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: ENST00000373960
MT speed 0 s - this script 3.340641 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DES	disease_causing_automatic	0.990665170931785	simple_aae			0	R406W	single base exchange	rs121913003		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.990665170931785 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM000368)
known disease mutation: rs16826 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:220286254C>TN/A show variant in all transcripts IGV

HGNC symbol

DES

Ensembl transcript ID

ENST00000373960

Genbank transcript ID

NM_001927

UniProt peptide

P17661

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1216C>T
cDNA.1302C>T
g.3156C>T

AA changes

R406W Score: 101 explain score(s)

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

406

frameshift

known variant

Reference ID: rs121913003
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16826 (pathogenic for Myofibrillar myopathy 1|Muscular dystrophy, limb-girdle, type 2R|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000368)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000368)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000368)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.079	1
	1.018	1
(flanking)	4.092	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

406

mutated

not conserved

406

Ptroglodytes

all identical

ENSPTRG00000012955

406

Mmulatta

all identical

ENSMMUG00000017933

406

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026208

405

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000019275

394

protein features

start (aa)	end (aa)	feature	details
109	412	REGION	Rod.	lost
296	412	REGION	Coil 2B.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1413 / 1413

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

471 / 471

position of stopcodon in wt / mu cDNA

1499 / 1499

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

87 / 87

chromosome

strand

last intron/exon boundary

1458

theoretical NMD boundary in CDS

1321

length of CDS

1413

coding sequence (CDS) position

1216

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

1302

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

3156

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

220286254

original gDNA sequence snippet

ATGTGGAGATTGCCACCTACCGGAAGCTGCTGGAGGGAGAG

altered gDNA sequence snippet

ATGTGGAGATTGCCACCTACTGGAAGCTGCTGGAGGGAGAG

original cDNA sequence snippet

ATGTGGAGATTGCCACCTACCGGAAGCTGCTGGAGGGAGAG

altered cDNA sequence snippet

ATGTGGAGATTGCCACCTACTGGAAGCTGCTGGAGGGAGAG

wildtype AA sequence

MSQAYSSSQR VSSYRRTFGG APGFPLGSPL SSPVFPRAGF GSKGSSSSVT SRVYQVSRTS
GGAGGLGSLR ASRLGTTRTP SSYGAGELLD FSLADAVNQE FLTTRTNEKV ELQELNDRFA
NYIEKVRFLE QQNAALAAEV NRLKGREPTR VAELYEEELR ELRRQVEVLT NQRARVDVER
DNLLDDLQRL KAKLQEEIQL KEEAENNLAA FRADVDAATL ARIDLERRIE SLNEEIAFLK
KVHEEEIREL QAQLQEQQVQ VEMDMSKPDL TAALRDIRAQ YETIAAKNIS EAEEWYKSKV
SDLTQAANKN NDALRQAKQE MMEYRHQIQS YTCEIDALKG TNDSLMRQMR ELEDRFASEA
SGYQDNIARL EEEIRHLKDE MARHLREYQD LLNVKMALDV EIATYRKLLE GEESRINLPI
QTYSALNFRE TSPEQRGSEV HTKKTVMIKT IETRDGEVVS EATQQQHEVL *

mutated AA sequence

MSQAYSSSQR VSSYRRTFGG APGFPLGSPL SSPVFPRAGF GSKGSSSSVT SRVYQVSRTS
GGAGGLGSLR ASRLGTTRTP SSYGAGELLD FSLADAVNQE FLTTRTNEKV ELQELNDRFA
NYIEKVRFLE QQNAALAAEV NRLKGREPTR VAELYEEELR ELRRQVEVLT NQRARVDVER
DNLLDDLQRL KAKLQEEIQL KEEAENNLAA FRADVDAATL ARIDLERRIE SLNEEIAFLK
KVHEEEIREL QAQLQEQQVQ VEMDMSKPDL TAALRDIRAQ YETIAAKNIS EAEEWYKSKV
SDLTQAANKN NDALRQAKQE MMEYRHQIQS YTCEIDALKG TNDSLMRQMR ELEDRFASEA
SGYQDNIARL EEEIRHLKDE MARHLREYQD LLNVKMALDV EIATYWKLLE GEESRINLPI
QTYSALNFRE TSPEQRGSEV HTKKTVMIKT IETRDGEVVS EATQQQHEVL *

speed

1.31 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

disease causing

Problems