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 5.232385 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HLA-DQA1	polymorphism_automatic	4.20469879920393e-05	simple_aae				F238L	single base exchange	rs1048430		show file
HLA-DQA1	polymorphism_automatic	4.20469879920393e-05	simple_aae				F238L	single base exchange	rs1048430		show file
HLA-DQA1	polymorphism_automatic	4.20469879920393e-05	simple_aae				F238L	single base exchange	rs1048430		show file
HLA-DQA1	polymorphism_automatic	4.20469879920393e-05	simple_aae				F238L	single base exchange	rs1048430		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999957953012008 (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)

chr6:32610487C>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.714C>G
cDNA.816C>G
g.14532C>G

AA changes

F238L Score: 22 explain score(s)

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

238

frameshift

known variant

Reference ID: rs1048430

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	4121	23884	28005

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)	2.548	0.139
	-0.566	0.136
(flanking)	2.548	0.666

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000014605

109

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036594

239

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000001832

229

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000031520

128

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost

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

714

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

816

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

14532

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

32610487

original gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

original cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

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

1.12 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: 0.999957953012008 (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)

chr6:32610487C>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.714C>G
cDNA.816C>G
g.14532C>G

AA changes

F238L Score: 22 explain score(s)

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

238

frameshift

known variant

Reference ID: rs1048430

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	4121	23884	28005

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.548	0.139
	-0.566	0.136
(flanking)	2.548	0.666

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000014605

109

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036594

239

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000001832

229

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000031520

128

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost

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

714

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

816

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

14532

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

32610487

original gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

original cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

wildtype AA sequence

mutated AA sequence

speed

1.09 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999957953012008 (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)

chr6:32610487C>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.714C>G
cDNA.772C>G
g.14532C>G

AA changes

F238L Score: 22 explain score(s)

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

238

frameshift

known variant

Reference ID: rs1048430

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	4121	23884	28005

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.548	0.139
	-0.566	0.136
(flanking)	2.548	0.666

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000014605

109

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036594

239

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000001832

229

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000031520

128

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost

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

714

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

772

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

14532

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

32610487

original gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

original cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

wildtype AA sequence

mutated AA sequence

speed

1.03 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999957953012008 (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)

chr6:32610487C>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.714C>G
cDNA.753C>G
g.14532C>G

AA changes

F238L Score: 22 explain score(s)

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

238

frameshift

known variant

Reference ID: rs1048430

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	4121	23884	28005

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.548	0.139
	-0.566	0.136
(flanking)	2.548	0.666

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

splice sites

no abrogation of potential splice sites

distance from splice site

101

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000014605

109

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036594

239

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000001832

229

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000031520

128

protein features

start (aa)	end (aa)	feature	details
217	239	TRANSMEM	Helical; (Potential).	lost

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

714

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

753

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

14532

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

32610487

original gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered gDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

original cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTCATCATCCAAGGCCTGCGTTC

altered cDNA sequence snippet

ATTGTGGTGGGCACTGTCTTGATCATCCAAGGCCTGCGTTC

wildtype AA sequence

mutated AA sequence

speed

0.98 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