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: ENST00000234389
MT speed 0.83 s - this script 3.007409 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GRIN3B	polymorphism_automatic	5.16936341499186e-06	simple_aae		affected		Q1006E	single base exchange	rs10401245		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999994830636585 (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)

chr19:1009485C>GN/A show variant in all transcripts IGV

HGNC symbol

GRIN3B

Ensembl transcript ID

ENST00000234389

Genbank transcript ID

NM_138690

UniProt peptide

O60391

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3016C>G
cDNA.3035C>G
g.9068C>G

AA changes

Q1006E Score: 29 explain score(s)

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

1006

frameshift

known variant

Reference ID: rs10401245

database	homozygous (G/G)	heterozygous	allele carriers
1000G	813	1139	1952
ExAC	2019	3346	5365

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.75	0.099
	0.745	0.558
(flanking)	1.408	0.857

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	9059	wt: 0.3683 / mu: 0.4005 (marginal change - not scored)	wt: GGCTCCGCCAGGCCCTGGTGCGGCGCGGCCAGCTCCTGGCA mu: GGCTCCGCCAGGCCCTGGTGCGGCGCGGCGAGCTCCTGGCA	gtgc\|GGCG
Donor gained	9062	0.41	mu: TGCGGCGCGGCGAGC	CGGC\|gcgg
Donor gained	9064	0.95	mu: CGGCGCGGCGAGCTC	GCGC\|ggcg

distance from splice site

247

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1006

mutated

all conserved

1006

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000035745

994

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000005364

1075

LQRTLVRQR

Dmelanogaster

no alignment

FBgn0053513

n/a

Celegans

no alignment

T01C3.10

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
852	1043	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3132 / 3132

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

1044 / 1044

position of stopcodon in wt / mu cDNA

3151 / 3151

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

20 / 20

chromosome

strand

last intron/exon boundary

2722

theoretical NMD boundary in CDS

2652

length of CDS

3132

coding sequence (CDS) position

3016

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

3035

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

9068

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

1009485

original gDNA sequence snippet

AGGCCCTGGTGCGGCGCGGCCAGCTCCTGGCACAGCTCGGG

altered gDNA sequence snippet

AGGCCCTGGTGCGGCGCGGCGAGCTCCTGGCACAGCTCGGG

original cDNA sequence snippet

AGGCCCTGGTGCGGCGCGGCCAGCTCCTGGCACAGCTCGGG

altered cDNA sequence snippet

AGGCCCTGGTGCGGCGCGGCGAGCTCCTGGCACAGCTCGGG

wildtype AA sequence

MEFVRALWLG LALALGPGSA GGHPQPCGVL ARLGGSVRLG ALLPRAPLAR ARARAALARA
ALAPRLPHNL SLELVVAAPP ARDPASLTRG LCQALVPPGV AALLAFPEAR PELLQLHFLA
AATETPVLSL LRREARAPLG APNPFHLQLH WASPLETLLD VLVAVLQAHA WEDVGLALCR
TQDPGGLVAL WTSRAGRPPQ LVLDLSRRDT GDAGLRARLA PMAAPVGGEA PVPAAVLLGC
DIARARRVLE AVPPGPHWLL GTPLPPKALP TAGLPPGLLA LGEVARPPLE AAIHDIVQLV
ARALGSAAQV QPKRALLPAP VNCGDLQPAG PESPGRFLAR FLANTSFQGR TGPVWVTGSS
QVHMSRHFKV WSLRRDPRGA PAWATVGSWR DGQLDLEPGG ASARPPPPQG AQVWPKLRVV
TLLEHPFVFA RDPDEDGQCP AGQLCLDPGT NDSATLDALF AALANGSAPR ALRKCCYGYC
IDLLERLAED TPFDFELYLV GDGKYGALRD GRWTGLVGDL LAGRAHMAVT SFSINSARSQ
VVDFTSPFFS TSLGIMVRAR DTASPIGAFM WPLHWSTWLG VFAALHLTAL FLTVYEWRSP
YGLTPRGRNR STVFSYSSAL NLCYAILFRR TVSSKTPKCP TGRLLMNLWA IFCLLVLSSY
TANLAAVMVG DKTFEELSGI HDPKLHHPAQ GFRFGTVWES SAEAYIKKSF PDMHAHMRRH
SAPTTPRGVA MLTSDPPKLN AFIMDKSLLD YEVSIDADCK LLTVGKPFAI EGYGIGLPQN
SPLTSNLSEF ISRYKSSGFI DLLHDKWYKM VPCGKRVFAV TETLQMSIYH FAGLFVLLCL
GLGSALLSSL GEHAFFRLAL PRIRKGSRLQ YWLHTSQKIH RALNTEPPEG SKEETAEAEP
SGPEVEQQQQ QQDQPTAPEG WKRARRAVDK ERRVRFLLEP AVVVAPEADA EAEAAPREGP
VWLCSYGRPP AARPTGAPQP GELQELERRI EVARERLRQA LVRRGQLLAQ LGDSARHRPR
RLLQARAAPA EAPPHSGRPG SQE*

mutated AA sequence

speed

0.83 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