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: ENST00000301466
MT speed 0.9 s - this script 2.945298 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SOAT2	polymorphism_automatic	0.0154360770802749	simple_aae		affected		T254I	single base exchange	rs2272296		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.984563922919725 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM055083)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:53509933C>TN/A show variant in all transcripts IGV

HGNC symbol

SOAT2

Ensembl transcript ID

ENST00000301466

Genbank transcript ID

NM_003578

UniProt peptide

O75908

alteration type

single base exchange

alteration region

CDS

DNA changes

c.761C>T
cDNA.821C>T
g.12632C>T

AA changes

T254I Score: 89 explain score(s)

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

254

frameshift

known variant

Reference ID: rs2272296

database	homozygous (T/T)	heterozygous	allele carriers
1000G	212	891	1103
ExAC	2599	18124	20723

known disease mutation at this position, please check HGMD for details (HGMD ID CM055083)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.524	0.977
	-0.005	0.971
(flanking)	1.416	0.994

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 increased	12637	wt: 0.23 / mu: 0.39	wt: AGGCTGTGCCTGGGACCCTTCGTGCCAGACGAGGTGAGGCC mu: AGGCTGTGCCTGGGATCCTTCGTGCCAGACGAGGTGAGGCC	cttc\|GTGC
Acc increased	12643	wt: 0.51 / mu: 0.63	wt: TGCCTGGGACCCTTCGTGCCAGACGAGGTGAGGCCTTCATC mu: TGCCTGGGATCCTTCGTGCCAGACGAGGTGAGGCCTTCATC	gcca\|GACG
Acc marginally increased	12639	wt: 0.3951 / mu: 0.4364 (marginal change - not scored)	wt: GCTGTGCCTGGGACCCTTCGTGCCAGACGAGGTGAGGCCTT mu: GCTGTGCCTGGGATCCTTCGTGCCAGACGAGGTGAGGCCTT	tcgt\|GCCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

254

mutated

not conserved

254

Ptroglodytes

all identical

ENSPTRG00000005002

258

Mmulatta

all identical

ENSMMUG00000020339

258

Fcatus

all identical

ENSFCAG00000000307

256

Mmusculus

not conserved

ENSMUSG00000023045

257

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000014440

164

NNP

Drerio

not conserved

ENSDARG00000059824

263

KNT

Dmelanogaster

no homologue

Celegans

not conserved

B0395.2

193

Xtropicalis

not conserved

ENSXETG00000001821

265

protein features

start (aa)	end (aa)	feature	details
262	282	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
304	324	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
344	366	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
434	434	ACT_SITE	Potential.	might get lost (downstream of altered splice site)
437	457	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
472	492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1569 / 1569

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

523 / 523

position of stopcodon in wt / mu cDNA

1629 / 1629

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

61 / 61

chromosome

strand

last intron/exon boundary

1579

theoretical NMD boundary in CDS

1468

length of CDS

1569

coding sequence (CDS) position

761

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

821

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

12632

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

53509933

original gDNA sequence snippet

GAGAGAGGCTGTGCCTGGGACCCTTCGTGCCAGACGAGGTG

altered gDNA sequence snippet

GAGAGAGGCTGTGCCTGGGATCCTTCGTGCCAGACGAGGTG

original cDNA sequence snippet

GAGAGAGGCTGTGCCTGGGACCCTTCGTGCCAGACGAGGTG

altered cDNA sequence snippet

GAGAGAGGCTGTGCCTGGGATCCTTCGTGCCAGACGAGGTG

wildtype AA sequence

MEPGGARLRL QRTEGLGGER ERQPCGDGNT ETHRAPDLVQ WTRHMEAVKA QLLEQAQGQL
RELLDRAMRE AIQSYPSQDK PLPPPPPGSL SRTQEPSLGK QKVFIIRKSL LDELMEVQHF
RTIYHMFIAG LCVFIISTLA IDFIDEGRLL LEFDLLIFSF GQLPLALVTW VPMFLSTLLA
PYQALRLWAR GTWTQATGLG CALLAAHAVV LCALPVHVAV EHQLPPASRC VLVFEQVRFL
MKSYSFLREA VPGTLRARRG EGIQAPSFSS YLYFLFCPTL IYRETYPRTP YVRWNYVAKN
FAQALGCVLY ACFILGRLCV PVFANMSREP FSTRALVLSI LHATLPGIFM LLLIFFAFLH
CWLNAFAEML RFGDRMFYRD WWNSTSFSNY YRTWNVVVHD WLYSYVYQDG LRLLGARARG
VAMLGVFLVS AVAHEYIFCF VLGFFYPVML ILFLVIGGML NFMMHDQRTG PAWNVLMWTM
LFLGQGIQVS LYCQEWYARR HCPLPQATFW GLVTPRSWSC HT*

mutated AA sequence

MEPGGARLRL QRTEGLGGER ERQPCGDGNT ETHRAPDLVQ WTRHMEAVKA QLLEQAQGQL
RELLDRAMRE AIQSYPSQDK PLPPPPPGSL SRTQEPSLGK QKVFIIRKSL LDELMEVQHF
RTIYHMFIAG LCVFIISTLA IDFIDEGRLL LEFDLLIFSF GQLPLALVTW VPMFLSTLLA
PYQALRLWAR GTWTQATGLG CALLAAHAVV LCALPVHVAV EHQLPPASRC VLVFEQVRFL
MKSYSFLREA VPGILRARRG EGIQAPSFSS YLYFLFCPTL IYRETYPRTP YVRWNYVAKN
FAQALGCVLY ACFILGRLCV PVFANMSREP FSTRALVLSI LHATLPGIFM LLLIFFAFLH
CWLNAFAEML RFGDRMFYRD WWNSTSFSNY YRTWNVVVHD WLYSYVYQDG LRLLGARARG
VAMLGVFLVS AVAHEYIFCF VLGFFYPVML ILFLVIGGML NFMMHDQRTG PAWNVLMWTM
LFLGQGIQVS LYCQEWYARR HCPLPQATFW GLVTPRSWSC HT*

speed

0.90 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