Yum, tasty mutations...

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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000377516
Querying Taster for transcript #2: ENST00000054668
MT speed 0 s - this script 3.39821 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
UTS2polymorphism_automatic5.09592368302947e-14simple_aaeaffectedT21Msingle base exchangers228648show file
UTS2polymorphism_automatic2.66511389201973e-06without_aaeaffectedsingle base exchangers228648show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999949 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM078165)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:7913430G>AN/A show variant in all transcripts   IGV
HGNC symbol UTS2
Ensembl transcript ID ENST00000054668
Genbank transcript ID NM_021995
UniProt peptide O95399
alteration type single base exchange
alteration region CDS
DNA changes c.62C>T
cDNA.62C>T
g.143C>T
AA changes T21M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 21
frameshift no
known variant Reference ID: rs228648
databasehomozygous (A/A)heterozygousallele carriers
1000G60911781787
ExAC17384-200115383

known disease mutation at this position, please check HGMD for details (HGMD ID CM078165)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3420.072
-0.3250.007
(flanking)-0.3380.012
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased151wt: 0.8501 / mu: 0.9122 (marginal change - not scored)wt: CTCATAAATCCACGTCTCTTTGCTTTGGCCACTTCAACTCA
mu: CTCATAAATCCATGTCTCTTTGCTTTGGCCACTTCAACTCA		 cttt|GCTT
Acc increased153wt: 0.77 / mu: 0.89wt: CATAAATCCACGTCTCTTTGCTTTGGCCACTTCAACTCATA
mu: CATAAATCCATGTCTCTTTGCTTTGGCCACTTCAACTCATA		 ttgc|TTTG
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      21LCVTSARTHKSTSLCFGHFNSYPS
mutated  not conserved    21LCVTSARTHKSMSLCFGHFNSYP
Ptroglodytes  not conserved  ENSPTRG00000000100  5YKLASCCLLFIGFLNPLL
Mmulatta  not conserved  ENSMMUG00000000625  5YKLASCCLLFIGFLNPLF
Fcatus  no alignment  ENSFCAG00000004372  n/a
Mmusculus  no alignment  ENSMUSG00000028963  n/a
Ggallus  no alignment  ENSGALG00000000556  n/a
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
21110PROPEP /FTId=PRO_0000036346.lost
114124PEPTIDEUrotensin-2. /FTId=PRO_0000036347.might get lost (downstream of altered splice site)
118118DISULFIDBy similarity.might get lost (downstream of altered splice site)
123123DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 420 / 420
position (AA) of stopcodon in wt / mu AA sequence 140 / 140
position of stopcodon in wt / mu cDNA 420 / 420
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 1 / 1
chromosome 1
strand -1
last intron/exon boundary 304
theoretical NMD boundary in CDS 253
length of CDS 420
coding sequence (CDS) position 62
cDNA position
(for ins/del: last normal base / first normal base)		 62
gDNA position
(for ins/del: last normal base / first normal base)		 143
chromosomal position
(for ins/del: last normal base / first normal base)		 7913430
original gDNA sequence snippet TGCTCGGACTCATAAATCCACGTCTCTTTGCTTTGGCCACT
altered gDNA sequence snippet TGCTCGGACTCATAAATCCATGTCTCTTTGCTTTGGCCACT
original cDNA sequence snippet TGCTCGGACTCATAAATCCACGTCTCTTTGCTTTGGCCACT
altered cDNA sequence snippet TGCTCGGACTCATAAATCCATGTCTCTTTGCTTTGGCCACT
wildtype AA sequence METNVFHLML CVTSARTHKS TSLCFGHFNS YPSLPLIHDL LLEISFQLSA PHEDARLTPE
ELERASLLQI LPEMLGAERG DILRKADSST NIFNPRGNLR KFQDFSGQDP NILLSHLLAR
IWKPYKKRET PDCFWKYCV*
mutated AA sequence METNVFHLML CVTSARTHKS MSLCFGHFNS YPSLPLIHDL LLEISFQLSA PHEDARLTPE
ELERASLLQI LPEMLGAERG DILRKADSST NIFNPRGNLR KFQDFSGQDP NILLSHLLAR
IWKPYKKRET PDCFWKYCV*
speed 0.78 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999997334886108 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM078165)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:7913430G>AN/A show variant in all transcripts   IGV
HGNC symbol UTS2
Ensembl transcript ID ENST00000377516
Genbank transcript ID N/A
UniProt peptide O95399
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.143C>T
g.143C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs228648
databasehomozygous (A/A)heterozygousallele carriers
1000G60911781787
ExAC17384-200115383

known disease mutation at this position, please check HGMD for details (HGMD ID CM078165)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3420.072
-0.3250.007
(flanking)-0.3380.012
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -55) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased151wt: 0.8501 / mu: 0.9122 (marginal change - not scored)wt: CTCATAAATCCACGTCTCTTTGCTTTGGCCACTTCAACTCA
mu: CTCATAAATCCATGTCTCTTTGCTTTGGCCACTTCAACTCA		 cttt|GCTT
Acc increased153wt: 0.77 / mu: 0.89wt: CATAAATCCACGTCTCTTTGCTTTGGCCACTTCAACTCATA
mu: CATAAATCCATGTCTCTTTGCTTTGGCCACTTCAACTCATA		 ttgc|TTTG
distance from splice site 64
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
120SIGNALmight get lost (downstream of altered splice site)
21110PROPEP /FTId=PRO_0000036346.might get lost (downstream of altered splice site)
114124PEPTIDEUrotensin-2. /FTId=PRO_0000036347.might get lost (downstream of altered splice site)
118118DISULFIDBy similarity.might get lost (downstream of altered splice site)
123123DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 322 / 322
chromosome 1
strand -1
last intron/exon boundary 734
theoretical NMD boundary in CDS 362
length of CDS 420
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 143
gDNA position
(for ins/del: last normal base / first normal base)		 143
chromosomal position
(for ins/del: last normal base / first normal base)		 7913430
original gDNA sequence snippet TGCTCGGACTCATAAATCCACGTCTCTTTGCTTTGGCCACT
altered gDNA sequence snippet TGCTCGGACTCATAAATCCATGTCTCTTTGCTTTGGCCACT
original cDNA sequence snippet TGCTCGGACTCATAAATCCACGTCTCTTTGCTTTGGCCACT
altered cDNA sequence snippet TGCTCGGACTCATAAATCCATGTCTCTTTGCTTTGGCCACT
wildtype AA sequence MYKLASCCLL FIGFLNPLLS LPLLDSREIS FQLSAPHEDA RLTPEELERA SLLQILPEML
GAERGDILRK ADSSTNIFNP RGNLRKFQDF SGQDPNILLS HLLARIWKPY KKQRRKLRQD
LRLWKKEPGL RIFKNYVWV*
mutated AA sequence N/A
speed 0.63 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

Problems