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: ENST00000343139
Querying Taster for transcript #2: ENST00000395364
Querying Taster for transcript #3: ENST00000395363
Querying Taster for transcript #4: ENST00000374949
MT speed 0 s - this script 5.010532 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-DQA1	polymorphism_automatic	3.12709714012094e-07	simple_aae		affected		M230V	single base exchange	rs9260		show file
HLA-DQA1	polymorphism_automatic	3.12709714012094e-07	simple_aae		affected		M230V	single base exchange	rs9260		show file
HLA-DQA1	polymorphism_automatic	3.12709714012094e-07	simple_aae		affected		M230V	single base exchange	rs9260		show file
HLA-DQA1	polymorphism_automatic	3.12709714012094e-07	simple_aae		affected		M230V	single base exchange	rs9260		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999687290286 (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)

chr6:32610461A>GN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQA1

Ensembl transcript ID

ENST00000395364

Genbank transcript ID

N/A

UniProt peptide

P01909

alteration type

single base exchange

alteration region

CDS

DNA changes

c.688A>G
cDNA.790A>G
g.14506A>G

AA changes

M230V Score: 21 explain score(s)

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

230

frameshift

known variant

Reference ID: rs9260

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1680	693	2373
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.019	0.341
	0.217	0.429
(flanking)	1.228	0.7

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
Acc marginally increased	14500	wt: 0.4308 / mu: 0.4354 (marginal change - not scored)	wt: GTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTG mu: GTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTG	gtgg\|GCCT
Acc marginally increased	14496	wt: 0.3512 / mu: 0.3826 (marginal change - not scored)	wt: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGT mu: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGT	gtct\|GTGG
Acc increased	14498	wt: 0.74 / mu: 0.81	wt: CTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGG mu: CTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGG	ctgt\|GGGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

230

mutated

all conserved

230

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000014605

101

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000036594

231

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000001832

221

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000031520

120

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost
240	254	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

768 / 768

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

256 / 256

position of stopcodon in wt / mu cDNA

870 / 870

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

103 / 103

chromosome

strand

last intron/exon boundary

891

theoretical NMD boundary in CDS

738

length of CDS

768

coding sequence (CDS) position

688

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

790

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

14506

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

32610461

original gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

original cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

wildtype AA sequence

MILNKALLLG ALALTTVMSP CGGEDIVADH VASCGVNLYQ FYGPSGQYTH EFDGDEQFYV
DLERKETAWR WPEFSKFGGF DPQGALRNMA VAKHNLNIMI KRYNSTAATN EVPEVTVFSK
SPVTLGQPNT LICLVDNIFP PVVNITWLSN GQSVTEGVSE TSFLSKSDHS FFKISYLTFL
PSADEIYDCK VEHWGLDQPL LKHWEPEIPA PMSELTETVV CALGLSVGLM GIVVGTVFII
QGLRSVGASR HQGPL*

mutated AA sequence

speed

0.77 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: 0.999999687290286 (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)

chr6:32610461A>GN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQA1

Ensembl transcript ID

ENST00000343139

Genbank transcript ID

NM_002122

UniProt peptide

P01909

alteration type

single base exchange

alteration region

CDS

DNA changes

c.688A>G
cDNA.790A>G
g.14506A>G

AA changes

M230V Score: 21 explain score(s)

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

230

frameshift

known variant

Reference ID: rs9260

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1680	693	2373
ExAC	-	-	-

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.019	0.341
	0.217	0.429
(flanking)	1.228	0.7

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
Acc marginally increased	14500	wt: 0.4308 / mu: 0.4354 (marginal change - not scored)	wt: GTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTG mu: GTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTG	gtgg\|GCCT
Acc marginally increased	14496	wt: 0.3512 / mu: 0.3826 (marginal change - not scored)	wt: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGT mu: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGT	gtct\|GTGG
Acc increased	14498	wt: 0.74 / mu: 0.81	wt: CTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGG mu: CTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGG	ctgt\|GGGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

230

mutated

all conserved

230

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000014605

101

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000036594

231

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000001832

221

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000031520

120

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost
240	254	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

768 / 768

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

256 / 256

position of stopcodon in wt / mu cDNA

870 / 870

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

103 / 103

chromosome

strand

last intron/exon boundary

891

theoretical NMD boundary in CDS

738

length of CDS

768

coding sequence (CDS) position

688

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

790

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

14506

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

32610461

original gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

original cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

wildtype AA sequence

mutated AA sequence

speed

0.75 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999687290286 (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)

chr6:32610461A>GN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQA1

Ensembl transcript ID

ENST00000395363

Genbank transcript ID

N/A

UniProt peptide

P01909

alteration type

single base exchange

alteration region

CDS

DNA changes

c.688A>G
cDNA.746A>G
g.14506A>G

AA changes

M230V Score: 21 explain score(s)

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

230

frameshift

known variant

Reference ID: rs9260

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1680	693	2373
ExAC	-	-	-

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.019	0.341
	0.217	0.429
(flanking)	1.228	0.7

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
Acc marginally increased	14500	wt: 0.4308 / mu: 0.4354 (marginal change - not scored)	wt: GTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTG mu: GTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTG	gtgg\|GCCT
Acc marginally increased	14496	wt: 0.3512 / mu: 0.3826 (marginal change - not scored)	wt: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGT mu: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGT	gtct\|GTGG
Acc increased	14498	wt: 0.74 / mu: 0.81	wt: CTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGG mu: CTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGG	ctgt\|GGGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

230

mutated

all conserved

230

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000014605

101

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000036594

231

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000001832

221

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000031520

120

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost
240	254	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

768 / 768

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

256 / 256

position of stopcodon in wt / mu cDNA

826 / 826

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

59 / 59

chromosome

strand

last intron/exon boundary

847

theoretical NMD boundary in CDS

738

length of CDS

768

coding sequence (CDS) position

688

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

746

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

14506

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

32610461

original gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

original cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

wildtype AA sequence

mutated AA sequence

speed

0.66 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999687290286 (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)

chr6:32610461A>GN/A show variant in all transcripts IGV

HGNC symbol

HLA-DQA1

Ensembl transcript ID

ENST00000374949

Genbank transcript ID

N/A

UniProt peptide

P01909

alteration type

single base exchange

alteration region

CDS

DNA changes

c.688A>G
cDNA.727A>G
g.14506A>G

AA changes

M230V Score: 21 explain score(s)

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

230

frameshift

known variant

Reference ID: rs9260

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1680	693	2373
ExAC	-	-	-

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.019	0.341
	0.217	0.429
(flanking)	1.228	0.7

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
Acc marginally increased	14500	wt: 0.4308 / mu: 0.4354 (marginal change - not scored)	wt: GTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTG mu: GTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTG	gtgg\|GCCT
Acc marginally increased	14496	wt: 0.3512 / mu: 0.3826 (marginal change - not scored)	wt: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGT mu: GTCTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGT	gtct\|GTGG
Acc increased	14498	wt: 0.74 / mu: 0.81	wt: CTGTGCCCTGGGGTTGTCTGTGGGCCTCATGGGCATTGTGG mu: CTGTGCCCTGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGG	ctgt\|GGGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

230

mutated

all conserved

230

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000014605

101

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000036594

231

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000001832

221

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000031520

120

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost
240	254	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

768 / 768

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

256 / 256

position of stopcodon in wt / mu cDNA

807 / 807

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

40 / 40

chromosome

strand

last intron/exon boundary

653

theoretical NMD boundary in CDS

563

length of CDS

768

coding sequence (CDS) position

688

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

727

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

14506

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

32610461

original gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered gDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

original cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCATGGGCATTGTGGTGGGCACT

altered cDNA sequence snippet

TGGGGTTGTCTGTGGGCCTCGTGGGCATTGTGGTGGGCACT

wildtype AA sequence

mutated AA sequence

speed

0.75 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