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: ENST00000301452
MT speed 0 s - this script 3.339544 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ACER1	polymorphism_automatic	0.757874752726058	simple_aae		affected		M74V	single base exchange	rs72981971		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.242125247273942 (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)

chr19:6312290T>CN/A show variant in all transcripts IGV

HGNC symbol

ACER1

Ensembl transcript ID

ENST00000301452

Genbank transcript ID

NM_133492

UniProt peptide

Q8TDN7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.220A>G
cDNA.298A>G
g.21351A>G

AA changes

M74V Score: 21 explain score(s)

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

frameshift

known variant

Reference ID: rs72981971

database	homozygous (C/C)	heterozygous	allele carriers
1000G	102	597	699
ExAC	1938	15281	17219

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.267	1
	0.801	1
(flanking)	0.83	1

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	21356	wt: 0.5250 / mu: 0.5538 (marginal change - not scored)	wt: GCAGGCCTGTTCTCCATGTATTTCCACATGACGCTCAGCTT mu: GCAGGCCTGTTCTCCGTGTATTTCCACATGACGCTCAGCTT	gtat\|TTCC
Acc increased	21350	wt: 0.32 / mu: 0.70	wt: GCCGCTGCAGGCCTGTTCTCCATGTATTTCCACATGACGCT mu: GCCGCTGCAGGCCTGTTCTCCGTGTATTTCCACATGACGCT	ctcc\|ATGT
Acc marginally increased	21352	wt: 0.8342 / mu: 0.8385 (marginal change - not scored)	wt: CGCTGCAGGCCTGTTCTCCATGTATTTCCACATGACGCTCA mu: CGCTGCAGGCCTGTTCTCCGTGTATTTCCACATGACGCTCA	ccat\|GTAT
Acc marginally increased	21362	wt: 0.9277 / mu: 0.9375 (marginal change - not scored)	wt: CTGTTCTCCATGTATTTCCACATGACGCTCAGCTTCCTGGG mu: CTGTTCTCCGTGTATTTCCACATGACGCTCAGCTTCCTGGG	ccac\|ATGA
Acc gained	21358	0.32	mu: AGGCCTGTTCTCCGTGTATTTCCACATGACGCTCAGCTTCC	attt\|CCAC
Acc gained	21360	0.30	mu: GCCTGTTCTCCGTGTATTTCCACATGACGCTCAGCTTCCTG	ttcc\|ACAT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000010358

Mmulatta

all identical

ENSMMUG00000005698

Fcatus

not conserved

ENSFCAG00000012508

Mmusculus

all identical

ENSMUSG00000045019

Ggallus

all identical

ENSGALG00000001592

Trubripes

not conserved

ENSTRUG00000008139

Drerio

all conserved

ENSDARG00000010347

Dmelanogaster

no homologue

Celegans

not conserved

W02F12.2

Xtropicalis

all identical

ENSXETG00000021873

protein features

start (aa)	end (aa)	feature	details
58	78	TRANSMEM	Helical; (Potential).	lost
79	81	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
82	102	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
103	119	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
120	137	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
138	138	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
139	159	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
160	176	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
177	197	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
198	206	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
207	227	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
228	264	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

795 / 795

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

265 / 265

position of stopcodon in wt / mu cDNA

873 / 873

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

79 / 79

chromosome

strand

-1

last intron/exon boundary

705

theoretical NMD boundary in CDS

576

length of CDS

795

coding sequence (CDS) position

220

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

298

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

21351

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

6312290

original gDNA sequence snippet

CCGCTGCAGGCCTGTTCTCCATGTATTTCCACATGACGCTC

altered gDNA sequence snippet

CCGCTGCAGGCCTGTTCTCCGTGTATTTCCACATGACGCTC

original cDNA sequence snippet

TGATCATAGGCCTGTTCTCCATGTATTTCCACATGACGCTC

altered cDNA sequence snippet

TGATCATAGGCCTGTTCTCCGTGTATTTCCACATGACGCTC

wildtype AA sequence

MPSIFAYQSS EVDWCESNFQ YSELVAEFYN TFSNIPFFIF GPLMMLLMHP YAQKRSRYIY
VVWVLFMIIG LFSMYFHMTL SFLGQLLDEI AILWLLGSGY SIWMPRCYFP SFLGGNRSQF
IRLVFITTVV STLLSFLRPT VNAYALNSIA LHILYIVCQE YRKTSNKELR HLIEVSVVLW
AVALTSWISD RLLCSFWQRI HFFYLHSIWH VLISITFPYG MVTMALVDAN YEMPGETLKV
RYWPRDSWPV GLPYVEIRGD DKDC*

mutated AA sequence

MPSIFAYQSS EVDWCESNFQ YSELVAEFYN TFSNIPFFIF GPLMMLLMHP YAQKRSRYIY
VVWVLFMIIG LFSVYFHMTL SFLGQLLDEI AILWLLGSGY SIWMPRCYFP SFLGGNRSQF
IRLVFITTVV STLLSFLRPT VNAYALNSIA LHILYIVCQE YRKTSNKELR HLIEVSVVLW
AVALTSWISD RLLCSFWQRI HFFYLHSIWH VLISITFPYG MVTMALVDAN YEMPGETLKV
RYWPRDSWPV GLPYVEIRGD DKDC*

speed

1.29 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