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: ENST00000258145
Querying Taster for transcript #2: ENST00000543646
Querying Taster for transcript #3: ENST00000542058
MT speed 0 s - this script 3.530096 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GNS	polymorphism_automatic	1.35003119794419e-13	simple_aae		affected		G84R	single base exchange	rs2620733		show file
GNS	polymorphism_automatic	2.74481378510494e-05	without_aae		affected			single base exchange	rs2620733		show file
GNS	polymorphism_automatic	2.74481378510494e-05	without_aae		affected			single base exchange	rs2620733		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999865 (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)

chr12:65150485C>TN/A show variant in all transcripts IGV

HGNC symbol

GNS

Ensembl transcript ID

ENST00000543646

Genbank transcript ID

N/A

UniProt peptide

P15586

alteration type

single base exchange

alteration region

CDS

DNA changes

c.250G>A
cDNA.380G>A
g.2743G>A

AA changes

G84R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs2620733

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1526	793	2319
ExAC	2267	2354	4621

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.066	0.103
	-0.067	0.013
(flanking)	0.133	0.005

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 marginally increased	2745	wt: 0.8438 / mu: 0.9211 (marginal change - not scored)	wt: CTAGGACAAGAGCAT mu: CTAAGACAAGAGCAT	AGGA\|caag
Donor increased	2738	wt: 0.91 / mu: 1.00	wt: GGAAGAGCTAGGACA mu: GGAAGAGCTAAGACA	AAGA\|gcta
Donor marginally increased	2743	wt: 0.9982 / mu: 0.9992 (marginal change - not scored)	wt: AGCTAGGACAAGAGC mu: AGCTAAGACAAGAGC	CTAG\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species	match	gene	aa	alignment
Human			84	N	C	Q	T	G	L	Q	G	E	E	L	G	Q	E	H	L	R	T	Y	L	E	P	S	R
mutated	not conserved		84	N	C	Q	T	G	L	Q	G	E	E	L	R	Q	E	H	L	R	T	Y	L	E	P	S
Ptroglodytes	not conserved	ENSPTRG00000005176	84	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Mmulatta	not conserved	ENSMMUG00000006481	84	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Fcatus	not conserved	ENSFCAG00000000437	85	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Mmusculus	not conserved	ENSMUSG00000034707	76	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Ggallus	not conserved	ENSGALG00000009856	76	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Trubripes	no homologue
Drerio	not conserved	ENSDARG00000023766	70	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Dmelanogaster	not conserved	FBgn0033836	65	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
Celegans	no homologue
Xtropicalis	not conserved	ENSXETG00000007318	90	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

protein features

start (aa)	end (aa)	feature	details
91	91	MOD_RES	3-oxoalanine (Cys) (By similarity).	might get lost (downstream of altered splice site)
91	91	METAL	Calcium; via 3-oxoalanine (By similarity).	might get lost (downstream of altered splice site)
111	111	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
117	117	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
183	183	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	198	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
210	210	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
252	252	CONFLICT	F -> C (in Ref. 2; BAD97204).	might get lost (downstream of altered splice site)
279	279	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
317	317	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
326	326	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
327	327	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
362	362	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
387	387	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
405	405	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
422	422	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
449	449	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
480	480	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1755 / 1755

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

585 / 585

position of stopcodon in wt / mu cDNA

1885 / 1885

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

131 / 131

chromosome

strand

-1

last intron/exon boundary

1807

theoretical NMD boundary in CDS

1626

length of CDS

1755

coding sequence (CDS) position

250

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

380

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

2743

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

65150485

original gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAGGACAAGAGCATTTGAGAACT

altered gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAAGACAAGAGCATTTGAGAACT

original cDNA sequence snippet

GACTCCAAGGGGAAGAGCTAGGACAAGAGCATTTGAGAACT

altered cDNA sequence snippet

GACTCCAAGGGGAAGAGCTAAGACAAGAGCATTTGAGAACT

wildtype AA sequence

MRLLPLAPGR LRRGSPRHLP SCSPALLLLV LGGCLGVFGV AAGTRRPNVV LLLTDDQDEV
LGGMAFSEYS TTNCQTGLQG EELGQEHLRT YLEPSRTPLK KTKALIGEMG MTFSSAYVPS
ALCCPSRASI LTGKYPHNHH VVNNTLEGNC SSKSWQKIQE PNTFPAILRS MCGYQTFFAG
KYLNEYGAPD AGGLEHVPLG WSYWYALEKN SKYYNYTLSI NGKARKHGEN YSVDYLTDVL
ANVSLDFLDY KSNFEPFFMM IATPAPHSPW TAAPQYQKAF QNVFAPRNKN FNIHGTNKHW
LIRQAKTPMT NSSIQFLDNA FRKRWQTLLS VDDLVEKLVK RLEFTGELNN TYIFYTSDNG
YHTGQFSLPI DKRQLYEFDI KVPLLVRGPG IKPNQTSKML VANIDLGPTI LDIAGYDLNK
TQMDGMSLLP ILRGASNLTW RSDVLVEYQG EGRNVTDPTC PSLSPGVSQC FPDCVCEDAY
NNTYACVRTM SALWNLQYCE FDDQEVFVEV YNLTADPDQI TNIAKTIDPE LLGKMNYRLM
MLQSCSGPTC RTPGVFDPGY RFDPRLMFSN RGSVRTRRFS KHLL*

mutated AA sequence

MRLLPLAPGR LRRGSPRHLP SCSPALLLLV LGGCLGVFGV AAGTRRPNVV LLLTDDQDEV
LGGMAFSEYS TTNCQTGLQG EELRQEHLRT YLEPSRTPLK KTKALIGEMG MTFSSAYVPS
ALCCPSRASI LTGKYPHNHH VVNNTLEGNC SSKSWQKIQE PNTFPAILRS MCGYQTFFAG
KYLNEYGAPD AGGLEHVPLG WSYWYALEKN SKYYNYTLSI NGKARKHGEN YSVDYLTDVL
ANVSLDFLDY KSNFEPFFMM IATPAPHSPW TAAPQYQKAF QNVFAPRNKN FNIHGTNKHW
LIRQAKTPMT NSSIQFLDNA FRKRWQTLLS VDDLVEKLVK RLEFTGELNN TYIFYTSDNG
YHTGQFSLPI DKRQLYEFDI KVPLLVRGPG IKPNQTSKML VANIDLGPTI LDIAGYDLNK
TQMDGMSLLP ILRGASNLTW RSDVLVEYQG EGRNVTDPTC PSLSPGVSQC FPDCVCEDAY
NNTYACVRTM SALWNLQYCE FDDQEVFVEV YNLTADPDQI TNIAKTIDPE LLGKMNYRLM
MLQSCSGPTC RTPGVFDPGY RFDPRLMFSN RGSVRTRRFS KHLL*

speed

0.74 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: without_aae, prob: 0.999972551862149 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr12:65150485C>TN/A show variant in all transcripts IGV

HGNC symbol

GNS

Ensembl transcript ID

ENST00000258145

Genbank transcript ID

NM_002076

UniProt peptide

P15586

alteration type

single base exchange

alteration region

intron

DNA changes

g.2743G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2620733

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1526	793	2319
ExAC	2267	2354	4621

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.066	0.103
	-0.067	0.013
(flanking)	0.133	0.005

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 marginally increased	2745	wt: 0.8438 / mu: 0.9211 (marginal change - not scored)	wt: CTAGGACAAGAGCAT mu: CTAAGACAAGAGCAT	AGGA\|caag
Donor increased	2738	wt: 0.91 / mu: 1.00	wt: GGAAGAGCTAGGACA mu: GGAAGAGCTAAGACA	AAGA\|gcta
Donor marginally increased	2743	wt: 0.9982 / mu: 0.9992 (marginal change - not scored)	wt: AGCTAGGACAAGAGC mu: AGCTAAGACAAGAGC	CTAG\|gaca

distance from splice site

2380

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
91	91	MOD_RES	3-oxoalanine (Cys) (By similarity).	might get lost (downstream of altered splice site)
91	91	METAL	Calcium; via 3-oxoalanine (By similarity).	might get lost (downstream of altered splice site)
111	111	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
117	117	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
183	183	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	198	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
210	210	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
252	252	CONFLICT	F -> C (in Ref. 2; BAD97204).	might get lost (downstream of altered splice site)
279	279	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
317	317	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
326	326	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
327	327	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
362	362	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
387	387	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
405	405	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
422	422	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
449	449	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
480	480	CARBOHYD	N-linked (GlcNAc...) (Potential).	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

172 / 172

chromosome

strand

-1

last intron/exon boundary

1752

theoretical NMD boundary in CDS

1530

length of CDS

1659

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)

2743

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

65150485

original gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAGGACAAGAGCATTTGAGAACT

altered gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAAGACAAGAGCATTTGAGAACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MRLLPLAPGR LRRGSPRHLP SCSPALLLLV LGGCLGVFGV AAGTRRPNVV LLLTDDQDEV
LGGMTPLKKT KALIGEMGMT FSSAYVPSAL CCPSRASILT GKYPHNHHVV NNTLEGNCSS
KSWQKIQEPN TFPAILRSMC GYQTFFAGKY LNEYGAPDAG GLEHVPLGWS YWYALEKNSK
YYNYTLSING KARKHGENYS VDYLTDVLAN VSLDFLDYKS NFEPFFMMIA TPAPHSPWTA
APQYQKAFQN VFAPRNKNFN IHGTNKHWLI RQAKTPMTNS SIQFLDNAFR KRWQTLLSVD
DLVEKLVKRL EFTGELNNTY IFYTSDNGYH TGQFSLPIDK RQLYEFDIKV PLLVRGPGIK
PNQTSKMLVA NIDLGPTILD IAGYDLNKTQ MDGMSLLPIL RGASNLTWRS DVLVEYQGEG
RNVTDPTCPS LSPGVSQCFP DCVCEDAYNN TYACVRTMSA LWNLQYCEFD DQEVFVEVYN
LTADPDQITN IAKTIDPELL GKMNYRLMML QSCSGPTCRT PGVFDPGYRF DPRLMFSNRG
SVRTRRFSKH LL*

mutated AA sequence

N/A

speed

0.60 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999972551862149 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr12:65150485C>TN/A show variant in all transcripts IGV

HGNC symbol

GNS

Ensembl transcript ID

ENST00000542058

Genbank transcript ID

N/A

UniProt peptide

P15586

alteration type

single base exchange

alteration region

intron

DNA changes

g.2743G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2620733

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1526	793	2319
ExAC	2267	2354	4621

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.066	0.103
	-0.067	0.013
(flanking)	0.133	0.005

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 marginally increased	2745	wt: 0.8438 / mu: 0.9211 (marginal change - not scored)	wt: CTAGGACAAGAGCAT mu: CTAAGACAAGAGCAT	AGGA\|caag
Donor increased	2738	wt: 0.91 / mu: 1.00	wt: GGAAGAGCTAGGACA mu: GGAAGAGCTAAGACA	AAGA\|gcta
Donor marginally increased	2743	wt: 0.9982 / mu: 0.9992 (marginal change - not scored)	wt: AGCTAGGACAAGAGC mu: AGCTAAGACAAGAGC	CTAG\|gaca

distance from splice site

2380

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
91	91	MOD_RES	3-oxoalanine (Cys) (By similarity).	might get lost (downstream of altered splice site)
91	91	METAL	Calcium; via 3-oxoalanine (By similarity).	might get lost (downstream of altered splice site)
111	111	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
117	117	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
183	183	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	198	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
210	210	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
252	252	CONFLICT	F -> C (in Ref. 2; BAD97204).	might get lost (downstream of altered splice site)
279	279	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
317	317	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
326	326	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
327	327	METAL	Calcium (By similarity).	might get lost (downstream of altered splice site)
362	362	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
387	387	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
405	405	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
422	422	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
449	449	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
480	480	CARBOHYD	N-linked (GlcNAc...) (Potential).	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

156 / 156

chromosome

strand

-1

last intron/exon boundary

1676

theoretical NMD boundary in CDS

1470

length of CDS

1599

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)

2743

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

65150485

original gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAGGACAAGAGCATTTGAGAACT

altered gDNA sequence snippet

GACTCCAAGGGGAAGAGCTAAGACAAGAGCATTTGAGAACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MRLLPLAPGR LRRGSPRHLP SCSPALLLLV LGGCLGVFGV AAGTRRPNVV LLLTDDQDEV
LGGMYVPSAL CCPSRASILT GKYPHNHHVV NNTLEGNCSS KSWQKIQEPN TFPAILRSMC
GYQTFFAGKY LNEYGAPDAG GLEHVPLGWS YWYALEKNSK YYNYTLSING KARKHGENYS
VDYLTDVLAN VSLDFLDYKS NFEPFFMMIA TPAPHSPWTA APQYQKAFQN VFAPRNKNFN
IHGTNKHWLI RQAKTPMTNS SIQFLDNAFR KRWQTLLSVD DLVEKLVKRL EFTGELNNTY
IFYTSDNGYH TGQFSLPIDK RQLYEFDIKV PLLVRGPGIK PNQTSKMLVA NIDLGPTILD
IAGYDLNKTQ MDGMSLLPIL RGASNLTWRS DVLVEYQGEG RNVTDPTCPS LSPGVSQCFP
DCVCEDAYNN TYACVRTMSA LWNLQYCEFD DQEVFVEVYN LTADPDQITN IAKTIDPELL
GKMNYRLMML QSCSGPTCRT PGVFDPGYRF DPRLMFSNRG SVRTRRFSKH LL*

mutated AA sequence

N/A

speed

0.81 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