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: ENST00000343216
MT speed 0.17 s - this script 2.228045 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RTP5	polymorphism_automatic	1.22013510406305e-13	simple_aae				A451V	single base exchange	rs28368764		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999878 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:242815059C>TN/A show variant in all transcripts IGV

HGNC symbol

RTP5

Ensembl transcript ID

ENST00000343216

Genbank transcript ID

NM_173821

UniProt peptide

Q14D33

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1352C>T
cDNA.1380C>T
g.3308C>T

AA changes

A451V Score: 64 explain score(s)

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

451

frameshift

known variant

Reference ID: rs28368764

database	homozygous (T/T)	heterozygous	allele carriers
1000G	152	446	598
ExAC	1778	7000	8778

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.382	0
	-0.472	0
(flanking)	-2.449	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 marginally increased	3310	wt: 0.2692 / mu: 0.3184 (marginal change - not scored)	wt: AAGGTGGCCTGGTCACCGCGGGTCACGACGCCCCTCTGGAG mu: AAGGTGGCCTGGTCACCGTGGGTCACGACGCCCCTCTGGAG	gcgg\|GTCA
Donor marginally increased	3313	wt: 0.2252 / mu: 0.2294 (marginal change - not scored)	wt: CGGGTCACGACGCCC mu: TGGGTCACGACGCCC	GGTC\|acga

distance from splice site

917

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

451

mutated

not conserved

451

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000011353

456

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1719 / 1719

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

573 / 573

position of stopcodon in wt / mu cDNA

1747 / 1747

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

29 / 29

chromosome

strand

last intron/exon boundary

187

theoretical NMD boundary in CDS

108

length of CDS

1719

coding sequence (CDS) position

1352

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

1380

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

3308

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

242815059

original gDNA sequence snippet

GGAAGGTGGCCTGGTCACCGCGGGTCACGACGCCCCTCTGG

altered gDNA sequence snippet

GGAAGGTGGCCTGGTCACCGTGGGTCACGACGCCCCTCTGG

original cDNA sequence snippet

GGAAGGTGGCCTGGTCACCGCGGGTCACGACGCCCCTCTGG

altered cDNA sequence snippet

GGAAGGTGGCCTGGTCACCGTGGGTCACGACGCCCCTCTGG

wildtype AA sequence

MDRAGADMWA STFTLAMAER KPQDVWVLLP EHSLVPGCLD GGGVQYLLVG LSRLQCGHCP
GTWDSAHVHV LFHLWWDRAS HRGLVKMRIW GQRCRLCPAP GDCQVRPPGE QPFLSRLVLH
ILQDCYGDGP GPARHPREAY EGCCEACELG VCFLQKAPDP AWSANATKGN FPATAWGGTG
TVSRGKPLST PGDDLGKGGV VIAIPFSLVG TSNDQVPIAE GPAPPAGASL PVTGSCEALV
IGQGSIFLSG DSVAMPGGKG FPVAIGDPLF HGPGLLGSSI QTFELKGFLF KGRGSLCSPV
GVAQGWGPIS LNNGLVPVGK HTPTVFYCVG LSASGEGSLT FPSSLTSIFT NTLSEPTDGP
VATKEASITF PFIFTDVKDA VAEVAEGNGK EGGGQGLVPV GHDALPETNA GGLPSQVKGS
LALPFPADVQ GKDAFTDITE GKEKEGGLVT AGHDAPLEAN AEGPITVSEG CITIPFAVFD
VIKRKGGGHV AYGPQGNGCF SQGYYQKRQL RSRFHKARCG CRREEDERPG RACRRPHAEP
YEDFWIWVSM TVCVFWLMCM CRLNPGIYPQ QV*

mutated AA sequence

MDRAGADMWA STFTLAMAER KPQDVWVLLP EHSLVPGCLD GGGVQYLLVG LSRLQCGHCP
GTWDSAHVHV LFHLWWDRAS HRGLVKMRIW GQRCRLCPAP GDCQVRPPGE QPFLSRLVLH
ILQDCYGDGP GPARHPREAY EGCCEACELG VCFLQKAPDP AWSANATKGN FPATAWGGTG
TVSRGKPLST PGDDLGKGGV VIAIPFSLVG TSNDQVPIAE GPAPPAGASL PVTGSCEALV
IGQGSIFLSG DSVAMPGGKG FPVAIGDPLF HGPGLLGSSI QTFELKGFLF KGRGSLCSPV
GVAQGWGPIS LNNGLVPVGK HTPTVFYCVG LSASGEGSLT FPSSLTSIFT NTLSEPTDGP
VATKEASITF PFIFTDVKDA VAEVAEGNGK EGGGQGLVPV GHDALPETNA GGLPSQVKGS
LALPFPADVQ GKDAFTDITE GKEKEGGLVT VGHDAPLEAN AEGPITVSEG CITIPFAVFD
VIKRKGGGHV AYGPQGNGCF SQGYYQKRQL RSRFHKARCG CRREEDERPG RACRRPHAEP
YEDFWIWVSM TVCVFWLMCM CRLNPGIYPQ QV*

speed

0.17 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