mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999988145541917 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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

ENST00000421133

Genbank transcript ID

NM_001082618

UniProt peptide

P20138

alteration type

single base exchange

alteration region

intron

DNA changes

g.322A>G

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

Reference ID: rs2455069

database	homozygous (G/G)	heterozygous	allele carriers
1000G	331	1016	1347
ExAC	8659	15449	24108

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

	PhyloP	PhastCons
(flanking)	-2.104	0
	-2.168	0
(flanking)	-4.282	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor gained	321	0.82	mu: ATATCCGGGGACTCT	ATCC\|gggg

distance from splice site

230

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	17	SIGNAL	Potential.	might get lost (downstream of altered splice site)
18	259	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
19	135	DOMAIN	Ig-like V-type.	might get lost (downstream of altered splice site)
36	36	DISULFID	By similarity.	might get lost (downstream of altered splice site)
41	41	DISULFID	By similarity.	might get lost (downstream of altered splice site)
100	100	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
101	101	DISULFID	By similarity.	might get lost (downstream of altered splice site)
113	113	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
119	119	BINDING	Sialic acid (By similarity).	might get lost (downstream of altered splice site)
145	228	DOMAIN	Ig-like C2-type.	might get lost (downstream of altered splice site)
160	160	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
163	163	DISULFID	Potential.	might get lost (downstream of altered splice site)
169	169	DISULFID	By similarity.	might get lost (downstream of altered splice site)
209	209	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
212	212	DISULFID	Potential.	might get lost (downstream of altered splice site)
230	230	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
260	282	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
283	364	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
338	343	MOTIF	ITIM motif 1.	might get lost (downstream of altered splice site)
340	340	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
340	340	MUTAGEN	Y->A: Abolishes binding to PTPN6 and PTPN11. Increases binding of red blood cells.	might get lost (downstream of altered splice site)
356	361	MOTIF	ITIM motif 2.	might get lost (downstream of altered splice site)
358	358	MUTAGEN	Y->A,F: Reduces binding to PTPN6.	might get lost (downstream of altered splice site)
358	358	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

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

41 / 41

chromosome

strand

last intron/exon boundary

584

theoretical NMD boundary in CDS

493

length of CDS

714

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)

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

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MPLLLLLPLL WADLTHRPKI LIPGTLEPGH SKNLTCSVSW ACEQGTPPIF SWLSAAPTSL
GPRTTHSSVL IITPRPQDHG TNLTCQVKFA GAGVTTERTI QLNVTYVPQN PTTGIFPGDG
SGKQETRAGV VHGAIGGAGV TALLALCLCL IFFIVKTHRR KAARTAVGRN DTHPTTGSAS
PKHQKKSKLH GPTETSSCSG AAPTVEMDEE LHYASLNFHG MNPSKDTSTE YSEVRTQ*

mutated AA sequence

N/A

speed

0.56 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