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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000447419
Querying Taster for transcript #2: ENST00000440447
Querying Taster for transcript #3: ENST00000293922
MT speed 0 s - this script 4.322341 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PTX4polymorphism_automatic7.72049091324334e-13simple_aaeaffectedG2Esingle base exchangers2745103show file
PTX4polymorphism_automatic1.60882971944609e-07without_aaeaffectedsingle base exchangers2745103show file
PTX4polymorphism_automatic1.60882971944609e-07without_aaeaffectedsingle base exchangers2745103show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999228 (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) chr16:1538464C>TN/A show variant in all transcripts   IGV
HGNC symbol PTX4
Ensembl transcript ID ENST00000293922
Genbank transcript ID NM_001013658
UniProt peptide Q96A99
alteration type single base exchange
alteration region CDS
DNA changes c.5G>A
cDNA.5G>A
g.519G>A
AA changes G2E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 2
frameshift no
known variant Reference ID: rs2745103
databasehomozygous (T/T)heterozygousallele carriers
1000G2108711081
ExAC39802138725367
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5350
0.5360.003
(flanking)0.1050.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased523wt: 0.47 / mu: 0.63wt: GGGAGTGGAAACTGG
mu: GAGAGTGGAAACTGG		 GAGT|ggaa
Donor increased511wt: 0.80 / mu: 0.91wt: GGTAGTGTCATGGGG
mu: GGTAGTGTCATGGAG		 TAGT|gtca
Donor marginally increased516wt: 0.9532 / mu: 0.9560 (marginal change - not scored)wt: TGTCATGGGGAGTGG
mu: TGTCATGGAGAGTGG		 TCAT|gggg
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      2 MGSGNWEVTGPPCG
mutated  not conserved    2 MESGNWEVTGPPCGSRCERPPG
Ptroglodytes  no alignment  ENSPTRG00000007595  n/a
Mmulatta  no alignment  ENSMMUG00000007049  n/a
Fcatus  no alignment  ENSFCAG00000010651  n/a
Mmusculus  no alignment  ENSMUSG00000044172  n/a
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000038072  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000009128  n/a
protein features
start (aa)end (aa)featuredetails 
125SIGNALPotential.lost
6767CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9191CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
271469DOMAINPentaxin.might get lost (downstream of altered splice site)
300300DISULFIDBy similarity.might get lost (downstream of altered splice site)
323323METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
364364DISULFIDBy similarity.might get lost (downstream of altered splice site)
406406METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
406406METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
407407METALCalcium 1; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1422 / 1422
position (AA) of stopcodon in wt / mu AA sequence 474 / 474
position of stopcodon in wt / mu cDNA 1422 / 1422
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 16
strand -1
last intron/exon boundary 782
theoretical NMD boundary in CDS 731
length of CDS 1422
coding sequence (CDS) position 5
cDNA position
(for ins/del: last normal base / first normal base)		 5
gDNA position
(for ins/del: last normal base / first normal base)		 519
chromosomal position
(for ins/del: last normal base / first normal base)		 1538464
original gDNA sequence snippet GGGGCCGGGTAGTGTCATGGGGAGTGGAAACTGGGAGGTCA
altered gDNA sequence snippet GGGGCCGGGTAGTGTCATGGAGAGTGGAAACTGGGAGGTCA
original cDNA sequence snippet ATGGGGAGTGGAAACTGGGAGGTCA
altered cDNA sequence snippet ATGGAGAGTGGAAACTGGGAGGTCA
wildtype AA sequence MGSGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTRNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*
mutated AA sequence MESGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTRNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*
speed 1.26 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: 0.999999839117028 (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) chr16:1538464C>TN/A show variant in all transcripts   IGV
HGNC symbol PTX4
Ensembl transcript ID ENST00000440447
Genbank transcript ID N/A
UniProt peptide Q96A99
alteration type single base exchange
alteration region intron
DNA changes g.519G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2745103
databasehomozygous (T/T)heterozygousallele carriers
1000G2108711081
ExAC39802138725367
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5350
0.5360.003
(flanking)0.1050.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased523wt: 0.47 / mu: 0.63wt: GGGAGTGGAAACTGG
mu: GAGAGTGGAAACTGG		 GAGT|ggaa
Donor increased511wt: 0.80 / mu: 0.91wt: GGTAGTGTCATGGGG
mu: GGTAGTGTCATGGAG		 TAGT|gtca
Donor marginally increased516wt: 0.9532 / mu: 0.9560 (marginal change - not scored)wt: TGTCATGGGGAGTGG
mu: TGTCATGGAGAGTGG		 TCAT|gggg
distance from splice site 306
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
6767CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9191CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
271469DOMAINPentaxin.might get lost (downstream of altered splice site)
300300DISULFIDBy similarity.might get lost (downstream of altered splice site)
323323METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
364364DISULFIDBy similarity.might get lost (downstream of altered splice site)
406406METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
406406METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
407407METALCalcium 1; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 1 (By 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 73 / 73
chromosome 16
strand -1
last intron/exon boundary 424
theoretical NMD boundary in CDS 301
length of CDS 579
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)		 519
chromosomal position
(for ins/del: last normal base / first normal base)		 1538464
original gDNA sequence snippet GGGGCCGGGTAGTGTCATGGGGAGTGGAAACTGGGAGGTCA
altered gDNA sequence snippet GGGGCCGGGTAGTGTCATGGAGAGTGGAAACTGGGAGGTCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKFAA
WAPPSFSQTP PPGTWSSSAL VSSLPCEPCP SAAGSARPPA AWAPSCPTPP RTMTTSWCCT
AETPCCPDPS TS*
mutated AA sequence N/A
speed 1.05 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: 0.999999839117028 (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) chr16:1538464C>TN/A show variant in all transcripts   IGV
HGNC symbol PTX4
Ensembl transcript ID ENST00000447419
Genbank transcript ID N/A
UniProt peptide Q96A99
alteration type single base exchange
alteration region intron
DNA changes g.519G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2745103
databasehomozygous (T/T)heterozygousallele carriers
1000G2108711081
ExAC39802138725367
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5350
0.5360.003
(flanking)0.1050.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased523wt: 0.47 / mu: 0.63wt: GGGAGTGGAAACTGG
mu: GAGAGTGGAAACTGG		 GAGT|ggaa
Donor increased511wt: 0.80 / mu: 0.91wt: GGTAGTGTCATGGGG
mu: GGTAGTGTCATGGAG		 TAGT|gtca
Donor marginally increased516wt: 0.9532 / mu: 0.9560 (marginal change - not scored)wt: TGTCATGGGGAGTGG
mu: TGTCATGGAGAGTGG		 TCAT|gggg
distance from splice site 306
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
6767CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9191CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
271469DOMAINPentaxin.might get lost (downstream of altered splice site)
300300DISULFIDBy similarity.might get lost (downstream of altered splice site)
323323METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
364364DISULFIDBy similarity.might get lost (downstream of altered splice site)
406406METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
406406METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
407407METALCalcium 1; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
408408METALCalcium 1 (By 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 27 / 27
chromosome 16
strand -1
last intron/exon boundary 823
theoretical NMD boundary in CDS 746
length of CDS 1437
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)		 519
chromosomal position
(for ins/del: last normal base / first normal base)		 1538464
original gDNA sequence snippet GGGGCCGGGTAGTGTCATGGGGAGTGGAAACTGGGAGGTCA
altered gDNA sequence snippet GGGGCCGGGTAGTGTCATGGAGAGTGGAAACTGGGAGGTCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGCSWRKTLS FFLVFVPIYL HGASSQEAAP VGPRKPFFER LRRLEEQFRR FQEVTWTHLQ
NIASNYNVSY NVDVRFRSLA EESQAVAQAV NRSQASVQGE LAQLKAWVRK LQRRGRKVDT
RLRALDLTLG ERSQQRARER KAHKAQRDAL QDSLARLEGL VHSQGARLAA LEGRLPVAHP
GTAALGPALV PTPTQPEELG PTSLKLQRDR QELRAASEHR GPPQDSSAPL QGRREPPASG
SHRVLSGTAP KDPRQQAWSP QVPGEICGVG PTLVFPNAST RNVVFLSPGF VTALRALSFC
SWVRTASGRL GTLLSYATED NDNKLVLHGR DSLLPGSIHF VIGDPAFREL PLQLLLDGQW
HHICVIWTST QGRYWLHVDR RLVATGSRFR EGYEIPPGGS LVLGQEQDSV GGGFDSSEAF
VGSMSGLAIW DRALVPGEVA NLAIGKEFPT GAILTLANAA LAGGFVQGAN CTCLERCP*
mutated AA sequence N/A
speed 1.07 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