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: ENST00000264193
MT speed 0.46 s - this script 3.23469 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CPOX	disease_causing_automatic	0.994662122205684	simple_aae		affected	0	R331W	single base exchange	rs121917866		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.994662122205684 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940320)
known disease mutation: rs451 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:98304466G>AN/A show variant in all transcripts IGV

HGNC symbol

CPOX

Ensembl transcript ID

ENST00000264193

Genbank transcript ID

NM_000097

UniProt peptide

P36551

alteration type

single base exchange

alteration region

CDS

DNA changes

c.991C>T
cDNA.1210C>T
g.8102C>T

AA changes

R331W Score: 101 explain score(s)

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

331

frameshift

known variant

Reference ID: rs121917866
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs451 (pathogenic for Coproporphyria) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940320)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940320)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940320)

regulatory features

Cfos, Transcription Factor, Cfos TF binding
Cjun, Transcription Factor, Cjun TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL1, Transcription Factor, FOSL1 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Jund, Transcription Factor, Jund TF binding
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.459	1
	1.529	1
(flanking)	1.457	1

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	8095	wt: 0.42 / mu: 0.48	wt: TACTTCTTTATAGCCCATCGTGGAGAACGGCGGGGCATTGG mu: TACTTCTTTATAGCCCATCGTGGAGAATGGCGGGGCATTGG	tcgt\|GGAG
Donor marginally increased	8096	wt: 0.4192 / mu: 0.4198 (marginal change - not scored)	wt: ATCGTGGAGAACGGC mu: ATCGTGGAGAATGGC	CGTG\|gaga
Donor gained	8095	0.42	mu: CATCGTGGAGAATGG	TCGT\|ggag
Donor gained	8098	0.36	mu: CGTGGAGAATGGCGG	TGGA\|gaat

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

331

mutated

not conserved

331

Ptroglodytes

all identical

ENSPTRG00000015151

331

Mmulatta

all identical

ENSMMUG00000010833

330

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022742

320

Ggallus

all identical

ENSGALG00000015240

234

Trubripes

not conserved

ENSTRUG00000017671

333

Drerio

not conserved

ENSDARG00000062025

327

Dmelanogaster

not conserved

FBgn0021944

268

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000002047

281

protein features

start (aa)	end (aa)	feature	details
330	342	STRAND		lost
347	359	HELIX		might get lost (downstream of altered splice site)
361	372	HELIX		might get lost (downstream of altered splice site)
371	371	MOD_RES	N6-acetyllysine (By similarity).	might get lost (downstream of altered splice site)
379	399	HELIX		might get lost (downstream of altered splice site)
392	418	MUTAGEN	Missing: Loss for dimerization.	might get lost (downstream of altered splice site)
392	428	REGION	Important for dimerization.	might get lost (downstream of altered splice site)
406	408	HELIX		might get lost (downstream of altered splice site)
409	411	STRAND		might get lost (downstream of altered splice site)
411	416	REGION	Substrate binding.	might get lost (downstream of altered splice site)
414	420	HELIX		might get lost (downstream of altered splice site)
438	447	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1365 / 1365

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

455 / 455

position of stopcodon in wt / mu cDNA

1584 / 1584

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

220 / 220

chromosome

strand

-1

last intron/exon boundary

1497

theoretical NMD boundary in CDS

1227

length of CDS

1365

coding sequence (CDS) position

991

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

1210

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

8102

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

98304466

original gDNA sequence snippet

TTATAGCCCATCGTGGAGAACGGCGGGGCATTGGTGGTATC

altered gDNA sequence snippet

TTATAGCCCATCGTGGAGAATGGCGGGGCATTGGTGGTATC

original cDNA sequence snippet

TTATAGCCCATCGTGGAGAACGGCGGGGCATTGGTGGTATC

altered cDNA sequence snippet

TTATAGCCCATCGTGGAGAATGGCGGGGCATTGGTGGTATC

wildtype AA sequence

MALQLGRLSS GPCWLVARGG CGGPRAWSQC GGGGLRAWSQ RSAAGRVCRP PGPAGTEQSR
GLGHGSTSRG GPWVGTGLAA ALAGLVGLAT AAFGHVQRAE MLPKTSGTRA TSLGRPEEEE
DELAHRCSSF MAPPVTDLGE LRRRPGDMKT KMELLILETQ AQVCQALAQV DGGANFSVDR
WERKEGGGGI SCVLQDGCVF EKAGVSISVV HGNLSEEAAK QMRSRGKVLK TKDGKLPFCA
MGVSSVIHPK NPHAPTIHFN YRYFEVEEAD GNKQWWFGGG CDLTPTYLNQ EDAVHFHRTL
KEACDQHGPD LYPKFKKWCD DYFFIAHRGE RRGIGGIFFD DLDSPSKEEV FRFVQSCARA
VVPSYIPLVK KHCDDSFTPQ EKLWQQLRRG RYVEFNLLYD RGTKFGLFTP GSRIESILMS
LPLTARWEYM HSPSENSKEA EILEVLRHPR DWVR*

mutated AA sequence

MALQLGRLSS GPCWLVARGG CGGPRAWSQC GGGGLRAWSQ RSAAGRVCRP PGPAGTEQSR
GLGHGSTSRG GPWVGTGLAA ALAGLVGLAT AAFGHVQRAE MLPKTSGTRA TSLGRPEEEE
DELAHRCSSF MAPPVTDLGE LRRRPGDMKT KMELLILETQ AQVCQALAQV DGGANFSVDR
WERKEGGGGI SCVLQDGCVF EKAGVSISVV HGNLSEEAAK QMRSRGKVLK TKDGKLPFCA
MGVSSVIHPK NPHAPTIHFN YRYFEVEEAD GNKQWWFGGG CDLTPTYLNQ EDAVHFHRTL
KEACDQHGPD LYPKFKKWCD DYFFIAHRGE WRGIGGIFFD DLDSPSKEEV FRFVQSCARA
VVPSYIPLVK KHCDDSFTPQ EKLWQQLRRG RYVEFNLLYD RGTKFGLFTP GSRIESILMS
LPLTARWEYM HSPSENSKEA EILEVLRHPR DWVR*

speed

0.46 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