MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000262262
Querying Taster for transcript #2: ENST00000421133
Querying Taster for transcript #3: ENST00000391796
Querying Taster for transcript #4: ENST00000436584
MT speed 0 s - this script 3.984847 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CD33	polymorphism_automatic	3.99680288865056e-15	simple_aae		affected		R69G	single base exchange	rs2455069		show file
CD33	polymorphism_automatic	3.99680288865056e-15	simple_aae		affected		R69G	single base exchange	rs2455069		show file
CD33	polymorphism_automatic	1.18544580830493e-05	without_aae		affected			single base exchange	rs2455069		show file
CD33	polymorphism_automatic	1.18544580830493e-05	without_aae		affected			single base exchange	rs2455069		show file

Taster files

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

frameshift

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

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000011375

Mmulatta

not conserved

ENSMMUG00000009486

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000039013

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
18	259	TOPO_DOM	Extracellular (Potential).	lost
19	135	DOMAIN	Ig-like V-type.	lost
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	MOD_RES	Phosphotyrosine.	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)

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

strand

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

0.70 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
back to results table

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

ENST00000391796

Genbank transcript ID

NM_001177608

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

frameshift

known variant

Reference ID: rs2455069

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

regulatory features

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

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000011375

Mmulatta

not conserved

ENSMMUG00000009486

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000039013

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
18	259	TOPO_DOM	Extracellular (Potential).	lost
19	135	DOMAIN	Ig-like V-type.	lost
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	MOD_RES	Phosphotyrosine.	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)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

933 / 933

position (AA) of stopcodon in wt / mu AA sequence

311 / 311

position of stopcodon in wt / mu cDNA

973 / 973

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

965

theoretical NMD boundary in CDS

874

length of CDS

933

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

mutated AA sequence

speed

0.77 s

mutation t@sting

documentation

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

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

0.58 s

mutation t@sting

documentation

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

ENST00000436584

Genbank transcript ID

N/A

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

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

56 / 56

chromosome

strand

last intron/exon boundary

517

theoretical NMD boundary in CDS

411

length of CDS

639

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

mutated AA sequence

N/A

speed

0.53 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems