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MutationTaster - study a chromosomal position

 MTQE documentation
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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 s - this script 2.669528 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CPOXdisease_causing_automatic0.999999999815077simple_aaeaffected0S208Fsingle base exchangers121917872show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999815077 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM024099)
  • known disease mutation: rs460 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:98309933G>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.623C>T
cDNA.842C>T
g.2635C>T
AA changes S208F Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 208
frameshift no
known variant Reference ID: rs121917872
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs460 (pathogenic for Coproporphyria) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024099)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024099)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024099)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0420.995
5.0431
(flanking)4.1791
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2644wt: 0.49 / mu: 0.64wt: GGTGAGCATTTCTGTTGTTCATGGAAATCTTTCAGAGGAAG
mu: GGTGAGCATTTTTGTTGTTCATGGAAATCTTTCAGAGGAAG		 ttca|TGGA
Acc marginally increased2643wt: 0.8483 / mu: 0.9050 (marginal change - not scored)wt: GGGTGAGCATTTCTGTTGTTCATGGAAATCTTTCAGAGGAA
mu: GGGTGAGCATTTTTGTTGTTCATGGAAATCTTTCAGAGGAA		 gttc|ATGG
Acc increased2646wt: 0.24 / mu: 0.35wt: TGAGCATTTCTGTTGTTCATGGAAATCTTTCAGAGGAAGCT
mu: TGAGCATTTTTGTTGTTCATGGAAATCTTTCAGAGGAAGCT		 catg|GAAA
Acc increased2645wt: 0.73 / mu: 0.82wt: GTGAGCATTTCTGTTGTTCATGGAAATCTTTCAGAGGAAGC
mu: GTGAGCATTTTTGTTGTTCATGGAAATCTTTCAGAGGAAGC		 tcat|GGAA
distance from splice site 67
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      208GCVFEKAGVSISVVHGNLSEEAAK
mutated  not conserved    208GCVFEKAGVSIFVVHGNLSEEAA
Ptroglodytes  all identical  ENSPTRG00000015151  208GCVFEKAGVSISVVHGNLSEEAA
Mmulatta  all identical  ENSMMUG00000010833  207GCVFEKAGVSISVVHGNLSEEAA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022742  197GRVFEKAGVSISVVHGNLSEEAA
Ggallus  all identical  ENSGALG00000015240  110GEVFEKAGVNVSVVFGQLSEEAA
Trubripes  all identical  ENSTRUG00000017671  210GKVFEKAGVNVSVVSGYLTEEAA
Drerio  all identical  ENSDARG00000062025  204GKIFEKAGVNVSVVYGNLTEEAA
Dmelanogaster  all identical  FBgn0021944  146GDVFEKAGVNISVVTGSLPPAAV
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000002047  158GKVFEKAGVNVSVVHGYLSEESI
protein features
start (aa)end (aa)featuredetails 
198213STRANDlost
216224HELIXmight get lost (downstream of altered splice site)
237251STRANDmight get lost (downstream of altered splice site)
244244BINDINGSubstrate.might get lost (downstream of altered splice site)
247247CONFLICTI -> T (in Ref. 7; CAA82250).might get lost (downstream of altered splice site)
256267STRANDmight get lost (downstream of altered splice site)
258258ACT_SITEProton donor.might get lost (downstream of altered splice site)
260262REGIONSubstrate binding.might get lost (downstream of altered splice site)
273284STRANDmight get lost (downstream of altered splice site)
290305HELIXmight get lost (downstream of altered splice site)
311322HELIXmight get lost (downstream of altered splice site)
326328HELIXmight get lost (downstream of altered splice site)
327327SITEImportant for dimerization.might get lost (downstream of altered splice site)
330342STRANDmight get lost (downstream of altered splice site)
347359HELIXmight get lost (downstream of altered splice site)
361372HELIXmight get lost (downstream of altered splice site)
371371MOD_RESN6-acetyllysine (By similarity).might get lost (downstream of altered splice site)
379399HELIXmight get lost (downstream of altered splice site)
392418MUTAGENMissing: Loss for dimerization.might get lost (downstream of altered splice site)
392428REGIONImportant for dimerization.might get lost (downstream of altered splice site)
406408HELIXmight get lost (downstream of altered splice site)
409411STRANDmight get lost (downstream of altered splice site)
411416REGIONSubstrate binding.might get lost (downstream of altered splice site)
414420HELIXmight get lost (downstream of altered splice site)
438447HELIXmight 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 3
strand -1
last intron/exon boundary 1497
theoretical NMD boundary in CDS 1227
length of CDS 1365
coding sequence (CDS) position 623
cDNA position
(for ins/del: last normal base / first normal base)		 842
gDNA position
(for ins/del: last normal base / first normal base)		 2635
chromosomal position
(for ins/del: last normal base / first normal base)		 98309933
original gDNA sequence snippet AAAGGCTGGGGTGAGCATTTCTGTTGTTCATGGAAATCTTT
altered gDNA sequence snippet AAAGGCTGGGGTGAGCATTTTTGTTGTTCATGGAAATCTTT
original cDNA sequence snippet AAAGGCTGGGGTGAGCATTTCTGTTGTTCATGGAAATCTTT
altered cDNA sequence snippet AAAGGCTGGGGTGAGCATTTTTGTTGTTCATGGAAATCTTT
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 EKAGVSIFVV 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*
speed 0.60 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
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