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: ENST00000300057
MT speed 0 s - this script 2.95827 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MESP1	polymorphism_automatic	2.19824158875781e-14	simple_aae		affected		L61R	single base exchange	rs28368490		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999978 (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)

chr15:90294281A>CN/A show variant in all transcripts IGV

HGNC symbol

MESP1

Ensembl transcript ID

ENST00000300057

Genbank transcript ID

NM_018670

UniProt peptide

Q9BRJ9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.182T>G
cDNA.261T>G
g.261T>G

AA changes

L61R Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs28368490

database	homozygous (C/C)	heterozygous	allele carriers
1000G	206	868	1074
ExAC	6	147	153

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Ini1, Transcription Factor, Ini1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Nrf1, Transcription Factor, Nrf1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.737	0.009
	-0.665	0
(flanking)	0.717	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 marginally increased	253	wt: 0.9048 / mu: 0.9070 (marginal change - not scored)	wt: CGGCCAGGCACCCTC mu: CGGCCAGGCACCCGC	GCCA\|ggca
Donor gained	260	0.68	mu: GCACCCGCCGGGACC	ACCC\|gccg

distance from splice site

261

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000007439

Mmulatta

not conserved

ENSMMUG00000010586

Fcatus

not conserved

ENSFCAG00000008973

Mmusculus

not conserved

ENSMUSG00000030544

Ggallus

not conserved

ENSGALG00000008275

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000030347

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000027628

PYIASQEIF

GLRH

protein features

start (aa)	end (aa)	feature	details
82	136	DOMAIN	bHLH.	might get lost (downstream of altered splice site)
163	167	MOTIF	CPLCP.	might get lost (downstream of altered splice site)
182	183	REPEAT	1.	might get lost (downstream of altered splice site)
182	185	REGION	2 X 2 AA tandem repeats of G-Q.	might get lost (downstream of altered splice site)
184	185	REPEAT	2.	might get lost (downstream of altered splice site)
223	223	CONFLICT	F -> L (in Ref. 2; CAB93425/CAB93426).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

807 / 807

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

269 / 269

position of stopcodon in wt / mu cDNA

886 / 886

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

80 / 80

chromosome

strand

-1

last intron/exon boundary

803

theoretical NMD boundary in CDS

673

length of CDS

807

coding sequence (CDS) position

182

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

261

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

261

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

90294281

original gDNA sequence snippet

CCCCGCGCGGCCAGGCACCCTCCGGGACCCCCGCGCCCCCT

altered gDNA sequence snippet

CCCCGCGCGGCCAGGCACCCGCCGGGACCCCCGCGCCCCCT

original cDNA sequence snippet

CCCCGCGCGGCCAGGCACCCTCCGGGACCCCCGCGCCCCCT

altered cDNA sequence snippet

CCCCGCGCGGCCAGGCACCCGCCGGGACCCCCGCGCCCCCT

wildtype AA sequence

MAQPLCPPLS ESWMLSAAWG PTRRPPPSDK DCGRSLVSSP DSWGSTPADS PVASPARPGT
LRDPRAPSVG RRGARSSRLG SGQRQSASER EKLRMRTLAR ALHELRRFLP PSVAPAGQSL
TKIETLRLAI RYIGHLSAVL GLSEESLQRR CRQRGDAGSP RGCPLCPDDC PAQMQTRTQA
EGQGQGRGLG LVSAVRAGAS WGSPPACPGA RAAPEPRDPP ALFAEAACPE GQAMEPSPPS
PLLPGDVLAL LETWMPLSPL EWLPEEPK*

mutated AA sequence

MAQPLCPPLS ESWMLSAAWG PTRRPPPSDK DCGRSLVSSP DSWGSTPADS PVASPARPGT
RRDPRAPSVG RRGARSSRLG SGQRQSASER EKLRMRTLAR ALHELRRFLP PSVAPAGQSL
TKIETLRLAI RYIGHLSAVL GLSEESLQRR CRQRGDAGSP RGCPLCPDDC PAQMQTRTQA
EGQGQGRGLG LVSAVRAGAS WGSPPACPGA RAAPEPRDPP ALFAEAACPE GQAMEPSPPS
PLLPGDVLAL LETWMPLSPL EWLPEEPK*

speed

0.95 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