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: ENST00000355973
Querying Taster for transcript #2: ENST00000383640
MT speed 3.02 s - this script 9.235119 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR2H2polymorphism_automatic4.9960036108132e-15simple_aaeaffectedA48Vsingle base exchangers1233387show file
GABBR1polymorphism_automatic7.40594969794728e-08without_aaeaffectedsingle base exchangers1233387show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (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) chr6:29555864C>TN/A show variant in all transcripts   IGV
HGNC symbol OR2H2
Ensembl transcript ID ENST00000383640
Genbank transcript ID NM_007160
UniProt peptide O95918
alteration type single base exchange
alteration region CDS
DNA changes c.143C>T
cDNA.182C>T
g.182C>T
AA changes A48V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
48
frameshift no
known variant Reference ID: rs1233387
databasehomozygous (T/T)heterozygousallele carriers
1000G32110761397
ExAC57962117526971
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9670
0.0140
(flanking)-0.1860
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 increased186wt: 0.7125 / mu: 0.7516 (marginal change - not scored)wt: ATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACTCTCC
mu: ATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACTCTCC
 gctg|GACC
Acc increased184wt: 0.33 / mu: 0.37wt: TCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACTCT
mu: TCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACTCT
 gcgc|TGGA
Acc increased180wt: 0.67 / mu: 0.84wt: ACACTCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCA
mu: ACACTCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCA
 gtct|GCGC
Acc increased187wt: 0.42 / mu: 0.61wt: TCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACTCTCCA
mu: TCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACTCTCCA
 ctgg|ACCC
distance from splice site 182
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      48LVGNTLIILLSALDPKLHSPMYFF
mutated  not conserved    48LVGNTLIILLSVLDPKLHSPMYF
Ptroglodytes  not conserved  ENSPTRG00000017900  48LVGNTLIILLSVLDPKLHSPMYF
Mmulatta  not conserved  ENSMMUG00000021482  48LVANTLIILLSVLDPRLHSPMYF
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
2447TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
4855TOPO_DOMCytoplasmic (Potential).lost
5151CONFLICTP -> T (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
5677TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
7898TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
8181CONFLICTV -> A (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
9595DISULFIDBy similarity.might get lost (downstream of altered splice site)
99118TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
113114CONFLICTLT -> MK (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
119137TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
138156TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
153153CONFLICTE -> G (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
157193TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
187187DISULFIDBy similarity.might get lost (downstream of altered splice site)
194217TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
218234TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
230232CONFLICTKGR -> TAW (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
235257TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
258270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
267267CONFLICTE -> G (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
271290TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
287287CONFLICTI -> V (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
291312TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
295296CONFLICTVT -> IK (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
299299CONFLICTF -> L (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
307312CONFLICTMGLTQS -> RDSRESWRAA (in Ref. 1; AAB36567).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 939 / 939
position (AA) of stopcodon in wt / mu AA sequence 313 / 313
position of stopcodon in wt / mu cDNA 978 / 978
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 40 / 40
chromosome 6
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 939
coding sequence (CDS) position 143
cDNA position
(for ins/del: last normal base / first normal base)
182
gDNA position
(for ins/del: last normal base / first normal base)
182
chromosomal position
(for ins/del: last normal base / first normal base)
29555864
original gDNA sequence snippet ACTCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACT
altered gDNA sequence snippet ACTCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACT
original cDNA sequence snippet ACTCATCATCCTGCTGTCTGCGCTGGACCCCAAGCTCCACT
altered cDNA sequence snippet ACTCATCATCCTGCTGTCTGTGCTGGACCCCAAGCTCCACT
wildtype AA sequence MVNQSSTPGF LLLGFSEHPG LERTLFVVVL TSYLLTLVGN TLIILLSALD PKLHSPMYFF
LSNLSFLDLC FTTSCVPQML VNLWGPKKTI SFLDCSVQIF IFLSLGTTEC ILLTVMAFDR
YVAVCQPLHY ATIIHPRLCW QLASVAWVIG LVESVVQTPS TLHLPFCPDR QVDDFVCEVP
ALIRLSCEDT SYNEIQVAVA SVFILVVPLS LILVSYGAIT WAVLRINSAK GRRKAFGTCS
SHLTVVTLFY SSVIAVYLQP KNPYAQERGK FFGLFYAVGT PSLNPLIYTL RNKEVTRAFR
RLLGKEMGLT QS*
mutated AA sequence MVNQSSTPGF LLLGFSEHPG LERTLFVVVL TSYLLTLVGN TLIILLSVLD PKLHSPMYFF
LSNLSFLDLC FTTSCVPQML VNLWGPKKTI SFLDCSVQIF IFLSLGTTEC ILLTVMAFDR
YVAVCQPLHY ATIIHPRLCW QLASVAWVIG LVESVVQTPS TLHLPFCPDR QVDDFVCEVP
ALIRLSCEDT SYNEIQVAVA SVFILVVPLS LILVSYGAIT WAVLRINSAK GRRKAFGTCS
SHLTVVTLFY SSVIAVYLQP KNPYAQERGK FFGLFYAVGT PSLNPLIYTL RNKEVTRAFR
RLLGKEMGLT QS*
speed 1.32 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: 0.999999925940503 (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) chr6:29555864C>TN/A show variant in all transcripts   IGV
HGNC symbol GABBR1
Ensembl transcript ID ENST00000355973
Genbank transcript ID N/A
UniProt peptide Q9UBS5
alteration type single base exchange
alteration region intron
DNA changes g.45890G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs1233387
databasehomozygous (T/T)heterozygousallele carriers
1000G32110761397
ExAC57962117526971
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9670
0.0140
(flanking)-0.1860
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 846)
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased45882wt: 0.33 / mu: 0.63wt: CTTGGGGTCCAGCGC
mu: CTTGGGGTCCAGCAC
 TGGG|gtcc
Donor marginally increased45892wt: 0.8479 / mu: 0.8719 (marginal change - not scored)wt: AGCGCAGACAGCAGG
mu: AGCACAGACAGCAGG
 CGCA|gaca
distance from splice site 15454
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 N/A
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)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
45890
chromosomal position
(for ins/del: last normal base / first normal base)
29555864
original gDNA sequence snippet AGTGGAGCTTGGGGTCCAGCGCAGACAGCAGGATGATGAGT
altered gDNA sequence snippet AGTGGAGCTTGGGGTCCAGCACAGACAGCAGGATGATGAGT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 1.70 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