MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000399082
Querying Taster for transcript #2: ENST00000399079
Querying Taster for transcript #3: ENST00000374943
Querying Taster for transcript #4: ENST00000434651
Querying Taster for transcript #5: ENST00000399084
MT speed 0 s - this script 4.36259 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-DQB1	polymorphism_automatic	2.26934104841092e-09	simple_aae				T127I	single base exchange	rs1130399		show file
HLA-DQB1	polymorphism_automatic	1.70676840438588e-08	simple_aae				T217I	single base exchange	rs1130399		show file
HLA-DQB1	polymorphism_automatic	1.70676840438588e-08	simple_aae				T217I	single base exchange	rs1130399		show file
HLA-DQB1	polymorphism_automatic	1.70676840438588e-08	simple_aae				T217I	single base exchange	rs1130399		show file
HLA-DQB1	polymorphism_automatic	1.70676840438588e-08	simple_aae				T217I	single base exchange	rs1130399		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999997730659 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:32629755G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQB1

Ensembl transcript ID

ENST00000399082

Genbank transcript ID

N/A

UniProt peptide

P01920

alteration type

single base exchange

alteration region

CDS

DNA changes

c.380C>T
cDNA.425C>T
g.6406C>T

AA changes

T127I Score: 89 explain score(s)

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

127

frameshift

known variant

Reference ID: rs1130399

database	homozygous (A/A)	heterozygous	allele carriers
1000G	189	896	1085
ExAC	3561	18858	22419

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.24	0.002
	0.153	0.006
(flanking)	0.226	0.022

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 marginally increased	6407	wt: 0.9821 / mu: 0.9867 (marginal change - not scored)	wt: ATCACCGTGGAGTGG mu: ATCATCGTGGAGTGG	CACC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

127

mutated

not conserved

127

Ptroglodytes

all identical

ENSPTRG00000018018

217

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000073421

213

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000079105

202

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
33	230	TOPO_DOM	Extracellular (Potential).	lost
127	220	REGION	Beta-2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

405 / 405

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

135 / 135

position of stopcodon in wt / mu cDNA

450 / 450

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

46 / 46

chromosome

strand

-1

last intron/exon boundary

437

theoretical NMD boundary in CDS

341

length of CDS

405

coding sequence (CDS) position

380

cDNA position
(for ins/del: last normal base / first normal base)

425

gDNA position
(for ins/del: last normal base / first normal base)

6406

chromosomal position
(for ins/del: last normal base / first normal base)

32629755

original gDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGTAAGGGGA

altered gDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGTAAGGGGA

original cDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGGCTTCTGC

altered cDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGGCTTCTGC

wildtype AA sequence

MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS
VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP
SLQSPITVEW RLLH*

mutated AA sequence

MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS
VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP
SLQSPIIVEW RLLH*

speed

0.46 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: 0.999999982932316 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:32629755G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQB1

Ensembl transcript ID

ENST00000399079

Genbank transcript ID

N/A

UniProt peptide

P01920

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650C>T
cDNA.707C>T
g.6406C>T

AA changes

T217I Score: 89 explain score(s)

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

217

frameshift

known variant

Reference ID: rs1130399

database	homozygous (A/A)	heterozygous	allele carriers
1000G	189	896	1085
ExAC	3561	18858	22419

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.24	0.002
	0.153	0.006
(flanking)	0.226	0.022

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 marginally increased	6407	wt: 0.9821 / mu: 0.9867 (marginal change - not scored)	wt: ATCACCGTGGAGTGG mu: ATCATCGTGGAGTGG	CACC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

not conserved

217

Ptroglodytes

all identical

ENSPTRG00000018018

217

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000073421

213

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000079105

202

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
33	230	TOPO_DOM	Extracellular (Potential).	lost
127	220	REGION	Beta-2.	lost
129	233	DOMAIN	Ig-like C1-type.	lost
216	220	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

675 / 675

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

225 / 225

position of stopcodon in wt / mu cDNA

732 / 732

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

58 / 58

chromosome

strand

-1

last intron/exon boundary

719

theoretical NMD boundary in CDS

611

length of CDS

675

coding sequence (CDS) position

650

cDNA position
(for ins/del: last normal base / first normal base)

707

gDNA position
(for ins/del: last normal base / first normal base)

6406

chromosomal position
(for ins/del: last normal base / first normal base)

32629755

original gDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGTAAGGGGA

altered gDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGTAAGGGGA

original cDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGGCTTCTGC

altered cDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGGCTTCTGC

wildtype AA sequence

MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RLLH*

mutated AA sequence

speed

0.44 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999982932316 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:32629755G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQB1

Ensembl transcript ID

ENST00000374943

Genbank transcript ID

NM_001243961

UniProt peptide

P01920

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650C>T
cDNA.727C>T
g.6406C>T

AA changes

T217I Score: 89 explain score(s)

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

217

frameshift

known variant

Reference ID: rs1130399

database	homozygous (A/A)	heterozygous	allele carriers
1000G	189	896	1085
ExAC	3561	18858	22419

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.24	0.002
	0.153	0.006
(flanking)	0.226	0.022

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 marginally increased	6407	wt: 0.9821 / mu: 0.9867 (marginal change - not scored)	wt: ATCACCGTGGAGTGG mu: ATCATCGTGGAGTGG	CACC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

not conserved

217

Ptroglodytes

all identical

ENSPTRG00000018018

217

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000073421

213

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000079105

202

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
33	230	TOPO_DOM	Extracellular (Potential).	lost
127	220	REGION	Beta-2.	lost
129	233	DOMAIN	Ig-like C1-type.	lost
216	220	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

810 / 810

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

270 / 270

position of stopcodon in wt / mu cDNA

887 / 887

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

78 / 78

chromosome

strand

-1

last intron/exon boundary

874

theoretical NMD boundary in CDS

746

length of CDS

810

coding sequence (CDS) position

650

cDNA position
(for ins/del: last normal base / first normal base)

727

gDNA position
(for ins/del: last normal base / first normal base)

6406

chromosomal position
(for ins/del: last normal base / first normal base)

32629755

original gDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGTAAGGGGA

altered gDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGTAAGGGGA

original cDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGGGCTCAGT

altered cDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGGGCTCAGT

wildtype AA sequence

mutated AA sequence

speed

0.91 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999982932316 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:32629755G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQB1

Ensembl transcript ID

ENST00000434651

Genbank transcript ID

NM_002123

UniProt peptide

P01920

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650C>T
cDNA.737C>T
g.6406C>T

AA changes

T217I Score: 89 explain score(s)

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

217

frameshift

known variant

Reference ID: rs1130399

database	homozygous (A/A)	heterozygous	allele carriers
1000G	189	896	1085
ExAC	3561	18858	22419

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.24	0.002
	0.153	0.006
(flanking)	0.226	0.022

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 marginally increased	6407	wt: 0.9821 / mu: 0.9867 (marginal change - not scored)	wt: ATCACCGTGGAGTGG mu: ATCATCGTGGAGTGG	CACC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

not conserved

217

Ptroglodytes

all identical

ENSPTRG00000018018

217

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000073421

213

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000079105

202

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
33	230	TOPO_DOM	Extracellular (Potential).	lost
127	220	REGION	Beta-2.	lost
129	233	DOMAIN	Ig-like C1-type.	lost
216	220	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

786 / 786

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

262 / 262

position of stopcodon in wt / mu cDNA

873 / 873

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

88 / 88

chromosome

strand

-1

last intron/exon boundary

860

theoretical NMD boundary in CDS

722

length of CDS

786

coding sequence (CDS) position

650

cDNA position
(for ins/del: last normal base / first normal base)

737

gDNA position
(for ins/del: last normal base / first normal base)

6406

chromosomal position
(for ins/del: last normal base / first normal base)

32629755

original gDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGTAAGGGGA

altered gDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGTAAGGGGA

original cDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGGGCTCAGT

altered cDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGGGCTCAGT

wildtype AA sequence

mutated AA sequence

speed

0.51 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999982932316 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:32629755G>AN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQB1

Ensembl transcript ID

ENST00000399084

Genbank transcript ID

N/A

UniProt peptide

P01920

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650C>T
cDNA.829C>T
g.6406C>T

AA changes

T217I Score: 89 explain score(s)

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

217

frameshift

known variant

Reference ID: rs1130399

database	homozygous (A/A)	heterozygous	allele carriers
1000G	189	896	1085
ExAC	3561	18858	22419

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.24	0.002
	0.153	0.006
(flanking)	0.226	0.022

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 marginally increased	6407	wt: 0.9821 / mu: 0.9867 (marginal change - not scored)	wt: ATCACCGTGGAGTGG mu: ATCATCGTGGAGTGG	CACC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

not conserved

217

Ptroglodytes

all identical

ENSPTRG00000018018

217

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000073421

213

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000079105

202

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
33	230	TOPO_DOM	Extracellular (Potential).	lost
127	220	REGION	Beta-2.	lost
129	233	DOMAIN	Ig-like C1-type.	lost
216	220	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

786 / 786

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

262 / 262

position of stopcodon in wt / mu cDNA

965 / 965

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

180 / 180

chromosome

strand

-1

last intron/exon boundary

952

theoretical NMD boundary in CDS

722

length of CDS

786

coding sequence (CDS) position

650

cDNA position
(for ins/del: last normal base / first normal base)

829

gDNA position
(for ins/del: last normal base / first normal base)

6406

chromosomal position
(for ins/del: last normal base / first normal base)

32629755

original gDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGTAAGGGGA

altered gDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGTAAGGGGA

original cDNA sequence snippet

CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGGGCTCAGT

altered cDNA sequence snippet

CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGGGCTCAGT

wildtype AA sequence

mutated AA sequence

speed

0.92 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

mutation t@sting

Prediction

polymorphism

Problems