MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000261195
MT speed 0 s - this script 2.919157 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GYS2	polymorphism_automatic	6.21845151109746e-05	simple_aae		affected		M363V	single base exchange	rs2306180		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999937815484889 (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)

chr12:21713402T>CN/A show variant in all transcripts IGV

HGNC symbol

GYS2

Ensembl transcript ID

ENST00000261195

Genbank transcript ID

NM_021957

UniProt peptide

P54840

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1087A>G
cDNA.1342A>G
g.44380A>G

AA changes

M363V Score: 21 explain score(s)

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

363

frameshift

known variant

Reference ID: rs2306180

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1391	927	2318
ExAC	-	-	-

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.808	1
	1.784	1
(flanking)	0.1	0.997

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 gained	44379	0.33	mu: ACAGTGGTGGTGTTT	AGTG\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

363

mutated

all conserved

363

Ptroglodytes

all conserved

ENSPTRG00000004761

363

Mmulatta

all conserved

ENSMMUG00000016171

363

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000030244

363

Ggallus

all conserved

ENSGALG00000013265

364

Trubripes

all conserved

ENSTRUG00000010601

369

Drerio

all conserved

ENSDARG00000004904

364

Dmelanogaster

all conserved

FBgn0038293

394

Celegans

all conserved

Y46G5A.31

381

TTSDP

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
441	441	CONFLICT	P -> A (in Ref. 3; BAA06154).	might get lost (downstream of altered splice site)
576	577	CONFLICT	KQ -> NM (in Ref. 3; BAA06154).	might get lost (downstream of altered splice site)
583	583	CONFLICT	I -> F (in Ref. 3; BAA06154).	might get lost (downstream of altered splice site)
626	626	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
641	641	MOD_RES	Phosphoserine; by GSK3-alpha and GSK3- beta (By similarity).	might get lost (downstream of altered splice site)
645	645	MOD_RES	Phosphoserine; by GSK3-alpha and GSK3- beta (By similarity).	might get lost (downstream of altered splice site)
649	649	MOD_RES	Phosphoserine; by GSK3-alpha and GSK3- beta (By similarity).	might get lost (downstream of altered splice site)
653	653	MOD_RES	Phosphoserine; by GSK3-alpha and GSK3- beta (By similarity).	might get lost (downstream of altered splice site)
657	657	MOD_RES	Phosphoserine; by CK2 (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

2112 / 2112

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

704 / 704

position of stopcodon in wt / mu cDNA

2367 / 2367

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

256 / 256

chromosome

strand

-1

last intron/exon boundary

2146

theoretical NMD boundary in CDS

1840

length of CDS

2112

coding sequence (CDS) position

1087

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

1342

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

44380

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

21713402

original gDNA sequence snippet

ATAAAAGTGACATCACAGTGATGGTGTTTTTCATTATGCCT

altered gDNA sequence snippet

ATAAAAGTGACATCACAGTGGTGGTGTTTTTCATTATGCCT

original cDNA sequence snippet

ATAAAAGTGACATCACAGTGATGGTGTTTTTCATTATGCCT

altered cDNA sequence snippet

ATAAAAGTGACATCACAGTGGTGGTGTTTTTCATTATGCCT

wildtype AA sequence

MLRGRSLSVT SLGGLPQWEV EELPVEELLL FEVAWEVTNK VGGIYTVIQT KAKTTADEWG
ENYFLIGPYF EHNMKTQVEQ CEPVNDAVRR AVDAMNKHGC QVHFGRWLIE GSPYVVLFDI
GYSAWNLDRW KGDLWEACSV GIPYHDREAN DMLIFGSLTA WFLKEVTDHA DGKYVVAQFH
EWQAGIGLIL SRARKLPIAT IFTTHATLLG RYLCAANIDF YNHLDKFNID KEAGERQIYH
RYCMERASVH CAHVFTTVSE ITAIEAEHML KRKPDVVTPN GLNVKKFSAV HEFQNLHAMY
KARIQDFVRG HFYGHLDFDL EKTLFLFIAG RYEFSNKGAD IFLESLSRLN FLLRMHKSDI
TVMVFFIMPA KTNNFNVETL KGQAVRKQLW DVAHSVKEKF GKKLYDALLR GEIPDLNDIL
DRDDLTIMKR AIFSTQRQSL PPVTTHNMID DSTDPILSTI RRIGLFNNRT DRVKVILHPE
FLSSTSPLLP MDYEEFVRGC HLGVFPSYYE PWGYTPAECT VMGIPSVTTN LSGFGCFMQE
HVADPTAYGI YIVDRRFRSP DDSCNQLTKF LYGFCKQSRR QRIIQRNRTE RLSDLLDWRY
LGRYYQHARH LTLSRAFPDK FHVELTSPPT TEGFKYPRPS SVPPSPSGSQ ASSPQSSDVE
DEVEDERYDE EEEAERDRLN IKSPFSLSHV PHGKKKLHGE YKN*

mutated AA sequence

MLRGRSLSVT SLGGLPQWEV EELPVEELLL FEVAWEVTNK VGGIYTVIQT KAKTTADEWG
ENYFLIGPYF EHNMKTQVEQ CEPVNDAVRR AVDAMNKHGC QVHFGRWLIE GSPYVVLFDI
GYSAWNLDRW KGDLWEACSV GIPYHDREAN DMLIFGSLTA WFLKEVTDHA DGKYVVAQFH
EWQAGIGLIL SRARKLPIAT IFTTHATLLG RYLCAANIDF YNHLDKFNID KEAGERQIYH
RYCMERASVH CAHVFTTVSE ITAIEAEHML KRKPDVVTPN GLNVKKFSAV HEFQNLHAMY
KARIQDFVRG HFYGHLDFDL EKTLFLFIAG RYEFSNKGAD IFLESLSRLN FLLRMHKSDI
TVVVFFIMPA KTNNFNVETL KGQAVRKQLW DVAHSVKEKF GKKLYDALLR GEIPDLNDIL
DRDDLTIMKR AIFSTQRQSL PPVTTHNMID DSTDPILSTI RRIGLFNNRT DRVKVILHPE
FLSSTSPLLP MDYEEFVRGC HLGVFPSYYE PWGYTPAECT VMGIPSVTTN LSGFGCFMQE
HVADPTAYGI YIVDRRFRSP DDSCNQLTKF LYGFCKQSRR QRIIQRNRTE RLSDLLDWRY
LGRYYQHARH LTLSRAFPDK FHVELTSPPT TEGFKYPRPS SVPPSPSGSQ ASSPQSSDVE
DEVEDERYDE EEEAERDRLN IKSPFSLSHV PHGKKKLHGE YKN*

speed

0.86 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems