Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000377050
Querying Taster for transcript #2: ENST00000355973
MT speed 0 s - this script 3.615498 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
UBDpolymorphism_automatic4.87609952415369e-11simple_aaeaffectedS95Psingle base exchangers2076486show file
GABBR1polymorphism_automatic9.67732419754341e-08without_aaeaffectedsingle base exchangers2076486show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999951239 (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) chr6:29523872A>GN/A show variant in all transcripts   IGV
HGNC symbol UBD
Ensembl transcript ID ENST00000377050
Genbank transcript ID NM_006398
UniProt peptide O15205
alteration type single base exchange
alteration region CDS
DNA changes c.283T>C
cDNA.507T>C
g.3831T>C
AA changes S95P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 95
frameshift no
known variant Reference ID: rs2076486
databasehomozygous (G/G)heterozygousallele carriers
1000G181638819
ExAC129876938991
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3790
-0.7880
(flanking)-0.0710.017
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 increased3826wt: 0.8023 / mu: 0.8796 (marginal change - not scored)wt: GGAGCTGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAA
mu: GGAGCTGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAA		 ttgt|GGAG
Donor increased3833wt: 0.51 / mu: 0.61wt: GAGTCAGGTGATGAG
mu: GAGCCAGGTGATGAG		 GTCA|ggtg
Donor marginally increased3829wt: 0.9922 / mu: 0.9926 (marginal change - not scored)wt: TGTGGAGTCAGGTGA
mu: TGTGGAGCCAGGTGA		 TGGA|gtca
distance from splice site 256
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      95SDEELPLFLVESGDEAKRHLLQVR
mutated  not conserved    95SDEELPLFLVEPGDEAKRHLLQV
Ptroglodytes  all identical  ENSPTRG00000017901  95GDEELPLFLVESVDEGKRHLLQV
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000035186  92SDEELPLFLVESKNEGQRHLLRV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no alignment  F52C6.4  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
90163DOMAINUbiquitin-like 2.lost
109109MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
110110MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
111111MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
164165SITEActivation by thioester intermediate formation with UBA6.might get lost (downstream of altered splice site)
164165MUTAGENGG->AA: Impaired thioester formation- mediated activation by UBA6.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 498 / 498
position (AA) of stopcodon in wt / mu AA sequence 166 / 166
position of stopcodon in wt / mu cDNA 722 / 722
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 225 / 225
chromosome 6
strand -1
last intron/exon boundary 252
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 498
coding sequence (CDS) position 283
cDNA position
(for ins/del: last normal base / first normal base)		 507
gDNA position
(for ins/del: last normal base / first normal base)		 3831
chromosomal position
(for ins/del: last normal base / first normal base)		 29523872
original gDNA sequence snippet TGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAAAGAGG
altered gDNA sequence snippet TGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAAAGAGG
original cDNA sequence snippet TGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAAAGAGG
altered cDNA sequence snippet TGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAAAGAGG
wildtype AA sequence MAPNASCLCV HVRSEEWDLM TFDANPYDSV KKIKEHVRSK TKVPVQDQVL LLGSKILKPR
RSLSSYGIDK EKTIHLTLKV VKPSDEELPL FLVESGDEAK RHLLQVRRSS SVAQVKAMIE
TKTGIIPETQ IVTCNGKRLE DGKMMADYGI RKGNLLFLAC YCIGG*
mutated AA sequence MAPNASCLCV HVRSEEWDLM TFDANPYDSV KKIKEHVRSK TKVPVQDQVL LLGSKILKPR
RSLSSYGIDK EKTIHLTLKV VKPSDEELPL FLVEPGDEAK RHLLQVRRSS SVAQVKAMIE
TKTGIIPETQ IVTCNGKRLE DGKMMADYGI RKGNLLFLAC YCIGG*
speed 0.82 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: 0.999999903226758 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:29523872A>GN/A show variant in all transcripts   IGV
HGNC symbol GABBR1
Ensembl transcript ID ENST00000355973
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.3040T>C
g.77882T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2076486
databasehomozygous (G/G)heterozygousallele carriers
1000G181638819
ExAC129876938991
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3790
-0.7880
(flanking)-0.0710.017
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 932)
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased77877wt: 0.8023 / mu: 0.8796 (marginal change - not scored)wt: GGAGCTGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAA
mu: GGAGCTGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAA		 ttgt|GGAG
Donor marginally increased77880wt: 0.9922 / mu: 0.9926 (marginal change - not scored)wt: TGTGGAGTCAGGTGA
mu: TGTGGAGCCAGGTGA		 TGGA|gtca
Donor increased77884wt: 0.51 / mu: 0.61wt: GAGTCAGGTGATGAG
mu: GAGCCAGGTGATGAG		 GTCA|ggtg
distance from splice site 256
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 signal is predicted to be ok
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 248 / 248
chromosome 6
strand -1
last intron/exon boundary 2785
theoretical NMD boundary in CDS 2487
length of CDS 2535
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 3040
gDNA position
(for ins/del: last normal base / first normal base)		 77882
chromosomal position
(for ins/del: last normal base / first normal base)		 29523872
original gDNA sequence snippet TGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAAAGAGG
altered gDNA sequence snippet TGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAAAGAGG
original cDNA sequence snippet TGCCCTTGTTTCTTGTGGAGTCAGGTGATGAGGCAAAGAGG
altered cDNA sequence snippet TGCCCTTGTTTCTTGTGGAGCCAGGTGATGAGGCAAAGAGG
wildtype AA sequence MGPGAPFARV GWPLPLLVVM AAGVAPVWAS HSPHLPRPHS RVPPHPSSER RAVYIGALFP
MSGGWPGGQA CQPAVEMALE DVNSRRDILP DYELKLIHHD SKCDPGQATK YLYELLYNDP
IKIILMPGCS SVSTLVAEAA RMWNLIVLSY GSSSPALSNR QRFPTFFRTH PSATLHNPTR
VKLFEKWGWK KIATIQQTTE VFTSTLDDLE ERVKEAGIEI TFRQSFFSDP AVPVKNLKRQ
DARIIVGLFY ETEARKVFCE VYKERLFGKK YVWFLIGWYA DNWFKIYDPS INCTVDEMTE
AVEGHITTEI VMLNPANTRS ISNMTSQEFV EKLTKRLKRH PEETGGFQEA PLAYDAIWAL
ALALNKTSGG GGRSGVRLED FNYNNQTITD QIYRAMNSSS FEGVSGHVVF DASGSRMAWT
LIEQLQGGSY KKIGYYDSTK DDLSWSKTDK WIGGSPPADQ TLVIKTFRFL SQKLFISVSV
LSSLGIVLAV VCLSFNIYNS HVRYIQNSQP NLNNLTAVGC SLALAAVFPL GLDGYHIGRN
QFPFVCQARL WLLGLGFSLG YGSMFTKIWW VHTVFTKKEE KKEWRKTLEP WKLYATVGLL
VGMDVLTLAI WQIVDPLHRT IETFAKEEPK EDIDVSILPQ LEHCSSRKMN TWLGIFYGYK
GLLLLLGIFL AYETKSVSTE KINDHRAVGM AIYNVAVLCL ITAPVTMILS SQQDAAFAFA
SLAIVFSSYI TLVVLFVPKM RRLITRGEWQ SEAQDTMKTG SSTNNNEEEK SRLLEKENRE
LEKIIAEKEE RVSELRHQLQ SRQQLRSRRH PPTPPEPSGG LPRGPPEPPD RLSCDGSRVH
LLYK*
mutated AA sequence N/A
speed 0.86 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

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