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: ENST00000323013
MT speed 0 s - this script 2.914511 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RRP7A	polymorphism_automatic	0.040076508053417	simple_aae		affected		V85I	single base exchange	rs1812240		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.959923491946583 (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)

chr22:42912106C>TN/A show variant in all transcripts IGV

HGNC symbol

RRP7A

Ensembl transcript ID

ENST00000323013

Genbank transcript ID

NM_015703

UniProt peptide

Q9Y3A4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.253G>A
cDNA.269G>A
g.3703G>A

AA changes

V85I Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs1812240

database	homozygous (T/T)	heterozygous	allele carriers
1000G	316	625	941
ExAC	3046	9687	12733

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.456	0.528
	0.144	0.096
(flanking)	-1.212	0

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	3706	wt: 0.70 / mu: 0.87	wt: TGTCCACCTGTGGCCTCGTCCAGTCTGTAGAGTTGCAGGAG mu: TGTCCACCTGTGGCCTCATCCAGTCTGTAGAGTTGCAGGAG	gtcc\|AGTC

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

no alignment

ENSPTRG00000033935

n/a

Mmulatta

all identical

ENSMMUG00000009716

Fcatus

no alignment

ENSFCAG00000012607

n/a

Mmusculus

all conserved

ENSMUSG00000018040

Ggallus

all identical

ENSGALG00000011866

Trubripes

all identical

ENSTRUG00000006442

Drerio

all identical

ENSDARG00000044853

Dmelanogaster

all conserved

FBgn0031764

Celegans

all identical

ZC434.4

Xtropicalis

all identical

ENSXETG00000013414

protein features

start (aa)	end (aa)	feature	details
61	90	DOMAIN	RRM.	lost
99	99	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
102	102	CONFLICT	E -> K (in Ref. 2; BAG37211).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

843 / 843

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

281 / 281

position of stopcodon in wt / mu cDNA

859 / 859

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

17 / 17

chromosome

strand

-1

last intron/exon boundary

774

theoretical NMD boundary in CDS

707

length of CDS

843

coding sequence (CDS) position

253

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

269

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

3703

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

42912106

original gDNA sequence snippet

TCCTGTCCACCTGTGGCCTCGTCCAGTCTGTAGAGTTGCAG

altered gDNA sequence snippet

TCCTGTCCACCTGTGGCCTCATCCAGTCTGTAGAGTTGCAG

original cDNA sequence snippet

TCCTGTCCACCTGTGGCCTCGTCCAGTCTGTAGAGTTGCAG

altered cDNA sequence snippet

TCCTGTCCACCTGTGGCCTCATCCAGTCTGTAGAGTTGCAG

wildtype AA sequence

MVARRRKCAA RDPEDRIPSP LGYAAIPIKF SEKQQASHYL YVRAHGVRQG TKSTWPQKRT
LFVLNVPPYC TEESLSRLLS TCGLVQSVEL QEKPDLAESP KESRSKFFHP KPVPGFQVAY
VVFQKPSGVS AALALKGPLL VSTESHPVKS GIHKWISDYA DSVPDPEALR VEVDTFMEAY
DQKIAEEEAK AKEEEGVPDE EGWVKVTRRG RRPVLPRTEA ASLRVLERER RKRSRKELLN
FYAWQHRESK MEHLAQLRKK FEEDKQRIEL LRAQRKFRPY *

mutated AA sequence

MVARRRKCAA RDPEDRIPSP LGYAAIPIKF SEKQQASHYL YVRAHGVRQG TKSTWPQKRT
LFVLNVPPYC TEESLSRLLS TCGLIQSVEL QEKPDLAESP KESRSKFFHP KPVPGFQVAY
VVFQKPSGVS AALALKGPLL VSTESHPVKS GIHKWISDYA DSVPDPEALR VEVDTFMEAY
DQKIAEEEAK AKEEEGVPDE EGWVKVTRRG RRPVLPRTEA ASLRVLERER RKRSRKELLN
FYAWQHRESK MEHLAQLRKK FEEDKQRIEL LRAQRKFRPY *

speed

0.91 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