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: ENST00000226460
MT speed 0 s - this script 2.568911 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SMR3A	polymorphism_automatic	1.397992832608e-12	simple_aae		affected		G28R	single base exchange	rs10031844		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998602 (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)

chr4:71232388G>AN/A show variant in all transcripts IGV

HGNC symbol

SMR3A

Ensembl transcript ID

ENST00000226460

Genbank transcript ID

NM_012390

UniProt peptide

Q99954

alteration type

single base exchange

alteration region

CDS

DNA changes

c.82G>A
cDNA.178G>A
g.5911G>A

AA changes

G28R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs10031844

database	homozygous (A/A)	heterozygous	allele carriers
1000G	284	914	1198
ExAC	5617	21533	27150

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.277	0
	-1.471	0
(flanking)	0.909	0.004

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	5906	0.87	mu: AGGCCCCAGGAGACC	GCCC\|cagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000016128

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000029280

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
26	134	COMPBIAS	Pro-rich.	lost
37	41	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
77	83	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

405 / 405

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

135 / 135

position of stopcodon in wt / mu cDNA

501 / 501

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

97 / 97

chromosome

strand

last intron/exon boundary

151

theoretical NMD boundary in CDS

length of CDS

405

coding sequence (CDS) position

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

178

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

5911

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

71232388

original gDNA sequence snippet

AGAGTCAAAGAGGCCCCAGGGGACCATATCCACCTGGACCA

altered gDNA sequence snippet

AGAGTCAAAGAGGCCCCAGGAGACCATATCCACCTGGACCA

original cDNA sequence snippet

AGAGTCAAAGAGGCCCCAGGGGACCATATCCACCTGGACCA

altered cDNA sequence snippet

AGAGTCAAAGAGGCCCCAGGAGACCATATCCACCTGGACCA

wildtype AA sequence

MKSLTWILGL WALAACFTPG ESQRGPRGPY PPGPLAPPPP PCFPFGTGFV PPPHPPPYGP
GRFPPPLSPP YGPGRIPPSP PPPYGPGRIQ SHSLPPPYGP GYPQPPSQPR PYPPGPPFFP
VNSPTDPALP TPAP*

mutated AA sequence

MKSLTWILGL WALAACFTPG ESQRGPRRPY PPGPLAPPPP PCFPFGTGFV PPPHPPPYGP
GRFPPPLSPP YGPGRIPPSP PPPYGPGRIQ SHSLPPPYGP GYPQPPSQPR PYPPGPPFFP
VNSPTDPALP TPAP*

speed

0.56 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