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: ENST00000261623
Querying Taster for transcript #2: ENST00000567174
Querying Taster for transcript #3: ENST00000569359
MT speed 0 s - this script 3.717767 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CYBA	disease_causing_automatic	0.999998364863648	simple_aae		affected	0	G24R	single base exchange	rs28941476		show file
CYBA	disease_causing_automatic	0.999998364863648	simple_aae		affected	0	G24R	single base exchange	rs28941476		show file
CYBA	disease_causing_automatic	0.999998364863648	simple_aae		affected	0	G24R	single base exchange	rs28941476		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998364863648 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001112)
known disease mutation: rs2265 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:88714511C>TN/A show variant in all transcripts IGV

HGNC symbol

CYBA

Ensembl transcript ID

ENST00000261623

Genbank transcript ID

NM_000101

UniProt peptide

P13498

alteration type

single base exchange

alteration region

CDS

DNA changes

c.70G>A
cDNA.209G>A
g.3050G>A

AA changes

G24R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs28941476

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs2265 (pathogenic for Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative|Chronic granulomatous disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001112)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001112)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001112)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.803	0.999
	4.278	1
(flanking)	-0.354	0.966

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	3051	wt: 0.4490 / mu: 0.4613 (marginal change - not scored)	wt: CCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCTG mu: CCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCTG	ccgg\|GGGC
Acc marginally increased	3050	wt: 0.9105 / mu: 0.9283 (marginal change - not scored)	wt: TCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCT mu: TCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCT	accg\|GGGG
Acc increased	3047	wt: 0.62 / mu: 0.71	wt: TTCTCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACA mu: TTCTCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACA	atca\|CCGG
Donor gained	3050	0.62	mu: TCACCAGGGGCATCG	ACCA\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000008458

Mmulatta

all identical

ENSMMUG00000014325

Fcatus

not conserved

ENSFCAG00000006655

Mmusculus

all identical

ENSMUSG00000006519

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018180

Drerio

all identical

ENSDARG00000018283

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017431

protein features

start (aa)	end (aa)	feature	details
91	127	INTRAMEM		might get lost (downstream of altered splice site)
94	94	METAL	Iron (heme axial ligand) (Potential).	might get lost (downstream of altered splice site)
133	189	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
147	147	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
157	157	MUTAGEN	P->Q: Loss of interaction with NOXO1.	might get lost (downstream of altered splice site)
161	165	HELIX		might get lost (downstream of altered splice site)
168	168	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

588 / 588

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

196 / 196

position of stopcodon in wt / mu cDNA

727 / 727

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

140 / 140

chromosome

strand

-1

last intron/exon boundary

509

theoretical NMD boundary in CDS

319

length of CDS

588

coding sequence (CDS) position

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

209

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

3050

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

88714511

original gDNA sequence snippet

TCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCT

altered gDNA sequence snippet

TCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCT

original cDNA sequence snippet

CCGGCCTGATCCTCATCACCGGGGGCATCGTGGCCACAGCT

altered cDNA sequence snippet

CCGGCCTGATCCTCATCACCAGGGGCATCGTGGCCACAGCT

wildtype AA sequence

MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLAAVRGEQ WTPIEPKPRE RPQIGGTIKQ PPSNPPPRPP AEARKKPSEE EAAVAAGGPP
GGPQVNPIPV TDEVV*

mutated AA sequence

MGQIEWAMWA NEQALASGLI LITRGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLAAVRGEQ WTPIEPKPRE RPQIGGTIKQ PPSNPPPRPP AEARKKPSEE EAAVAAGGPP
GGPQVNPIPV TDEVV*

speed

0.93 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

disease causing

Model: simple_aae, prob: 0.999998364863648 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001112)
known disease mutation: rs2265 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:88714511C>TN/A show variant in all transcripts IGV

HGNC symbol

CYBA

Ensembl transcript ID

ENST00000567174

Genbank transcript ID

N/A

UniProt peptide

P13498

alteration type

single base exchange

alteration region

CDS

DNA changes

c.70G>A
cDNA.98G>A
g.3050G>A

AA changes

G24R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs28941476

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.803	0.999
	4.278	1
(flanking)	-0.354	0.966

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	3051	wt: 0.4490 / mu: 0.4613 (marginal change - not scored)	wt: CCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCTG mu: CCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCTG	ccgg\|GGGC
Acc marginally increased	3050	wt: 0.9105 / mu: 0.9283 (marginal change - not scored)	wt: TCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCT mu: TCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCT	accg\|GGGG
Acc increased	3047	wt: 0.62 / mu: 0.71	wt: TTCTCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACA mu: TTCTCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACA	atca\|CCGG
Donor gained	3050	0.62	mu: TCACCAGGGGCATCG	ACCA\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000008458

Mmulatta

all identical

ENSMMUG00000014325

Fcatus

not conserved

ENSFCAG00000006655

Mmusculus

all identical

ENSMUSG00000006519

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018180

Drerio

all identical

ENSDARG00000018283

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017431

protein features

start (aa)	end (aa)	feature	details
91	127	INTRAMEM		might get lost (downstream of altered splice site)
94	94	METAL	Iron (heme axial ligand) (Potential).	might get lost (downstream of altered splice site)
133	189	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
147	147	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
157	157	MUTAGEN	P->Q: Loss of interaction with NOXO1.	might get lost (downstream of altered splice site)
161	165	HELIX		might get lost (downstream of altered splice site)
168	168	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

633 / 633

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

211 / 211

position of stopcodon in wt / mu cDNA

661 / 661

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

29 / 29

chromosome

strand

-1

last intron/exon boundary

398

theoretical NMD boundary in CDS

319

length of CDS

633

coding sequence (CDS) position

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

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

3050

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

88714511

original gDNA sequence snippet

TCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCT

altered gDNA sequence snippet

TCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCT

original cDNA sequence snippet

CCGGCCTGATCCTCATCACCGGGGGCATCGTGGCCACAGCT

altered cDNA sequence snippet

CCGGCCTGATCCTCATCACCAGGGGCATCGTGGCCACAGCT

wildtype AA sequence

MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLSQVPPAR RGNCPPLAVR LLVCVRGKGA ALSVYAFRVW KWSSVSSLTD LPPAELSFRT
PSCCQVLIWA VALFSGGHPH PPRLPAATHS *

mutated AA sequence

MGQIEWAMWA NEQALASGLI LITRGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLSQVPPAR RGNCPPLAVR LLVCVRGKGA ALSVYAFRVW KWSSVSSLTD LPPAELSFRT
PSCCQVLIWA VALFSGGHPH PPRLPAATHS *

speed

1.03 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998364863648 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001112)
known disease mutation: rs2265 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:88714511C>TN/A show variant in all transcripts IGV

HGNC symbol

CYBA

Ensembl transcript ID

ENST00000569359

Genbank transcript ID

N/A

UniProt peptide

P13498

alteration type

single base exchange

alteration region

CDS

DNA changes

c.70G>A
cDNA.87G>A
g.3050G>A

AA changes

G24R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs28941476

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.803	0.999
	4.278	1
(flanking)	-0.354	0.966

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	3051	wt: 0.4490 / mu: 0.4613 (marginal change - not scored)	wt: CCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCTG mu: CCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCTG	ccgg\|GGGC
Acc marginally increased	3050	wt: 0.9105 / mu: 0.9283 (marginal change - not scored)	wt: TCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCT mu: TCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCT	accg\|GGGG
Acc increased	3047	wt: 0.62 / mu: 0.71	wt: TTCTCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACA mu: TTCTCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACA	atca\|CCGG
Donor gained	3050	0.62	mu: TCACCAGGGGCATCG	ACCA\|gggg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000008458

Mmulatta

all identical

ENSMMUG00000014325

Fcatus

not conserved

ENSFCAG00000006655

Mmusculus

all identical

ENSMUSG00000006519

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000018180

Drerio

all identical

ENSDARG00000018283

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017431

protein features

start (aa)	end (aa)	feature	details
91	127	INTRAMEM		might get lost (downstream of altered splice site)
94	94	METAL	Iron (heme axial ligand) (Potential).	might get lost (downstream of altered splice site)
133	189	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
147	147	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
157	157	MUTAGEN	P->Q: Loss of interaction with NOXO1.	might get lost (downstream of altered splice site)
161	165	HELIX		might get lost (downstream of altered splice site)
168	168	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

387 / 387

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

129 / 129

position of stopcodon in wt / mu cDNA

404 / 404

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

18 / 18

chromosome

strand

-1

last intron/exon boundary

305

theoretical NMD boundary in CDS

237

length of CDS

387

coding sequence (CDS) position

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

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

3050

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

88714511

original gDNA sequence snippet

TCCCCGCAGTCCTCATCACCGGGGGCATCGTGGCCACAGCT

altered gDNA sequence snippet

TCCCCGCAGTCCTCATCACCAGGGGCATCGTGGCCACAGCT

original cDNA sequence snippet

CCGGCCTGATCCTCATCACCGGGGGCATCGTGGCCACAGCT

altered cDNA sequence snippet

CCGGCCTGATCCTCATCACCAGGGGCATCGTGGCCACAGCT

wildtype AA sequence

MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLVSGAL*

mutated AA sequence

MGQIEWAMWA NEQALASGLI LITRGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLVSGAL*

speed

0.59 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems