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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000592383
Querying Taster for transcript #2: ENST00000253801
Querying Taster for transcript #3: ENST00000585489
MT speed 0 s - this script 4.720878 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
G6PC	disease_causing_automatic	0.999999988197877	simple_aae		affected	0	A124T	single base exchange	rs104894568		show file
G6PC	disease_causing_automatic	0.999999988197877	simple_aae		affected	0	A124T	single base exchange	rs104894568		show file
G6PC	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs104894568		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999988197877 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960670)
known disease mutation: rs12006 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:41059569G>AN/A show variant in all transcripts IGV

HGNC symbol

G6PC

Ensembl transcript ID

ENST00000585489

Genbank transcript ID

N/A

UniProt peptide

P35575

alteration type

single base exchange

alteration region

CDS

DNA changes

c.370G>A
cDNA.447G>A
g.6756G>A

AA changes

A124T Score: 58 explain score(s)

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

124

frameshift

known variant

Reference ID: rs104894568
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs12006 (pathogenic for Glycogen storage disease due to glucose-6-phosphatase deficiency type IA) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960670)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.086	0.969
	5.827	1
(flanking)	5.827	1

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 increased	6758	wt: 0.39 / mu: 0.51	wt: ACAGCAGGTGTATAC mu: ACAACAGGTGTATAC	AGCA\|ggtg
Donor gained	6756	0.86	mu: GCACAACAGGTGTAT	ACAA\|cagg
Donor gained	6754	0.43	mu: GGGCACAACAGGTGT	GCAC\|aaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

124

mutated

not conserved

124

Ptroglodytes

all identical

ENSPTRG00000009229

124

Mmulatta

all identical

ENSMMUG00000008087

124

Fcatus

all identical

ENSFCAG00000013139

124

Mmusculus

all identical

ENSMUSG00000078650

124

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013721

124

Dmelanogaster

not conserved

FBgn0031463

130

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012583

124

protein features

start (aa)	end (aa)	feature	details
118	138	TRANSMEM	Helical; (Potential).	lost
139	147	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
148	168	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
169	179	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
170	170	BINDING	Substrate (Potential).	might get lost (downstream of altered splice site)
176	176	ACT_SITE	Nucleophile.	might get lost (downstream of altered splice site)
176	176	MUTAGEN	H->A: Loss of catalytic activity.	might get lost (downstream of altered splice site)
179	179	MUTAGEN	H->A: Loss of catalytic activity.	might get lost (downstream of altered splice site)
180	202	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
192	192	CONFLICT	A -> T (in Ref. 1; AAA16222).	might get lost (downstream of altered splice site)
197	197	MUTAGEN	H->T: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
203	209	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
210	230	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
231	254	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
252	252	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
255	275	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
276	291	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
292	312	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
307	307	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
313	320	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
321	341	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
342	357	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
353	353	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

492 / 492

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

164 / 164

position of stopcodon in wt / mu cDNA

569 / 569

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

last intron/exon boundary

524

theoretical NMD boundary in CDS

396

length of CDS

492

coding sequence (CDS) position

370

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

447

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

6756

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

41059569

original gDNA sequence snippet

CTGGCCATGCCATGGGCACAGCAGGTGTATACTACGTGATG

altered gDNA sequence snippet

CTGGCCATGCCATGGGCACAACAGGTGTATACTACGTGATG

original cDNA sequence snippet

CTGGCCATGCCATGGGCACAGCAGGTGTATACTACGTGATG

altered cDNA sequence snippet

CTGGCCATGCCATGGGCACAACAGGTGTATACTACGTGATG

wildtype AA sequence

MEEGMNVLHD FGIQSTHYLQ VNYQDSQDWF ILVSVIADLR NAFYVLFPIW FHLQEAVGIK
LLWVAVIGDW LNLVFKWILF GQRPYWWVLD TDYYSNTSVP LIKQFPVTCE TGPGSPSGHA
MGTAGVYYVM VTSTLSIFQG KIKPTYRFRH CCCRNFQPHP QHL*

mutated AA sequence

MEEGMNVLHD FGIQSTHYLQ VNYQDSQDWF ILVSVIADLR NAFYVLFPIW FHLQEAVGIK
LLWVAVIGDW LNLVFKWILF GQRPYWWVLD TDYYSNTSVP LIKQFPVTCE TGPGSPSGHA
MGTTGVYYVM VTSTLSIFQG KIKPTYRFRH CCCRNFQPHP QHL*

speed

1.24 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: 0.999999988197877 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960670)
known disease mutation: rs12006 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:41059569G>AN/A show variant in all transcripts IGV

HGNC symbol

G6PC

Ensembl transcript ID

ENST00000253801

Genbank transcript ID

NM_000151

UniProt peptide

P35575

alteration type

single base exchange

alteration region

CDS

DNA changes

c.370G>A
cDNA.449G>A
g.6756G>A

AA changes

A124T Score: 58 explain score(s)

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

124

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.086	0.969
	5.827	1
(flanking)	5.827	1

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 increased	6758	wt: 0.39 / mu: 0.51	wt: ACAGCAGGTGTATAC mu: ACAACAGGTGTATAC	AGCA\|ggtg
Donor gained	6756	0.86	mu: GCACAACAGGTGTAT	ACAA\|cagg
Donor gained	6754	0.43	mu: GGGCACAACAGGTGT	GCAC\|aaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

124

mutated

not conserved

124

Ptroglodytes

all identical

ENSPTRG00000009229

124

Mmulatta

all identical

ENSMMUG00000008087

124

Fcatus

all identical

ENSFCAG00000013139

124

Mmusculus

all identical

ENSMUSG00000078650

124

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000013721

124

Dmelanogaster

not conserved

FBgn0031463

131

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012583

124

protein features

start (aa)	end (aa)	feature	details
118	138	TRANSMEM	Helical; (Potential).	lost
139	147	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
148	168	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
169	179	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
170	170	BINDING	Substrate (Potential).	might get lost (downstream of altered splice site)
176	176	ACT_SITE	Nucleophile.	might get lost (downstream of altered splice site)
176	176	MUTAGEN	H->A: Loss of catalytic activity.	might get lost (downstream of altered splice site)
179	179	MUTAGEN	H->A: Loss of catalytic activity.	might get lost (downstream of altered splice site)
180	202	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
192	192	CONFLICT	A -> T (in Ref. 1; AAA16222).	might get lost (downstream of altered splice site)
197	197	MUTAGEN	H->T: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
203	209	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
210	230	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
231	254	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
252	252	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
255	275	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
276	291	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
292	312	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
307	307	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
313	320	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
321	341	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
342	357	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
353	353	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1074 / 1074

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

358 / 358

position of stopcodon in wt / mu cDNA

1153 / 1153

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

80 / 80

chromosome

strand

last intron/exon boundary

642

theoretical NMD boundary in CDS

512

length of CDS

1074

coding sequence (CDS) position

370

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

449

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

6756

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

41059569

original gDNA sequence snippet

CTGGCCATGCCATGGGCACAGCAGGTGTATACTACGTGATG

altered gDNA sequence snippet

CTGGCCATGCCATGGGCACAACAGGTGTATACTACGTGATG

original cDNA sequence snippet

CTGGCCATGCCATGGGCACAGCAGGTGTATACTACGTGATG

altered cDNA sequence snippet

CTGGCCATGCCATGGGCACAACAGGTGTATACTACGTGATG

wildtype AA sequence

MEEGMNVLHD FGIQSTHYLQ VNYQDSQDWF ILVSVIADLR NAFYVLFPIW FHLQEAVGIK
LLWVAVIGDW LNLVFKWILF GQRPYWWVLD TDYYSNTSVP LIKQFPVTCE TGPGSPSGHA
MGTAGVYYVM VTSTLSIFQG KIKPTYRFRC LNVILWLGFW AVQLNVCLSR IYLAAHFPHQ
VVAGVLSGIA VAETFSHIHS IYNASLKKYF LITFFLFSFA IGFYLLLKGL GVDLLWTLEK
AQRWCEQPEW VHIDTTPFAS LLKNLGTLFG LGLALNSSMY RESCKGKLSK WLPFRLSSIV
ASLVLLHVFD SLKPPSQVEL VFYVLSFCKS AVVPLASVSV IPYCLAQVLG QPHKKSL*

mutated AA sequence

MEEGMNVLHD FGIQSTHYLQ VNYQDSQDWF ILVSVIADLR NAFYVLFPIW FHLQEAVGIK
LLWVAVIGDW LNLVFKWILF GQRPYWWVLD TDYYSNTSVP LIKQFPVTCE TGPGSPSGHA
MGTTGVYYVM VTSTLSIFQG KIKPTYRFRC LNVILWLGFW AVQLNVCLSR IYLAAHFPHQ
VVAGVLSGIA VAETFSHIHS IYNASLKKYF LITFFLFSFA IGFYLLLKGL GVDLLWTLEK
AQRWCEQPEW VHIDTTPFAS LLKNLGTLFG LGLALNSSMY RESCKGKLSK WLPFRLSSIV
ASLVLLHVFD SLKPPSQVEL VFYVLSFCKS AVVPLASVSV IPYCLAQVLG QPHKKSL*

speed

1.44 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM960670)
known disease mutation: rs12006 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:41059569G>AN/A show variant in all transcripts IGV

HGNC symbol

G6PC

Ensembl transcript ID

ENST00000592383

Genbank transcript ID

N/A

UniProt peptide

P35575

alteration type

single base exchange

alteration region

intron

DNA changes

g.6756G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.086	0.969
	5.827	1
(flanking)	5.827	1

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 increased	6758	wt: 0.39 / mu: 0.51	wt: ACAGCAGGTGTATAC mu: ACAACAGGTGTATAC	AGCA\|ggtg
Donor gained	6756	0.86	mu: GCACAACAGGTGTAT	ACAA\|cagg
Donor gained	6754	0.43	mu: GGGCACAACAGGTGT	GCAC\|aaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
82	117	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
118	138	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
119	119	ACT_SITE	Proton donor (Potential).	might get lost (downstream of altered splice site)
119	119	MUTAGEN	H->A: Loss of catalytic activity.	might get lost (downstream of altered splice site)
139	147	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
148	168	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
169	179	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
170	170	BINDING	Substrate (Potential).	might get lost (downstream of altered splice site)
176	176	MUTAGEN	H->A: Loss of catalytic activity.	might get lost (downstream of altered splice site)
176	176	ACT_SITE	Nucleophile.	might get lost (downstream of altered splice site)
179	179	MUTAGEN	H->A: Loss of catalytic activity.	might get lost (downstream of altered splice site)
180	202	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
192	192	CONFLICT	A -> T (in Ref. 1; AAA16222).	might get lost (downstream of altered splice site)
197	197	MUTAGEN	H->T: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
203	209	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
210	230	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
231	254	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
252	252	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
255	275	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
276	291	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
292	312	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
307	307	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)
313	320	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
321	341	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
342	357	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
353	353	MUTAGEN	H->A: Partial loss of catalytic activity.	might get lost (downstream of altered splice site)

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

81 / 81

chromosome

strand

last intron/exon boundary

566

theoretical NMD boundary in CDS

435

length of CDS

531

coding sequence (CDS) position

N/A

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

N/A

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

6756

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

41059569

original gDNA sequence snippet

CTGGCCATGCCATGGGCACAGCAGGTGTATACTACGTGATG

altered gDNA sequence snippet

CTGGCCATGCCATGGGCACAACAGGTGTATACTACGTGATG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEEGMNVLHD FGIQSTHYLQ VNYQDSQDWF ILVSVIADLR NAFYVLFPIW FHLQEAVGIK
LLWVAVIGDW LNLVFKWILF GQRPYWWVLD TDYYSNTSVP LIKQFPVTCE TGPGKDKADL
QISVLECHFV VGILGCAAEC LSVTNLPCCS FSSSSCCWSP VRHCCCRNFQ PHPQHL*

mutated AA sequence

N/A

speed

1.10 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