MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000507039
Querying Taster for transcript #2: ENST00000340083
Querying Taster for transcript #3: ENST00000389653
MT speed 0 s - this script 3.612891 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DOK7	polymorphism_automatic	2.6104119976722e-09	simple_aae		affected		Q296R	single base exchange	rs6811423		show file
DOK7	polymorphism_automatic	2.6104119976722e-09	simple_aae		affected		Q296R	single base exchange	rs6811423		show file
DOK7	polymorphism_automatic	0.000270187798031007	without_aae		affected			single base exchange	rs6811423		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999997389588 (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)

chr4:3494600A>GN/A show variant in all transcripts IGV

HGNC symbol

DOK7

Ensembl transcript ID

ENST00000340083

Genbank transcript ID

NM_173660

UniProt peptide

Q18PE1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.887A>G
cDNA.952A>G
g.29568A>G

AA changes

Q296R Score: 43 explain score(s)

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

296

frameshift

known variant

Reference ID: rs6811423

database	homozygous (G/G)	heterozygous	allele carriers
1000G	201	690	891
ExAC	2920	17435	20355

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.445	0.112
	-0.069	0.119
(flanking)	0.358	0.348

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 increased	29558	wt: 0.36 / mu: 0.50	wt: AGCAATCCTCGTCGTCAGCCAGCACGTCACAGGAGGGGCCT mu: AGCAATCCTCGTCGTCAGCCAGCACGTCACGGGAGGGGCCT	gcca\|GCAC
Acc increased	29562	wt: 0.43 / mu: 0.47	wt: ATCCTCGTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGAC mu: ATCCTCGTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGAC	gcac\|GTCA
Donor increased	29562	wt: 0.54 / mu: 0.99	wt: CAGCACGTCACAGGA mu: CAGCACGTCACGGGA	GCAC\|gtca
Donor gained	29567	0.97	mu: CGTCACGGGAGGGGC	TCAC\|ggga

distance from splice site

115

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

296

mutated

all conserved

296

Ptroglodytes

all identical

ENSPTRG00000015858

151

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000044716

259

Ggallus

not conserved

ENSGALG00000015615

255

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000060236

306

HPTPVEPPPPPP

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
262	359	COMPBIAS	Ser-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1515 / 1515

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

505 / 505

position of stopcodon in wt / mu cDNA

1580 / 1580

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

66 / 66

chromosome

strand

last intron/exon boundary

838

theoretical NMD boundary in CDS

722

length of CDS

1515

coding sequence (CDS) position

887

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

952

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

29568

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

3494600

original gDNA sequence snippet

GTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGACCAGCAG

altered gDNA sequence snippet

GTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGACCAGCAG

original cDNA sequence snippet

GTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGACCAGCAG

altered cDNA sequence snippet

GTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGACCAGCAG

wildtype AA sequence

MTEAALVEGQ VKLRDGKKWK SRWLVLRKPS PVADCLLMLV YKDKSERIKG LRERSSLTLE
DICGLEPGLP YEGLVHTLAI VCLSQAIMLG FDSHEAMCAW DARIRYALGE VHRFHVTVAP
GTKLESGPAT LHLCNDVLVL ARDIPPAVTG QWKLSDLRRY GAVPSGFIFE GGTRCGYWAG
VFFLSSAEGE QISFLFDCIV RGISPTKGPF GLRPVLPDPS PPGPSTVEER VAQEALETLQ
LEKRLSLLSH AGRPGSGGDD RSLSSSSSEA SHLDVSASSR LTAWPEQSSS SASTSQEGPR
PAAAQAAGEA MVGASRPPPK PLRPRQLQEV GRQSSSDSGI ATGSHSSYSS SLSSYAGSSL
DVWRATDELG SLLSLPAAGA PEPSLCTCLP GTVEYQVPTS LRAHYDTPRS LCLAPRDHSP
PSQGSPGNSA ARDSGGQTSA GCPSGWLGTR RRGLVMEAPQ GSEATLPGPA PGEPWEAGGP
HAGPPPAFFS ACPVCGGLKV NPPP*

mutated AA sequence

MTEAALVEGQ VKLRDGKKWK SRWLVLRKPS PVADCLLMLV YKDKSERIKG LRERSSLTLE
DICGLEPGLP YEGLVHTLAI VCLSQAIMLG FDSHEAMCAW DARIRYALGE VHRFHVTVAP
GTKLESGPAT LHLCNDVLVL ARDIPPAVTG QWKLSDLRRY GAVPSGFIFE GGTRCGYWAG
VFFLSSAEGE QISFLFDCIV RGISPTKGPF GLRPVLPDPS PPGPSTVEER VAQEALETLQ
LEKRLSLLSH AGRPGSGGDD RSLSSSSSEA SHLDVSASSR LTAWPEQSSS SASTSREGPR
PAAAQAAGEA MVGASRPPPK PLRPRQLQEV GRQSSSDSGI ATGSHSSYSS SLSSYAGSSL
DVWRATDELG SLLSLPAAGA PEPSLCTCLP GTVEYQVPTS LRAHYDTPRS LCLAPRDHSP
PSQGSPGNSA ARDSGGQTSA GCPSGWLGTR RRGLVMEAPQ GSEATLPGPA PGEPWEAGGP
HAGPPPAFFS ACPVCGGLKV NPPP*

speed

0.44 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: 0.999999997389588 (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)

chr4:3494600A>GN/A show variant in all transcripts IGV

HGNC symbol

DOK7

Ensembl transcript ID

ENST00000389653

Genbank transcript ID

N/A

UniProt peptide

Q18PE1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.887A>G
cDNA.957A>G
g.29568A>G

AA changes

Q296R Score: 43 explain score(s)

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

296

frameshift

known variant

Reference ID: rs6811423

database	homozygous (G/G)	heterozygous	allele carriers
1000G	201	690	891
ExAC	2920	17435	20355

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.445	0.112
	-0.069	0.119
(flanking)	0.358	0.348

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 increased	29558	wt: 0.36 / mu: 0.50	wt: AGCAATCCTCGTCGTCAGCCAGCACGTCACAGGAGGGGCCT mu: AGCAATCCTCGTCGTCAGCCAGCACGTCACGGGAGGGGCCT	gcca\|GCAC
Acc increased	29562	wt: 0.43 / mu: 0.47	wt: ATCCTCGTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGAC mu: ATCCTCGTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGAC	gcac\|GTCA
Donor increased	29562	wt: 0.54 / mu: 0.99	wt: CAGCACGTCACAGGA mu: CAGCACGTCACGGGA	GCAC\|gtca
Donor gained	29567	0.97	mu: CGTCACGGGAGGGGC	TCAC\|ggga

distance from splice site

115

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

296

mutated

all conserved

296

Ptroglodytes

all identical

ENSPTRG00000015858

151

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000044716

259

Ggallus

not conserved

ENSGALG00000015615

255

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000060236

306

HPTPVEPPPPPP

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
262	359	COMPBIAS	Ser-rich.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1827 / 1827

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

609 / 609

position of stopcodon in wt / mu cDNA

1897 / 1897

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

71 / 71

chromosome

strand

last intron/exon boundary

1764

theoretical NMD boundary in CDS

1643

length of CDS

1827

coding sequence (CDS) position

887

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

957

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

29568

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

3494600

original gDNA sequence snippet

GTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGACCAGCAG

altered gDNA sequence snippet

GTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGACCAGCAG

original cDNA sequence snippet

GTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGACCAGCAG

altered cDNA sequence snippet

GTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGACCAGCAG

wildtype AA sequence

mutated AA sequence

MTEAALVEGQ VKLRDGKKWK SRWLVLRKPS PVADCLLMLV YKDKSERIKG LRERSSLTLE
DICGLEPGLP YEGLVHTLAI VCLSQAIMLG FDSHEAMCAW DARIRYALGE VHRFHVTVAP
GTKLESGPAT LHLCNDVLVL ARDIPPAVTG QWKLSDLRRY GAVPSGFIFE GGTRCGYWAG
VFFLSSAEGE QISFLFDCIV RGISPTKGPF GLRPVLPDPS PPGPSTVEER VAQEALETLQ
LEKRLSLLSH AGRPGSGGDD RSLSSSSSEA SHLDVSASSR LTAWPEQSSS SASTSREGPR
PAAAQAAGEA MVGASRPPPK PLRPRQLQEV GRQSSSDSGI ATGSHSSYSS SLSSYAGSSL
DVWRATDELG SLLSLPAAGA PEPSLCTCLP GTVEYQVPTS LRAHYDTPRS LCLAPRDHSP
PSQGSPGNSA ARDSGGQTSA GCPSGWLGTR RRGLVMEAPQ GSEATLPGPA PGEPWEAGGP
HAGPPPAFFS ACPVCGGLKG AAASAPGPAT AHSGSPGPVA VDSPGPERPR GESPTYVNIP
VSPSSRKQLH YMGLELQEAS EGVRGAGASL YAQIDIMATE TAHRVGVRHA RAREEQLSEL
EQRKAAPQ*

speed

0.86 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999729812201969 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:3494600A>GN/A show variant in all transcripts IGV

HGNC symbol

DOK7

Ensembl transcript ID

ENST00000507039

Genbank transcript ID

NM_001164673

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.941A>G
g.29568A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs6811423

database	homozygous (G/G)	heterozygous	allele carriers
1000G	201	690	891
ExAC	2920	17435	20355

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.445	0.112
	-0.069	0.119
(flanking)	0.358	0.348

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

splice sites

splice site change occurs after stopcodon (at aa 288) splice site change occurs after stopcodon (at aa 290) splice site change occurs after stopcodon (at aa 291)

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	29558	wt: 0.36 / mu: 0.50	wt: AGCAATCCTCGTCGTCAGCCAGCACGTCACAGGAGGGGCCT mu: AGCAATCCTCGTCGTCAGCCAGCACGTCACGGGAGGGGCCT	gcca\|GCAC
Acc increased	29562	wt: 0.43 / mu: 0.47	wt: ATCCTCGTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGAC mu: ATCCTCGTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGAC	gcac\|GTCA
Donor increased	29562	wt: 0.54 / mu: 0.99	wt: CAGCACGTCACAGGA mu: CAGCACGTCACGGGA	GCAC\|gtca
Donor gained	29567	0.97	mu: CGTCACGGGAGGGGC	TCAC\|ggga

distance from splice site

115

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

66 / 66

chromosome

strand

last intron/exon boundary

827

theoretical NMD boundary in CDS

711

length of CDS

768

coding sequence (CDS) position

N/A

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

941

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

29568

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

3494600

original gDNA sequence snippet

GTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGACCAGCAG

altered gDNA sequence snippet

GTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGACCAGCAG

original cDNA sequence snippet

GTCGTCAGCCAGCACGTCACAGGAGGGGCCTAGACCAGCAG

altered cDNA sequence snippet

GTCGTCAGCCAGCACGTCACGGGAGGGGCCTAGACCAGCAG

wildtype AA sequence

mutated AA sequence

N/A

speed

0.45 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems