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: ENST00000306729
Querying Taster for transcript #2: ENST00000306739
Querying Taster for transcript #3: ENST00000580534
MT speed 0 s - this script 3.847786 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ASPSCR1	polymorphism_automatic	0.996398282062417	simple_aae		affected		L252Q	single base exchange	rs8074498		show file
ASPSCR1	polymorphism_automatic	0.996398282062417	simple_aae		affected		L175Q	single base exchange	rs8074498		show file
ASPSCR1	polymorphism_automatic	0.996740626262166	simple_aae		affected		L252Q	single base exchange	rs8074498		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00360171793758351 (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)

chr17:79954544T>AN/A show variant in all transcripts IGV

HGNC symbol

ASPSCR1

Ensembl transcript ID

ENST00000306739

Genbank transcript ID

NM_024083

UniProt peptide

Q9BZE9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.755T>A
cDNA.852T>A
g.19862T>A

AA changes

L252Q Score: 113 explain score(s)

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

252

frameshift

known variant

Reference ID: rs8074498

database	homozygous (A/A)	heterozygous	allele carriers
1000G	413	1091	1504
ExAC	15662	1443	17105

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.484	0.994
	2.923	1
(flanking)	0.294	0.999

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	19858	wt: 0.53 / mu: 0.97	wt: GACAGAGACTGGGGG mu: GACAGAGACAGGGGG	CAGA\|gact
Donor marginally increased	19856	wt: 0.8748 / mu: 0.9058 (marginal change - not scored)	wt: GGGACAGAGACTGGG mu: GGGACAGAGACAGGG	GACA\|gaga
Donor gained	19862	0.87	mu: GAGACAGGGGGGCCC	GACA\|gggg

distance from splice site

179

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

252

mutated

not conserved

252

Ptroglodytes

all identical

ENSPTRG00000009782

248

Mmulatta

all identical

ENSMMUG00000010887

174

Fcatus

all identical

ENSFCAG00000011662

257

Mmusculus

all identical

ENSMUSG00000025142

266

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000089727

160

Dmelanogaster

not conserved

FBgn0064126

204

Celegans

not conserved

B0024.10

247

SNIQDSTVMDTTESQQRDVLQE

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
257	257	CONFLICT	G -> E (in Ref. 2; BAB71595).	might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
264	264	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
311	312	SITE	Breakpoint for translocation to form ASPSCR1-TFE3.	might get lost (downstream of altered splice site)
317	380	REGION	Interaction with GLUT4 (By similarity).	might get lost (downstream of altered splice site)
386	462	DOMAIN	UBX.	might get lost (downstream of altered splice site)
444	444	CONFLICT	D -> G (in Ref. 2; BAB71595).	might get lost (downstream of altered splice site)
500	500	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
502	502	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1662 / 1662

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

554 / 554

position of stopcodon in wt / mu cDNA

1759 / 1759

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

98 / 98

chromosome

strand

last intron/exon boundary

1746

theoretical NMD boundary in CDS

1598

length of CDS

1662

coding sequence (CDS) position

755

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

852

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

19862

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

79954544

original gDNA sequence snippet

CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA

altered gDNA sequence snippet

CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA

original cDNA sequence snippet

CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA

altered cDNA sequence snippet

CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA

wildtype AA sequence

MAAPAGGGGS AVSVLAPNGR RHTVKVTPST VLLQVLEDTC RRQDFNPCEY DLKFQRSVLD
LSLQWRFANL PNNAKLEMVP ASRSREGPEN MVRIALQLDD GSRLQDSFCS GQTLWELLSH
FPQIRECLQH PGGATPVCVY TRDEVTGEAA LRGTTLQSLG LTGGSATIRF VMKCYDPVGK
TPGSLGSSAS AGQAAASAPL PLESGELSRG DLSRPEDADT SGPCCEHTQE KQSTRAPAAA
PFVPFSGGGQ RLGGPPGPTR PLTSSSAKLP KSLSSPGGPS KPKKSKSGQD PQQEQEQERE
RDPQQEQERE RPVDREPVDR EPVVCHPDLE ERLQAWPAEL PDEFFELTVD DVRRRLAQLK
SERKRLEEAP LVTKAFREAQ IKEKLERYPK VALRVLFPDR YVLQGFFRPS ETVGDLRDFV
RSHLGNPELS FYLFITPPKT VLDDHTQTLF QANLFPAALV HLGAEEPAGV YLEPGLLEHA
ISPSAADVLV ARYMSRAAGS PSPLPAPDPA PKSEPAAEEG ALVPPEPIPG TAQPVKRSLG
KVPKWLKLPA SKR*

mutated AA sequence

MAAPAGGGGS AVSVLAPNGR RHTVKVTPST VLLQVLEDTC RRQDFNPCEY DLKFQRSVLD
LSLQWRFANL PNNAKLEMVP ASRSREGPEN MVRIALQLDD GSRLQDSFCS GQTLWELLSH
FPQIRECLQH PGGATPVCVY TRDEVTGEAA LRGTTLQSLG LTGGSATIRF VMKCYDPVGK
TPGSLGSSAS AGQAAASAPL PLESGELSRG DLSRPEDADT SGPCCEHTQE KQSTRAPAAA
PFVPFSGGGQ RQGGPPGPTR PLTSSSAKLP KSLSSPGGPS KPKKSKSGQD PQQEQEQERE
RDPQQEQERE RPVDREPVDR EPVVCHPDLE ERLQAWPAEL PDEFFELTVD DVRRRLAQLK
SERKRLEEAP LVTKAFREAQ IKEKLERYPK VALRVLFPDR YVLQGFFRPS ETVGDLRDFV
RSHLGNPELS FYLFITPPKT VLDDHTQTLF QANLFPAALV HLGAEEPAGV YLEPGLLEHA
ISPSAADVLV ARYMSRAAGS PSPLPAPDPA PKSEPAAEEG ALVPPEPIPG TAQPVKRSLG
KVPKWLKLPA SKR*

speed

0.94 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: 0.00360171793758351 (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)

chr17:79954544T>AN/A show variant in all transcripts IGV

HGNC symbol

ASPSCR1

Ensembl transcript ID

ENST00000580534

Genbank transcript ID

N/A

UniProt peptide

Q9BZE9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.524T>A
cDNA.712T>A
g.19862T>A

AA changes

L175Q Score: 113 explain score(s)

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

175

frameshift

known variant

Reference ID: rs8074498

database	homozygous (A/A)	heterozygous	allele carriers
1000G	413	1091	1504
ExAC	15662	1443	17105

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.484	0.994
	2.923	1
(flanking)	0.294	0.999

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	19858	wt: 0.53 / mu: 0.97	wt: GACAGAGACTGGGGG mu: GACAGAGACAGGGGG	CAGA\|gact
Donor marginally increased	19856	wt: 0.8748 / mu: 0.9058 (marginal change - not scored)	wt: GGGACAGAGACTGGG mu: GGGACAGAGACAGGG	GACA\|gaga
Donor gained	19862	0.87	mu: GAGACAGGGGGGCCC	GACA\|gggg

distance from splice site

179

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

175

mutated

not conserved

175

Ptroglodytes

all identical

ENSPTRG00000009782

248

Mmulatta

all identical

ENSMMUG00000010887

174

Fcatus

all identical

ENSFCAG00000011662

257

Mmusculus

all identical

ENSMUSG00000025142

267

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000089727

160

Dmelanogaster

not conserved

FBgn0064126

221

Celegans

not conserved

B0024.10

269

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
257	257	CONFLICT	G -> E (in Ref. 2; BAB71595).	might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
264	264	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
311	312	SITE	Breakpoint for translocation to form ASPSCR1-TFE3.	might get lost (downstream of altered splice site)
317	380	REGION	Interaction with GLUT4 (By similarity).	might get lost (downstream of altered splice site)
386	462	DOMAIN	UBX.	might get lost (downstream of altered splice site)
444	444	CONFLICT	D -> G (in Ref. 2; BAB71595).	might get lost (downstream of altered splice site)
500	500	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
502	502	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1506 / 1506

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

502 / 502

position of stopcodon in wt / mu cDNA

1694 / 1694

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

189 / 189

chromosome

strand

last intron/exon boundary

1681

theoretical NMD boundary in CDS

1442

length of CDS

1506

coding sequence (CDS) position

524

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

712

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

19862

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

79954544

original gDNA sequence snippet

CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA

altered gDNA sequence snippet

CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA

original cDNA sequence snippet

CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA

altered cDNA sequence snippet

CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA

wildtype AA sequence

MVPASRSREG PENMVRIALQ LDDGSRLQDS FCSGQTLWEL LSHFPQIREC LQHPGGATPV
CVYTRDEVTG EAALRGTTLQ SLGLTGGSAT IRFVMKCYDP VGKTPGSLGS SASAGQAAAS
APLPLESGEL SRGDLSRPED ADTSGPCCEH TQEKQSTRAP AAAPFVPFSG GGQRLGGPPG
PTRPLTSSSA KLPKSLSSPG GPSKPKKSKS GQDPQQEQEQ ERERDPQQEQ ERERPVDREP
VDREPVVCHP DLEERLQAWP AELPDEFFEL TVDDVRRRLA QLKSERKRLE EAPLVTKAFR
EAQIKEKLER YPKVALRVLF PDRYVLQGFF RPSETVGDLR DFVRSHLGNP ELSFYLCLSS
FGRMDGRGPR CFLTRRCLLS SVITPPKTVL DDHTQTLFQA NLFPAALVHL GAEEPAGVYL
EPGLLEHAIS PSAADVLVAR YMSRAAGSPS PLPAPDPAPK SEPAAEEGAL VPPEPIPGTA
QPVKRSLGKV PKWLKLPASK R*

mutated AA sequence

MVPASRSREG PENMVRIALQ LDDGSRLQDS FCSGQTLWEL LSHFPQIREC LQHPGGATPV
CVYTRDEVTG EAALRGTTLQ SLGLTGGSAT IRFVMKCYDP VGKTPGSLGS SASAGQAAAS
APLPLESGEL SRGDLSRPED ADTSGPCCEH TQEKQSTRAP AAAPFVPFSG GGQRQGGPPG
PTRPLTSSSA KLPKSLSSPG GPSKPKKSKS GQDPQQEQEQ ERERDPQQEQ ERERPVDREP
VDREPVVCHP DLEERLQAWP AELPDEFFEL TVDDVRRRLA QLKSERKRLE EAPLVTKAFR
EAQIKEKLER YPKVALRVLF PDRYVLQGFF RPSETVGDLR DFVRSHLGNP ELSFYLCLSS
FGRMDGRGPR CFLTRRCLLS SVITPPKTVL DDHTQTLFQA NLFPAALVHL GAEEPAGVYL
EPGLLEHAIS PSAADVLVAR YMSRAAGSPS PLPAPDPAPK SEPAAEEGAL VPPEPIPGTA
QPVKRSLGKV PKWLKLPASK R*

speed

0.87 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00325937373783436 (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)

chr17:79954544T>AN/A show variant in all transcripts IGV

HGNC symbol

ASPSCR1

Ensembl transcript ID

ENST00000306729

Genbank transcript ID

NM_001251888

UniProt peptide

Q9BZE9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.755T>A
cDNA.852T>A
g.19862T>A

AA changes

L252Q Score: 113 explain score(s)

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

252

frameshift

known variant

Reference ID: rs8074498

database	homozygous (A/A)	heterozygous	allele carriers
1000G	413	1091	1504
ExAC	15662	1443	17105

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.484	0.994
	2.923	1
(flanking)	0.294	0.999

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	19858	wt: 0.53 / mu: 0.97	wt: GACAGAGACTGGGGG mu: GACAGAGACAGGGGG	CAGA\|gact
Donor marginally increased	19856	wt: 0.8748 / mu: 0.9058 (marginal change - not scored)	wt: GGGACAGAGACTGGG mu: GGGACAGAGACAGGG	GACA\|gaga
Donor gained	19862	0.87	mu: GAGACAGGGGGGCCC	GACA\|gggg

distance from splice site

179

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

252

mutated

not conserved

252

Ptroglodytes

all identical

ENSPTRG00000009782

248

Mmulatta

all identical

ENSMMUG00000010887

174

Fcatus

all identical

ENSFCAG00000011662

257

Mmusculus

all identical

ENSMUSG00000025142

267

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000089727

n/a

Dmelanogaster

not conserved

FBgn0064126

204

Celegans

not conserved

B0024.10

247

SNIQDSTVMDTTESQQRDVLQE

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
257	257	CONFLICT	G -> E (in Ref. 2; BAB71595).	might get lost (downstream of altered splice site)
263	263	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
264	264	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
311	312	SITE	Breakpoint for translocation to form ASPSCR1-TFE3.	might get lost (downstream of altered splice site)
317	380	REGION	Interaction with GLUT4 (By similarity).	might get lost (downstream of altered splice site)
386	462	DOMAIN	UBX.	might get lost (downstream of altered splice site)
444	444	CONFLICT	D -> G (in Ref. 2; BAB71595).	might get lost (downstream of altered splice site)
500	500	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
502	502	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1944 / 1944

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

648 / 648

position of stopcodon in wt / mu cDNA

2041 / 2041

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

98 / 98

chromosome

strand

last intron/exon boundary

2028

theoretical NMD boundary in CDS

1880

length of CDS

1944

coding sequence (CDS) position

755

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

852

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

19862

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

79954544

original gDNA sequence snippet

CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA

altered gDNA sequence snippet

CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA

original cDNA sequence snippet

CTCGGGTGGGGGACAGAGACTGGGGGGCCCTCCTGGGCCCA

altered cDNA sequence snippet

CTCGGGTGGGGGACAGAGACAGGGGGGCCCTCCTGGGCCCA

wildtype AA sequence

MAAPAGGGGS AVSVLAPNGR RHTVKVTPST VLLQVLEDTC RRQDFNPCEY DLKFQRSVLD
LSLQWRFANL PNNAKLEMVP ASRSREGPEN MVRIALQLDD GSRLQDSFCS GQTLWELLSH
FPQIRECLQH PGGATPVCVY TRDEVTGEAA LRGTTLQSLG LTGGSATIRF VMKCYDPVGK
TPGSLGSSAS AGQAAASAPL PLESGELSRG DLSRPEDADT SGPCCEHTQE KQSTRAPAAA
PFVPFSGGGQ RLGGPPGPTR PLTSSSAKLP KSLSSPGGPS KPKKSKSGQD PQQEQEQERE
RDPQQEQERE RPVDREPVDR EPVVCHPDLE ERLQAWPAEL PDEFFELTVD DVRRRLAQLK
SERKRLEEAP LVTKAFREAQ IKEKLERYPK VALRVLFPDR YVLQGFFRPS ETVGDLRDFV
RSHLGNPELS FYLFITPPKT VLDDHTQTLF QPQLGDRVAP FTLGPSLKRC LGPEQRTRLP
VVGDGGDVDS GRLLFWGPSR GRASPSTGQP PCHPVCRPSS PPSPRPSSGD PSRVKAGHKH
VGTGRANLFP AALVHLGAEE PAGVYLEPGL LEHAISPSAA DVLVARYMSR AAGSPSPLPA
PDPAPKSEPA AEEGALVPPE PIPGTAQPVK RSLGKVPKWL KLPASKR*

mutated AA sequence

MAAPAGGGGS AVSVLAPNGR RHTVKVTPST VLLQVLEDTC RRQDFNPCEY DLKFQRSVLD
LSLQWRFANL PNNAKLEMVP ASRSREGPEN MVRIALQLDD GSRLQDSFCS GQTLWELLSH
FPQIRECLQH PGGATPVCVY TRDEVTGEAA LRGTTLQSLG LTGGSATIRF VMKCYDPVGK
TPGSLGSSAS AGQAAASAPL PLESGELSRG DLSRPEDADT SGPCCEHTQE KQSTRAPAAA
PFVPFSGGGQ RQGGPPGPTR PLTSSSAKLP KSLSSPGGPS KPKKSKSGQD PQQEQEQERE
RDPQQEQERE RPVDREPVDR EPVVCHPDLE ERLQAWPAEL PDEFFELTVD DVRRRLAQLK
SERKRLEEAP LVTKAFREAQ IKEKLERYPK VALRVLFPDR YVLQGFFRPS ETVGDLRDFV
RSHLGNPELS FYLFITPPKT VLDDHTQTLF QPQLGDRVAP FTLGPSLKRC LGPEQRTRLP
VVGDGGDVDS GRLLFWGPSR GRASPSTGQP PCHPVCRPSS PPSPRPSSGD PSRVKAGHKH
VGTGRANLFP AALVHLGAEE PAGVYLEPGL LEHAISPSAA DVLVARYMSR AAGSPSPLPA
PDPAPKSEPA AEEGALVPPE PIPGTAQPVK RSLGKVPKWL KLPASKR*

speed

0.87 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