLSIVDARR RDNGSYFFRM
ERGSTKYSYK SPQLSVHVTD LTHRPKILIP GTLEPGHSKN LTCSVSWACE QGTPPIFSWL
SAAPTSLGPR TTHSSVLIIT PRPQDHGTNL TCQVKFAGAG VTTERTIQLN VTYVPQNPTT
GIFPGDGSGK QETRAGVVHG AIGGAGVTAL LALCLCLIFF IVKTHRRKAA RTAVGRNDTH
PTTGSASPKH QKKSKLHGPT ETSSCSGAAP TVEMDEELHY ASLNFHGMNP SKDTSTEYSE
VRTQ*
speed 0.66 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