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: ENST00000380390
Querying Taster for transcript #2: ENST00000380371
MT speed 0 s - this script 2.962512 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
OR51A2polymorphism_automatic1.99840144432528e-15simple_aaeaffectedE235Qsingle base exchangers2570571show file
MMP26polymorphism_automatic2.7969358051827e-08without_aaeaffectedsingle base exchangers2570571show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999998 (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) chr11:4976241C>GN/A show variant in all transcripts   IGV
HGNC symbol OR51A2
Ensembl transcript ID ENST00000380371
Genbank transcript ID NM_001004748
UniProt peptide Q8NGJ7
alteration type single base exchange
alteration region CDS
DNA changes c.703G>C
cDNA.703G>C
g.703G>C
AA changes E235Q Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 235
frameshift no
known variant Reference ID: rs2570571
databasehomozygous (G/G)heterozygousallele carriers
1000G311536847
ExAC6037874014777
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.430
-1.8010
(flanking)-4.4370
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased694wt: 0.54 / mu: 0.73wt: CATCCAAAAAGGAGG
mu: CATCCAAAAAGGAGC		 TCCA|aaaa
Donor increased698wt: 0.32 / mu: 0.67wt: CAAAAAGGAGGAGCT
mu: CAAAAAGGAGCAGCT		 AAAA|ggag
Donor increased701wt: 0.61 / mu: 0.77wt: AAAGGAGGAGCTTAA
mu: AAAGGAGCAGCTTAA		 AGGA|ggag
Donor increased705wt: 0.72 / mu: 0.91wt: GAGGAGCTTAAGGCT
mu: GAGCAGCTTAAGGCT		 GGAG|ctta
Donor marginally increased696wt: 0.9596 / mu: 0.9607 (marginal change - not scored)wt: TCCAAAAAGGAGGAG
mu: TCCAAAAAGGAGCAG		 CAAA|aagg
distance from splice site 240
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      235KTVPGIASKKEELKALNTCVSHIC
mutated  all conserved    235KTVPGIASKKEQLKALN
Ptroglodytes  no homologue    
Mmulatta  all conserved  ENSMMUG00000001065  235KTVLGIASKKEQLKALN
Fcatus  all conserved  ENSFCAG00000010994  235KTVLGIASRKEQLKALN
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 
219238TOPO_DOMCytoplasmic (Potential).lost
239259TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
260274TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
275295TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
296313TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 942 / 942
position (AA) of stopcodon in wt / mu AA sequence 314 / 314
position of stopcodon in wt / mu cDNA 942 / 942
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 11
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 942
coding sequence (CDS) position 703
cDNA position
(for ins/del: last normal base / first normal base)		 703
gDNA position
(for ins/del: last normal base / first normal base)		 703
chromosomal position
(for ins/del: last normal base / first normal base)		 4976241
original gDNA sequence snippet GAATTGCATCCAAAAAGGAGGAGCTTAAGGCTCTCAATACT
altered gDNA sequence snippet GAATTGCATCCAAAAAGGAGCAGCTTAAGGCTCTCAATACT
original cDNA sequence snippet GAATTGCATCCAAAAAGGAGGAGCTTAAGGCTCTCAATACT
altered cDNA sequence snippet GAATTGCATCCAAAAAGGAGCAGCTTAAGGCTCTCAATACT
wildtype AA sequence MSIINTSYVE ITTFFLVGMP GLEYAHIWIS IPICSMYLIA ILGNGTILFI IKTEPSLHGP
MYYFLSMLAM SDLGLSLSSL PTVLSIFLFN APETSSSACF AQEFFIHGFS VLESSVLLIM
SFDRFLAIHN PLRYTSILTT VRVAQIGIVF SFKSMLLVLP FPFTLRSLRY CKKNQLSHSY
CLHQDVMKLA CSDNRIDVIY GFFGALCLMV DFILIAVSYT LILKTVPGIA SKKEELKALN
TCVSHICAVI IFYLPIINLA VVHRFAGHVS PLINVLMANV LLLVPPLMKP IVYCVKTKQI
RVRVVAKLCQ WKI*
mutated AA sequence MSIINTSYVE ITTFFLVGMP GLEYAHIWIS IPICSMYLIA ILGNGTILFI IKTEPSLHGP
MYYFLSMLAM SDLGLSLSSL PTVLSIFLFN APETSSSACF AQEFFIHGFS VLESSVLLIM
SFDRFLAIHN PLRYTSILTT VRVAQIGIVF SFKSMLLVLP FPFTLRSLRY CKKNQLSHSY
CLHQDVMKLA CSDNRIDVIY GFFGALCLMV DFILIAVSYT LILKTVPGIA SKKEQLKALN
TCVSHICAVI IFYLPIINLA VVHRFAGHVS PLINVLMANV LLLVPPLMKP IVYCVKTKQI
RVRVVAKLCQ WKI*
speed 0.52 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: 0.999999972030642 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr11:4976241C>GN/A show variant in all transcripts   IGV
HGNC symbol MMP26
Ensembl transcript ID ENST00000380390
Genbank transcript ID NM_021801
UniProt peptide Q9NRE1
alteration type single base exchange
alteration region intron
DNA changes g.250085C>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2570571
databasehomozygous (G/G)heterozygousallele carriers
1000G311536847
ExAC6037874014777
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.430
-1.8010
(flanking)-4.4370
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -47) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor gained2500810.48mu: CCTTAAGCTGCTCCT TTAA|gctg
distance from splice site 33057
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
117SIGNALPotential.might get lost (downstream of altered splice site)
1889PROPEPBy similarity. /FTId=PRO_0000028855.might get lost (downstream of altered splice site)
6464CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
7171CONFLICTM -> I (in Ref. 1; AAF80180).might get lost (downstream of altered splice site)
8087MOTIFCysteine switch (By similarity).might get lost (downstream of altered splice site)
8282METALZinc; in inhibited form (By similarity).might get lost (downstream of altered splice site)
208208METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
209209ACT_SITEBy similarity.might get lost (downstream of altered splice site)
212212METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
218218METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
221221CARBOHYDN-linked (GlcNAc...) (Potential).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 217 / 217
chromosome 11
strand 1
last intron/exon boundary 974
theoretical NMD boundary in CDS 707
length of CDS 786
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)		 250085
chromosomal position
(for ins/del: last normal base / first normal base)		 4976241
original gDNA sequence snippet AGTATTGAGAGCCTTAAGCTCCTCCTTTTTGGATGCAATTC
altered gDNA sequence snippet AGTATTGAGAGCCTTAAGCTGCTCCTTTTTGGATGCAATTC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MQLVILRVTI FLPWCFAVPV PPAADHKGWD FVEGYFHQFF LTKKESPLLT QETQTQLLQQ
FHRNGTDLLD MQMHALLHQP HCGVPDGSDT SISPGRCKWN KHTLTYRIIN YPHDMKPSAV
KDSIYNAVSI WSNVTPLIFQ QVQNGDADIK VSFWQWAHED GWPFDGPGGI LGHAFLPNSG
NPGVVHFDKN EHWSASDTGY NLFLVATHEI GHSLGLQHSG NQSSIMYPTY WYHDPRTFQL
SADDIQRIQH LYGEKCSSDI P*
mutated AA sequence N/A
speed 0.43 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