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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000560371
Querying Taster for transcript #2: ENST00000392745
Querying Taster for transcript #3: ENST00000539721
Querying Taster for transcript #4: ENST00000351691
Querying Taster for transcript #5: ENST00000347662
MT speed 0 s - this script 4.1931 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TRAF3polymorphism_automatic3.99680288865056e-15simple_aaeaffectedM129Tsingle base exchangers1131877show file
TRAF3polymorphism_automatic9.99200722162641e-15simple_aaeaffectedM129Tsingle base exchangers1131877show file
TRAF3polymorphism_automatic9.99200722162641e-15simple_aaeaffectedM129Tsingle base exchangers1131877show file
TRAF3polymorphism_automatic9.99200722162641e-15simple_aaeaffectedM129Tsingle base exchangers1131877show file
TRAF3polymorphism_automatic9.99200722162641e-15simple_aaeaffectedM129Tsingle base exchangers1131877show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999996 (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) chr14:103342049T>CN/A show variant in all transcripts   IGV
HGNC symbol TRAF3
Ensembl transcript ID ENST00000539721
Genbank transcript ID NM_001199427
UniProt peptide Q13114
alteration type single base exchange
alteration region CDS
DNA changes c.386T>C
cDNA.477T>C
g.98237T>C
AA changes M129T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 129
frameshift no
known variant Reference ID: rs1131877
databasehomozygous (C/C)heterozygousallele carriers
1000G7658231588
ExAC80381669124729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0080
0.9520
(flanking)-5.3340
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased98231wt: 0.9494 / mu: 0.9521 (marginal change - not scored)wt: AGAGCAGTTAATGCT
mu: AGAGCAGTTAACGCT		 AGCA|gtta
Donor gained982320.30mu: GAGCAGTTAACGCTG GCAG|ttaa
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      129RNESRGCAEQLMLGHLLVHLKNDC
mutated  not conserved    129SRGCAEQLTLGHLLVHLKND
Ptroglodytes  not conserved  ENSPTRG00000006746  129SRGCAEQLTLGHLLVHLKND
Mmulatta  no homologue    
Fcatus  all conserved  ENSFCAG00000010003  123RADCKEKVLRRDLRDHVEKA
Mmusculus  not conserved  ENSMUSG00000021277  128GRGCAEQLTLGHLLVHLKNE
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000005547  139RSEANGCQEQMRLQQIPDHL-NT
Drerio  not conserved  ENSDARG00000022000  132RSEKNGCKEQMCLQQVMEHLVICPYFEVPCPLGKCKEKMMRKDMPEHLSRK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000012746  124TRGCKELITLGNLLIHLKSDCQFEELSCPRADCKEKVIRKDLSDHIEKT
protein features
start (aa)end (aa)featuredetails 
134134CONFLICTMissing (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
135190ZN_FINGTRAF-type 1.might get lost (downstream of altered splice site)
156156CROSSLNKGlycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).might get lost (downstream of altered splice site)
158158CONFLICTL -> F (in Ref. 6; BAH13910).might get lost (downstream of altered splice site)
191249ZN_FINGTRAF-type 2.might get lost (downstream of altered splice site)
218242CONFLICTMissing (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
267338COILEDPotential.might get lost (downstream of altered splice site)
339339CONFLICTP -> S (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
365373TURNmight get lost (downstream of altered splice site)
375377TURNmight get lost (downstream of altered splice site)
378410HELIXmight get lost (downstream of altered splice site)
405405CONFLICTR -> G (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
415423STRANDmight get lost (downstream of altered splice site)
415560DOMAINMATH.might get lost (downstream of altered splice site)
425433HELIXmight get lost (downstream of altered splice site)
438441STRANDmight get lost (downstream of altered splice site)
441441MUTAGENY->A: Abolishes interaction with RNF216; when associated with A-443.might get lost (downstream of altered splice site)
443443MUTAGENQ->A: Abolishes interaction with RNF216; when associated with A-441.might get lost (downstream of altered splice site)
445448STRANDmight get lost (downstream of altered splice site)
453459STRANDmight get lost (downstream of altered splice site)
459459MUTAGENY->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
464466HELIXmight get lost (downstream of altered splice site)
467469TURNmight get lost (downstream of altered splice site)
470478STRANDmight get lost (downstream of altered splice site)
483485HELIXmight get lost (downstream of altered splice site)
494498STRANDmight get lost (downstream of altered splice site)
502504STRANDmight get lost (downstream of altered splice site)
508512STRANDmight get lost (downstream of altered splice site)
512512MUTAGENF->E: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521521MUTAGENF->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521523STRANDmight get lost (downstream of altered splice site)
525528STRANDmight get lost (downstream of altered splice site)
532539STRANDmight get lost (downstream of altered splice site)
540545HELIXmight get lost (downstream of altered splice site)
553560STRANDmight get lost (downstream of altered splice site)
563565STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1458 / 1458
position (AA) of stopcodon in wt / mu AA sequence 486 / 486
position of stopcodon in wt / mu cDNA 1549 / 1549
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 92 / 92
chromosome 14
strand 1
last intron/exon boundary 978
theoretical NMD boundary in CDS 836
length of CDS 1458
coding sequence (CDS) position 386
cDNA position
(for ins/del: last normal base / first normal base)		 477
gDNA position
(for ins/del: last normal base / first normal base)		 98237
chromosomal position
(for ins/del: last normal base / first normal base)		 103342049
original gDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGA
altered gDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGA
original cDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGC
altered cDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGC
wildtype AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLML GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ VSLLQNESVE KNKSIQSLHN QICSFEIEIE RQKEMLRNNE SKILHLQRVI
DSQAEKLKEL DKEIRPFRQN WEEADSMKSS VESLQNRVTE LESVDKSAGQ VARNTGLLES
QLSRHDQMLS VHDIRLADMD LRFQVLETAS YNGVLIWKIR DYKRRKQEAV MGKTLSLYSQ
PFYTGYFGYK MCARVYLNGD GMGKGTHLSL FFVIMRGEYD ALLPWPFKQK VTLMLMDQGS
SRRHLGDAFK PDPNSSSFKK PTGEMNIASG CPVFVAQTVL ENGTYIKDDT IFIKVIVDTS
DLPDP*
mutated AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLTL GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ VSLLQNESVE KNKSIQSLHN QICSFEIEIE RQKEMLRNNE SKILHLQRVI
DSQAEKLKEL DKEIRPFRQN WEEADSMKSS VESLQNRVTE LESVDKSAGQ VARNTGLLES
QLSRHDQMLS VHDIRLADMD LRFQVLETAS YNGVLIWKIR DYKRRKQEAV MGKTLSLYSQ
PFYTGYFGYK MCARVYLNGD GMGKGTHLSL FFVIMRGEYD ALLPWPFKQK VTLMLMDQGS
SRRHLGDAFK PDPNSSSFKK PTGEMNIASG CPVFVAQTVL ENGTYIKDDT IFIKVIVDTS
DLPDP*
speed 0.61 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: simple_aae, prob: 0.99999999999999 (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) chr14:103342049T>CN/A show variant in all transcripts   IGV
HGNC symbol TRAF3
Ensembl transcript ID ENST00000560371
Genbank transcript ID NM_003300
UniProt peptide Q13114
alteration type single base exchange
alteration region CDS
DNA changes c.386T>C
cDNA.603T>C
g.98237T>C
AA changes M129T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 129
frameshift no
known variant Reference ID: rs1131877
databasehomozygous (C/C)heterozygousallele carriers
1000G7658231588
ExAC80381669124729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0080
0.9520
(flanking)-5.3340
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased98231wt: 0.9494 / mu: 0.9521 (marginal change - not scored)wt: AGAGCAGTTAATGCT
mu: AGAGCAGTTAACGCT		 AGCA|gtta
Donor gained982320.30mu: GAGCAGTTAACGCTG GCAG|ttaa
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      129RNESRGCAEQLMLGHLLVHLKNDC
mutated  not conserved    129SRGCAEQLTLGHLLVHLKND
Ptroglodytes  not conserved  ENSPTRG00000006746  129SRGCAEQLTLGHLLVHLKND
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000010003  109---------------HLKND
Mmusculus  not conserved  ENSMUSG00000021277  128GRGCAEQLTLGHLLVHLKNE
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000005547  139RSEANGCQEQMRLQQIPDHL-NT
Drerio  not conserved  ENSDARG00000022000  132RSEKNGCKEQMCLQQVMEHLVI-
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000012746  124TRGCKELITLGNLLIHLKSD
protein features
start (aa)end (aa)featuredetails 
134134CONFLICTMissing (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
135190ZN_FINGTRAF-type 1.might get lost (downstream of altered splice site)
156156CROSSLNKGlycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).might get lost (downstream of altered splice site)
158158CONFLICTL -> F (in Ref. 6; BAH13910).might get lost (downstream of altered splice site)
191249ZN_FINGTRAF-type 2.might get lost (downstream of altered splice site)
218242CONFLICTMissing (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
267338COILEDPotential.might get lost (downstream of altered splice site)
339339CONFLICTP -> S (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
365373TURNmight get lost (downstream of altered splice site)
375377TURNmight get lost (downstream of altered splice site)
378410HELIXmight get lost (downstream of altered splice site)
405405CONFLICTR -> G (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
415423STRANDmight get lost (downstream of altered splice site)
415560DOMAINMATH.might get lost (downstream of altered splice site)
425433HELIXmight get lost (downstream of altered splice site)
438441STRANDmight get lost (downstream of altered splice site)
441441MUTAGENY->A: Abolishes interaction with RNF216; when associated with A-443.might get lost (downstream of altered splice site)
443443MUTAGENQ->A: Abolishes interaction with RNF216; when associated with A-441.might get lost (downstream of altered splice site)
445448STRANDmight get lost (downstream of altered splice site)
453459STRANDmight get lost (downstream of altered splice site)
459459MUTAGENY->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
464466HELIXmight get lost (downstream of altered splice site)
467469TURNmight get lost (downstream of altered splice site)
470478STRANDmight get lost (downstream of altered splice site)
483485HELIXmight get lost (downstream of altered splice site)
494498STRANDmight get lost (downstream of altered splice site)
502504STRANDmight get lost (downstream of altered splice site)
508512STRANDmight get lost (downstream of altered splice site)
512512MUTAGENF->E: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521521MUTAGENF->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521523STRANDmight get lost (downstream of altered splice site)
525528STRANDmight get lost (downstream of altered splice site)
532539STRANDmight get lost (downstream of altered splice site)
540545HELIXmight get lost (downstream of altered splice site)
553560STRANDmight get lost (downstream of altered splice site)
563565STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1707 / 1707
position (AA) of stopcodon in wt / mu AA sequence 569 / 569
position of stopcodon in wt / mu cDNA 1924 / 1924
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 218 / 218
chromosome 14
strand 1
last intron/exon boundary 1353
theoretical NMD boundary in CDS 1085
length of CDS 1707
coding sequence (CDS) position 386
cDNA position
(for ins/del: last normal base / first normal base)		 603
gDNA position
(for ins/del: last normal base / first normal base)		 98237
chromosomal position
(for ins/del: last normal base / first normal base)		 103342049
original gDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGA
altered gDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGA
original cDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGC
altered cDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGC
wildtype AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLML GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSELSA HLSECVNAPS TCSFKRYGCV
FQGTNQQIKA HEASSAVQHV NLLKEWSNSL EKKVSLLQNE SVEKNKSIQS LHNQICSFEI
EIERQKEMLR NNESKILHLQ RVIDSQAEKL KELDKEIRPF RQNWEEADSM KSSVESLQNR
VTELESVDKS AGQVARNTGL LESQLSRHDQ MLSVHDIRLA DMDLRFQVLE TASYNGVLIW
KIRDYKRRKQ EAVMGKTLSL YSQPFYTGYF GYKMCARVYL NGDGMGKGTH LSLFFVIMRG
EYDALLPWPF KQKVTLMLMD QGSSRRHLGD AFKPDPNSSS FKKPTGEMNI ASGCPVFVAQ
TVLENGTYIK DDTIFIKVIV DTSDLPDP*
mutated AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLTL GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSELSA HLSECVNAPS TCSFKRYGCV
FQGTNQQIKA HEASSAVQHV NLLKEWSNSL EKKVSLLQNE SVEKNKSIQS LHNQICSFEI
EIERQKEMLR NNESKILHLQ RVIDSQAEKL KELDKEIRPF RQNWEEADSM KSSVESLQNR
VTELESVDKS AGQVARNTGL LESQLSRHDQ MLSVHDIRLA DMDLRFQVLE TASYNGVLIW
KIRDYKRRKQ EAVMGKTLSL YSQPFYTGYF GYKMCARVYL NGDGMGKGTH LSLFFVIMRG
EYDALLPWPF KQKVTLMLMD QGSSRRHLGD AFKPDPNSSS FKKPTGEMNI ASGCPVFVAQ
TVLENGTYIK DDTIFIKVIV DTSDLPDP*
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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999999 (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) chr14:103342049T>CN/A show variant in all transcripts   IGV
HGNC symbol TRAF3
Ensembl transcript ID ENST00000392745
Genbank transcript ID N/A
UniProt peptide Q13114
alteration type single base exchange
alteration region CDS
DNA changes c.386T>C
cDNA.661T>C
g.98237T>C
AA changes M129T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 129
frameshift no
known variant Reference ID: rs1131877
databasehomozygous (C/C)heterozygousallele carriers
1000G7658231588
ExAC80381669124729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0080
0.9520
(flanking)-5.3340
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased98231wt: 0.9494 / mu: 0.9521 (marginal change - not scored)wt: AGAGCAGTTAATGCT
mu: AGAGCAGTTAACGCT		 AGCA|gtta
Donor gained982320.30mu: GAGCAGTTAACGCTG GCAG|ttaa
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      129RNESRGCAEQLMLGHLLVHLKNDC
mutated  not conserved    129SRGCAEQLTLGHLLVHLKND
Ptroglodytes  not conserved  ENSPTRG00000006746  129SRGCAEQLTLGHLLVHLKND
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000010003  109---------------HLKND
Mmusculus  not conserved  ENSMUSG00000021277  128GRGCAEQLTLGHLLVHLKNE
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000005547  139RSEANGCQEQMRLQQIPDHL-NT
Drerio  not conserved  ENSDARG00000022000  132RSEKNGCKEQMCLQQVMEHLVI-
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000012746  124TRGCKELITLGNLLIHLKSD
protein features
start (aa)end (aa)featuredetails 
134134CONFLICTMissing (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
135190ZN_FINGTRAF-type 1.might get lost (downstream of altered splice site)
156156CROSSLNKGlycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).might get lost (downstream of altered splice site)
158158CONFLICTL -> F (in Ref. 6; BAH13910).might get lost (downstream of altered splice site)
191249ZN_FINGTRAF-type 2.might get lost (downstream of altered splice site)
218242CONFLICTMissing (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
267338COILEDPotential.might get lost (downstream of altered splice site)
339339CONFLICTP -> S (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
365373TURNmight get lost (downstream of altered splice site)
375377TURNmight get lost (downstream of altered splice site)
378410HELIXmight get lost (downstream of altered splice site)
405405CONFLICTR -> G (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
415423STRANDmight get lost (downstream of altered splice site)
415560DOMAINMATH.might get lost (downstream of altered splice site)
425433HELIXmight get lost (downstream of altered splice site)
438441STRANDmight get lost (downstream of altered splice site)
441441MUTAGENY->A: Abolishes interaction with RNF216; when associated with A-443.might get lost (downstream of altered splice site)
443443MUTAGENQ->A: Abolishes interaction with RNF216; when associated with A-441.might get lost (downstream of altered splice site)
445448STRANDmight get lost (downstream of altered splice site)
453459STRANDmight get lost (downstream of altered splice site)
459459MUTAGENY->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
464466HELIXmight get lost (downstream of altered splice site)
467469TURNmight get lost (downstream of altered splice site)
470478STRANDmight get lost (downstream of altered splice site)
483485HELIXmight get lost (downstream of altered splice site)
494498STRANDmight get lost (downstream of altered splice site)
502504STRANDmight get lost (downstream of altered splice site)
508512STRANDmight get lost (downstream of altered splice site)
512512MUTAGENF->E: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521521MUTAGENF->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521523STRANDmight get lost (downstream of altered splice site)
525528STRANDmight get lost (downstream of altered splice site)
532539STRANDmight get lost (downstream of altered splice site)
540545HELIXmight get lost (downstream of altered splice site)
553560STRANDmight get lost (downstream of altered splice site)
563565STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1707 / 1707
position (AA) of stopcodon in wt / mu AA sequence 569 / 569
position of stopcodon in wt / mu cDNA 1982 / 1982
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 276 / 276
chromosome 14
strand 1
last intron/exon boundary 1411
theoretical NMD boundary in CDS 1085
length of CDS 1707
coding sequence (CDS) position 386
cDNA position
(for ins/del: last normal base / first normal base)		 661
gDNA position
(for ins/del: last normal base / first normal base)		 98237
chromosomal position
(for ins/del: last normal base / first normal base)		 103342049
original gDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGA
altered gDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGA
original cDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGC
altered cDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGC
wildtype AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLML GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSELSA HLSECVNAPS TCSFKRYGCV
FQGTNQQIKA HEASSAVQHV NLLKEWSNSL EKKVSLLQNE SVEKNKSIQS LHNQICSFEI
EIERQKEMLR NNESKILHLQ RVIDSQAEKL KELDKEIRPF RQNWEEADSM KSSVESLQNR
VTELESVDKS AGQVARNTGL LESQLSRHDQ MLSVHDIRLA DMDLRFQVLE TASYNGVLIW
KIRDYKRRKQ EAVMGKTLSL YSQPFYTGYF GYKMCARVYL NGDGMGKGTH LSLFFVIMRG
EYDALLPWPF KQKVTLMLMD QGSSRRHLGD AFKPDPNSSS FKKPTGEMNI ASGCPVFVAQ
TVLENGTYIK DDTIFIKVIV DTSDLPDP*
mutated AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLTL GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSELSA HLSECVNAPS TCSFKRYGCV
FQGTNQQIKA HEASSAVQHV NLLKEWSNSL EKKVSLLQNE SVEKNKSIQS LHNQICSFEI
EIERQKEMLR NNESKILHLQ RVIDSQAEKL KELDKEIRPF RQNWEEADSM KSSVESLQNR
VTELESVDKS AGQVARNTGL LESQLSRHDQ MLSVHDIRLA DMDLRFQVLE TASYNGVLIW
KIRDYKRRKQ EAVMGKTLSL YSQPFYTGYF GYKMCARVYL NGDGMGKGTH LSLFFVIMRG
EYDALLPWPF KQKVTLMLMD QGSSRRHLGD AFKPDPNSSS FKKPTGEMNI ASGCPVFVAQ
TVLENGTYIK DDTIFIKVIV DTSDLPDP*
speed 0.94 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: simple_aae, prob: 0.99999999999999 (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) chr14:103342049T>CN/A show variant in all transcripts   IGV
HGNC symbol TRAF3
Ensembl transcript ID ENST00000351691
Genbank transcript ID N/A
UniProt peptide Q13114
alteration type single base exchange
alteration region CDS
DNA changes c.386T>C
cDNA.522T>C
g.98237T>C
AA changes M129T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 129
frameshift no
known variant Reference ID: rs1131877
databasehomozygous (C/C)heterozygousallele carriers
1000G7658231588
ExAC80381669124729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0080
0.9520
(flanking)-5.3340
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased98231wt: 0.9494 / mu: 0.9521 (marginal change - not scored)wt: AGAGCAGTTAATGCT
mu: AGAGCAGTTAACGCT		 AGCA|gtta
Donor gained982320.30mu: GAGCAGTTAACGCTG GCAG|ttaa
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      129RNESRGCAEQLMLGHLLVHLKNDC
mutated  not conserved    129SRGCAEQLTLGHLLVHLKND
Ptroglodytes  not conserved  ENSPTRG00000006746  129SRGCAEQLTLGHLLVHLKND
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000010003  109---------------HLKND
Mmusculus  not conserved  ENSMUSG00000021277  128GRGCAEQLTLGHLLVHLKNE
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000005547  139RSEANGCQEQMRLQQIPDHL-NT
Drerio  not conserved  ENSDARG00000022000  132RSEKNGCKEQMCLQQVMEHLVI-
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000012746  124TRGCKELITLGNLLIHLKSD
protein features
start (aa)end (aa)featuredetails 
134134CONFLICTMissing (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
135190ZN_FINGTRAF-type 1.might get lost (downstream of altered splice site)
156156CROSSLNKGlycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).might get lost (downstream of altered splice site)
158158CONFLICTL -> F (in Ref. 6; BAH13910).might get lost (downstream of altered splice site)
191249ZN_FINGTRAF-type 2.might get lost (downstream of altered splice site)
218242CONFLICTMissing (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
267338COILEDPotential.might get lost (downstream of altered splice site)
339339CONFLICTP -> S (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
365373TURNmight get lost (downstream of altered splice site)
375377TURNmight get lost (downstream of altered splice site)
378410HELIXmight get lost (downstream of altered splice site)
405405CONFLICTR -> G (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
415423STRANDmight get lost (downstream of altered splice site)
415560DOMAINMATH.might get lost (downstream of altered splice site)
425433HELIXmight get lost (downstream of altered splice site)
438441STRANDmight get lost (downstream of altered splice site)
441441MUTAGENY->A: Abolishes interaction with RNF216; when associated with A-443.might get lost (downstream of altered splice site)
443443MUTAGENQ->A: Abolishes interaction with RNF216; when associated with A-441.might get lost (downstream of altered splice site)
445448STRANDmight get lost (downstream of altered splice site)
453459STRANDmight get lost (downstream of altered splice site)
459459MUTAGENY->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
464466HELIXmight get lost (downstream of altered splice site)
467469TURNmight get lost (downstream of altered splice site)
470478STRANDmight get lost (downstream of altered splice site)
483485HELIXmight get lost (downstream of altered splice site)
494498STRANDmight get lost (downstream of altered splice site)
502504STRANDmight get lost (downstream of altered splice site)
508512STRANDmight get lost (downstream of altered splice site)
512512MUTAGENF->E: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521521MUTAGENF->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521523STRANDmight get lost (downstream of altered splice site)
525528STRANDmight get lost (downstream of altered splice site)
532539STRANDmight get lost (downstream of altered splice site)
540545HELIXmight get lost (downstream of altered splice site)
553560STRANDmight get lost (downstream of altered splice site)
563565STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1632 / 1632
position (AA) of stopcodon in wt / mu AA sequence 544 / 544
position of stopcodon in wt / mu cDNA 1768 / 1768
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 137 / 137
chromosome 14
strand 1
last intron/exon boundary 1197
theoretical NMD boundary in CDS 1010
length of CDS 1632
coding sequence (CDS) position 386
cDNA position
(for ins/del: last normal base / first normal base)		 522
gDNA position
(for ins/del: last normal base / first normal base)		 98237
chromosomal position
(for ins/del: last normal base / first normal base)		 103342049
original gDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGA
altered gDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGA
original cDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGC
altered cDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGC
wildtype AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLML GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSEGTN QQIKAHEASS AVQHVNLLKE
WSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS
QAEKLKELDK EIRPFRQNWE EADSMKSSVE SLQNRVTELE SVDKSAGQVA RNTGLLESQL
SRHDQMLSVH DIRLADMDLR FQVLETASYN GVLIWKIRDY KRRKQEAVMG KTLSLYSQPF
YTGYFGYKMC ARVYLNGDGM GKGTHLSLFF VIMRGEYDAL LPWPFKQKVT LMLMDQGSSR
RHLGDAFKPD PNSSSFKKPT GEMNIASGCP VFVAQTVLEN GTYIKDDTIF IKVIVDTSDL
PDP*
mutated AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLTL GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSEGTN QQIKAHEASS AVQHVNLLKE
WSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS
QAEKLKELDK EIRPFRQNWE EADSMKSSVE SLQNRVTELE SVDKSAGQVA RNTGLLESQL
SRHDQMLSVH DIRLADMDLR FQVLETASYN GVLIWKIRDY KRRKQEAVMG KTLSLYSQPF
YTGYFGYKMC ARVYLNGDGM GKGTHLSLFF VIMRGEYDAL LPWPFKQKVT LMLMDQGSSR
RHLGDAFKPD PNSSSFKKPT GEMNIASGCP VFVAQTVLEN GTYIKDDTIF IKVIVDTSDL
PDP*
speed 0.58 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: simple_aae, prob: 0.99999999999999 (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) chr14:103342049T>CN/A show variant in all transcripts   IGV
HGNC symbol TRAF3
Ensembl transcript ID ENST00000347662
Genbank transcript ID N/A
UniProt peptide Q13114
alteration type single base exchange
alteration region CDS
DNA changes c.386T>C
cDNA.739T>C
g.98237T>C
AA changes M129T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 129
frameshift no
known variant Reference ID: rs1131877
databasehomozygous (C/C)heterozygousallele carriers
1000G7658231588
ExAC80381669124729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0080
0.9520
(flanking)-5.3340
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased98231wt: 0.9494 / mu: 0.9521 (marginal change - not scored)wt: AGAGCAGTTAATGCT
mu: AGAGCAGTTAACGCT		 AGCA|gtta
Donor gained982320.30mu: GAGCAGTTAACGCTG GCAG|ttaa
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      129RNESRGCAEQLMLGHLLVHLKNDC
mutated  not conserved    129SRGCAEQLTLGHLLVHLKND
Ptroglodytes  not conserved  ENSPTRG00000006746  129SRGCAEQLTLGHLLVHLKND
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000010003  109---------------HLKND
Mmusculus  not conserved  ENSMUSG00000021277  128GRGCAEQLTLGHLLVHLKNE
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000005547  139RSEANGCQEQMRLQQIPDHL-NT
Drerio  not conserved  ENSDARG00000022000  132RSEKNGCKEQMCLQQVMEHLVI-
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000012746  124TRGCKELITLGNLLIHLKSD
protein features
start (aa)end (aa)featuredetails 
134134CONFLICTMissing (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
135190ZN_FINGTRAF-type 1.might get lost (downstream of altered splice site)
156156CROSSLNKGlycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).might get lost (downstream of altered splice site)
158158CONFLICTL -> F (in Ref. 6; BAH13910).might get lost (downstream of altered splice site)
191249ZN_FINGTRAF-type 2.might get lost (downstream of altered splice site)
218242CONFLICTMissing (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
267338COILEDPotential.might get lost (downstream of altered splice site)
339339CONFLICTP -> S (in Ref. 3; AAA68195).might get lost (downstream of altered splice site)
365373TURNmight get lost (downstream of altered splice site)
375377TURNmight get lost (downstream of altered splice site)
378410HELIXmight get lost (downstream of altered splice site)
405405CONFLICTR -> G (in Ref. 4; AAA56753).might get lost (downstream of altered splice site)
415423STRANDmight get lost (downstream of altered splice site)
415560DOMAINMATH.might get lost (downstream of altered splice site)
425433HELIXmight get lost (downstream of altered splice site)
438441STRANDmight get lost (downstream of altered splice site)
441441MUTAGENY->A: Abolishes interaction with RNF216; when associated with A-443.might get lost (downstream of altered splice site)
443443MUTAGENQ->A: Abolishes interaction with RNF216; when associated with A-441.might get lost (downstream of altered splice site)
445448STRANDmight get lost (downstream of altered splice site)
453459STRANDmight get lost (downstream of altered splice site)
459459MUTAGENY->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
464466HELIXmight get lost (downstream of altered splice site)
467469TURNmight get lost (downstream of altered splice site)
470478STRANDmight get lost (downstream of altered splice site)
483485HELIXmight get lost (downstream of altered splice site)
494498STRANDmight get lost (downstream of altered splice site)
502504STRANDmight get lost (downstream of altered splice site)
508512STRANDmight get lost (downstream of altered splice site)
512512MUTAGENF->E: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521521MUTAGENF->A: Abolishes interaction with LTBR, CD40 and TANK.might get lost (downstream of altered splice site)
521523STRANDmight get lost (downstream of altered splice site)
525528STRANDmight get lost (downstream of altered splice site)
532539STRANDmight get lost (downstream of altered splice site)
540545HELIXmight get lost (downstream of altered splice site)
553560STRANDmight get lost (downstream of altered splice site)
563565STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1632 / 1632
position (AA) of stopcodon in wt / mu AA sequence 544 / 544
position of stopcodon in wt / mu cDNA 1985 / 1985
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 354 / 354
chromosome 14
strand 1
last intron/exon boundary 1414
theoretical NMD boundary in CDS 1010
length of CDS 1632
coding sequence (CDS) position 386
cDNA position
(for ins/del: last normal base / first normal base)		 739
gDNA position
(for ins/del: last normal base / first normal base)		 98237
chromosomal position
(for ins/del: last normal base / first normal base)		 103342049
original gDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGA
altered gDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGA
original cDNA sequence snippet AGGTTGTGCAGAGCAGTTAATGCTGGGACATCTGCTGGTGC
altered cDNA sequence snippet AGGTTGTGCAGAGCAGTTAACGCTGGGACATCTGCTGGTGC
wildtype AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLML GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSEGTN QQIKAHEASS AVQHVNLLKE
WSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS
QAEKLKELDK EIRPFRQNWE EADSMKSSVE SLQNRVTELE SVDKSAGQVA RNTGLLESQL
SRHDQMLSVH DIRLADMDLR FQVLETASYN GVLIWKIRDY KRRKQEAVMG KTLSLYSQPF
YTGYFGYKMC ARVYLNGDGM GKGTHLSLFF VIMRGEYDAL LPWPFKQKVT LMLMDQGSSR
RHLGDAFKPD PNSSSFKKPT GEMNIASGCP VFVAQTVLEN GTYIKDDTIF IKVIVDTSDL
PDP*
mutated AA sequence MESSKKMDSP GALQTNPPLK LHTDRSAGTP VFVPEQGGYK EKFVKTVEDK YKCEKCHLVL
CSPKQTECGH RFCESCMAAL LSSSSPKCTA CQESIVKDKV FKDNCCKREI LALQIYCRNE
SRGCAEQLTL GHLLVHLKND CHFEELPCVR PDCKEKVLRK DLRDHVEKAC KYREATCSHC
KSQVPMIALQ KHEDTDCPCV VVSCPHKCSV QTLLRSEGTN QQIKAHEASS AVQHVNLLKE
WSNSLEKKVS LLQNESVEKN KSIQSLHNQI CSFEIEIERQ KEMLRNNESK ILHLQRVIDS
QAEKLKELDK EIRPFRQNWE EADSMKSSVE SLQNRVTELE SVDKSAGQVA RNTGLLESQL
SRHDQMLSVH DIRLADMDLR FQVLETASYN GVLIWKIRDY KRRKQEAVMG KTLSLYSQPF
YTGYFGYKMC ARVYLNGDGM GKGTHLSLFF VIMRGEYDAL LPWPFKQKVT LMLMDQGSSR
RHLGDAFKPD PNSSSFKKPT GEMNIASGCP VFVAQTVLEN GTYIKDDTIF IKVIVDTSDL
PDP*
speed 0.59 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