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 s - this script 2.879907 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
RTP5	polymorphism_automatic	3.77031739162703e-13	simple_aae		affected		I218T	single base exchange	rs28378061		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999623 (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)

chr2:242814360T>CN/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.653T>C
cDNA.681T>C
g.2609T>C

AA changes

I218T Score: 89 explain score(s)

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

218

frameshift

known variant

Reference ID: rs28378061

database	homozygous (C/C)	heterozygous	allele carriers
1000G	280	802	1082
ExAC	3160	14373	17533

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.458	0
	0.202	0
(flanking)	0.202	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
Donor increased	2600	wt: 0.42 / mu: 0.47	wt: TGACCAGGTGCCCAT mu: TGACCAGGTGCCCAC	ACCA\|ggtg
Donor marginally increased	2610	wt: 0.9877 / mu: 0.9950 (marginal change - not scored)	wt: CCCATCGCTGAGGGC mu: CCCACCGCTGAGGGC	CATC\|gctg

distance from splice site

495

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

218

mutated

not conserved

218

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000011353

220

DAR

Mmusculus

no homologue

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
241	241	CONFLICT	I -> T (in Ref. 1; BAC03544).	might get lost (downstream of altered splice site)
544	560	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

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

653

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

681

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

2609

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

242814360

original gDNA sequence snippet

CAGCAATGACCAGGTGCCCATCGCTGAGGGCCCTGCCCCCC

altered gDNA sequence snippet

CAGCAATGACCAGGTGCCCACCGCTGAGGGCCCTGCCCCCC

original cDNA sequence snippet

CAGCAATGACCAGGTGCCCATCGCTGAGGGCCCTGCCCCCC

altered cDNA sequence snippet

CAGCAATGACCAGGTGCCCACCGCTGAGGGCCCTGCCCCCC

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 TSNDQVPTAE 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*

speed

0.81 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