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: ENST00000265909
Querying Taster for transcript #2: ENST00000528555
Querying Taster for transcript #3: ENST00000530356
Querying Taster for transcript #4: ENST00000533214
Querying Taster for transcript #5: ENST00000539184
MT speed 0 s - this script 4.102649 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SNX19polymorphism_automatic0simple_aaeaffectedV361Lsingle base exchangers3751037show file
SNX19polymorphism_automatic0simple_aaeaffectedV361Lsingle base exchangers3751037show file
SNX19polymorphism_automatic1.07689010042655e-07without_aaeaffectedsingle base exchangers3751037show file
SNX19polymorphism_automatic1.07689010042655e-07without_aaeaffectedsingle base exchangers3751037show file
SNX19polymorphism_automatic1.07689010042655e-07without_aaeaffectedsingle base exchangers3751037show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1 (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) chr11:130784754C>GN/A show variant in all transcripts   IGV
HGNC symbol SNX19
Ensembl transcript ID ENST00000265909
Genbank transcript ID NM_014758
UniProt peptide Q92543
alteration type single base exchange
alteration region CDS
DNA changes c.1081G>C
cDNA.1651G>C
g.1651G>C
AA changes V361L Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 361
frameshift no
known variant Reference ID: rs3751037
databasehomozygous (G/G)heterozygousallele carriers
1000G13459682313
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4610.02
-0.4970
(flanking)0.240
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1642wt: 0.59 / mu: 0.69wt: ACAACTCATCTCATTTCCTACAGCCAAATGTTCGAGGTCCC
mu: ACAACTCATCTCATTTCCTACAGCCAAATCTTCGAGGTCCC		 ctac|AGCC
Donor increased1652wt: 0.66 / mu: 0.82wt: AAATGTTCGAGGTCC
mu: AAATCTTCGAGGTCC		 ATGT|tcga
Donor marginally increased1643wt: 0.9985 / mu: 0.9990 (marginal change - not scored)wt: CCTACAGCCAAATGT
mu: CCTACAGCCAAATCT		 TACA|gcca
distance from splice site 594
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      361GNNSSHFLQPNVRGPLFLCEDSEL
mutated  all conserved    361LRGPLFLCEDSE
Ptroglodytes  all conserved  ENSPTRG00000004487  361LRGPLFLCEDSE
Mmulatta  all conserved  ENSMMUG00000018119  360GNNSSHFLQPNLRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000031993  365SSHFLQPDIRGPLFLCEDSE
Ggallus  not conserved  ENSGALG00000001425  215EGVVLRPRGLGLLFPYEGLE
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079931  347GFSPRDYLRLSKPNPFYQET
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000021858  362DVFSGHYLQPPNPTSPFFLCEESE
protein features
start (aa)end (aa)featuredetails 
533663DOMAINPX.might get lost (downstream of altered splice site)
582582BINDINGPhosphatidylinositol 3-phosphate (By similarity).might get lost (downstream of altered splice site)
629629BINDINGPhosphatidylinositol 3-phosphate (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 2979 / 2979
position (AA) of stopcodon in wt / mu AA sequence 993 / 993
position of stopcodon in wt / mu cDNA 3549 / 3549
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 571 / 571
chromosome 11
strand -1
last intron/exon boundary 3417
theoretical NMD boundary in CDS 2796
length of CDS 2979
coding sequence (CDS) position 1081
cDNA position
(for ins/del: last normal base / first normal base)		 1651
gDNA position
(for ins/del: last normal base / first normal base)		 1651
chromosomal position
(for ins/del: last normal base / first normal base)		 130784754
original gDNA sequence snippet CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA
altered gDNA sequence snippet CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA
original cDNA sequence snippet CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA
altered cDNA sequence snippet CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA
wildtype AA sequence MKTETVPPFQ ETPAGSSCHL NNLLSSRKLM AVGVLLGWLL VIHLLVNVWL LCLLSALLVV
LGGWLGSSLA GVASGRLHLE RFIPLATCPP CPEAERQLER EINRTIQMII RDFVLSWYRS
VSQEPAFEEE MEAAMKGLVQ ELRRRMSVMD SHAVAQSVLT LCGCHLQSYI QAKEATAGKN
GPVEPSHLWE AYCRATAPHP AVHSPSAEVT YTRGVVNLLL QGLVPKPHLE TRTGRHVVVE
LITCNVILPL ISRLSDPDWI HLVLVGIFSK ARDPAPCPAS APEQPSVPTS LPLIAEVEQL
PEGRASPVAA PVFLSYSEPE GSAGPSPEVE EGHEAVEGDL GGMCEERKVG NNSSHFLQPN
VRGPLFLCED SELESPLSEL GKETIMLMTP GSFLSDRIQD ALCALESSQA LEPKDGEASE
GAEAEEGPGT ETETGLPVST LNSCPEIHID TADKEIEQGD VTASVTALLE GPEKTCPSRP
SCLEKDLTND VSSLDPTLPP VLLSSSPPGP LSSATFSFEP LSSPDGPVII QNLRITGTIT
AREHSGTGFH PYTLYTVKYE TALDGENSSG LQQLAYHTVN RRYREFLNLQ TRLEEKPDLR
KFIKNVKGPK KLFPDLPLGN MDSDRVEARK SLLESFLKQL CAIPEIANSE EVQEFLALNT
DARIAFVKKP FMVSRIDKMV VSAIVDTLKT AFPRSEPQSP TEELSEAETE SKPQTEGKKA
SKSRLRFSSS KISPALSVTE AQDKILYCLQ EGNVESETLS MSAMESFIEK QTKLLEMQPT
KAPEKDPEQP PKGRVDSCVS DAAVPAQDPS NSDPGTETEL ADTALDLLLL LLTEQWKWLC
TENMQKFLRL IFGTLVQRWL EVQVANLTSP QRWVQYLLLL QESIWPGGVL PKFPRPVRTQ
EQKLAAEKQA LQSLMGVLPD LVVEILGVNK CRLSWGLVLE SLQQPLINRH LIYCLGDIIL
EFLDLSASVE ESAATTSASD TPGNSKRMGV SS*
mutated AA sequence MKTETVPPFQ ETPAGSSCHL NNLLSSRKLM AVGVLLGWLL VIHLLVNVWL LCLLSALLVV
LGGWLGSSLA GVASGRLHLE RFIPLATCPP CPEAERQLER EINRTIQMII RDFVLSWYRS
VSQEPAFEEE MEAAMKGLVQ ELRRRMSVMD SHAVAQSVLT LCGCHLQSYI QAKEATAGKN
GPVEPSHLWE AYCRATAPHP AVHSPSAEVT YTRGVVNLLL QGLVPKPHLE TRTGRHVVVE
LITCNVILPL ISRLSDPDWI HLVLVGIFSK ARDPAPCPAS APEQPSVPTS LPLIAEVEQL
PEGRASPVAA PVFLSYSEPE GSAGPSPEVE EGHEAVEGDL GGMCEERKVG NNSSHFLQPN
LRGPLFLCED SELESPLSEL GKETIMLMTP GSFLSDRIQD ALCALESSQA LEPKDGEASE
GAEAEEGPGT ETETGLPVST LNSCPEIHID TADKEIEQGD VTASVTALLE GPEKTCPSRP
SCLEKDLTND VSSLDPTLPP VLLSSSPPGP LSSATFSFEP LSSPDGPVII QNLRITGTIT
AREHSGTGFH PYTLYTVKYE TALDGENSSG LQQLAYHTVN RRYREFLNLQ TRLEEKPDLR
KFIKNVKGPK KLFPDLPLGN MDSDRVEARK SLLESFLKQL CAIPEIANSE EVQEFLALNT
DARIAFVKKP FMVSRIDKMV VSAIVDTLKT AFPRSEPQSP TEELSEAETE SKPQTEGKKA
SKSRLRFSSS KISPALSVTE AQDKILYCLQ EGNVESETLS MSAMESFIEK QTKLLEMQPT
KAPEKDPEQP PKGRVDSCVS DAAVPAQDPS NSDPGTETEL ADTALDLLLL LLTEQWKWLC
TENMQKFLRL IFGTLVQRWL EVQVANLTSP QRWVQYLLLL QESIWPGGVL PKFPRPVRTQ
EQKLAAEKQA LQSLMGVLPD LVVEILGVNK CRLSWGLVLE SLQQPLINRH LIYCLGDIIL
EFLDLSASVE ESAATTSASD TPGNSKRMGV SS*
speed 0.87 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: 1 (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) chr11:130784754C>GN/A show variant in all transcripts   IGV
HGNC symbol SNX19
Ensembl transcript ID ENST00000533214
Genbank transcript ID N/A
UniProt peptide Q92543
alteration type single base exchange
alteration region CDS
DNA changes c.1081G>C
cDNA.1591G>C
g.1651G>C
AA changes V361L Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 361
frameshift no
known variant Reference ID: rs3751037
databasehomozygous (G/G)heterozygousallele carriers
1000G13459682313
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4610.02
-0.4970
(flanking)0.240
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1642wt: 0.59 / mu: 0.69wt: ACAACTCATCTCATTTCCTACAGCCAAATGTTCGAGGTCCC
mu: ACAACTCATCTCATTTCCTACAGCCAAATCTTCGAGGTCCC		 ctac|AGCC
Donor increased1652wt: 0.66 / mu: 0.82wt: AAATGTTCGAGGTCC
mu: AAATCTTCGAGGTCC		 ATGT|tcga
Donor marginally increased1643wt: 0.9985 / mu: 0.9990 (marginal change - not scored)wt: CCTACAGCCAAATGT
mu: CCTACAGCCAAATCT		 TACA|gcca
distance from splice site 594
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      361GNNSSHFLQPNVRGPLFLCEDSEL
mutated  all conserved    361LRGPLFLCEDSE
Ptroglodytes  all conserved  ENSPTRG00000004487  361LRGPLFLCEDSE
Mmulatta  all conserved  ENSMMUG00000018119  360GNNSSHFLQPNLRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000031993  365SSHFLQPDIRGPLFLCEDSE
Ggallus  not conserved  ENSGALG00000001425  215EGVVLRPRGLGLLFPYEGLE
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079931  347GFSPRDYLRLSKPNPFYQET
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000021858  362DVFSGHYLQPPNPTSPFFLCEESE
protein features
start (aa)end (aa)featuredetails 
533663DOMAINPX.might get lost (downstream of altered splice site)
582582BINDINGPhosphatidylinositol 3-phosphate (By similarity).might get lost (downstream of altered splice site)
629629BINDINGPhosphatidylinositol 3-phosphate (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 2412 / 2412
position (AA) of stopcodon in wt / mu AA sequence 804 / 804
position of stopcodon in wt / mu cDNA 2922 / 2922
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 511 / 511
chromosome 11
strand -1
last intron/exon boundary 2903
theoretical NMD boundary in CDS 2342
length of CDS 2412
coding sequence (CDS) position 1081
cDNA position
(for ins/del: last normal base / first normal base)		 1591
gDNA position
(for ins/del: last normal base / first normal base)		 1651
chromosomal position
(for ins/del: last normal base / first normal base)		 130784754
original gDNA sequence snippet CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA
altered gDNA sequence snippet CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA
original cDNA sequence snippet CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA
altered cDNA sequence snippet CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA
wildtype AA sequence MKTETVPPFQ ETPAGSSCHL NNLLSSRKLM AVGVLLGWLL VIHLLVNVWL LCLLSALLVV
LGGWLGSSLA GVASGRLHLE RFIPLATCPP CPEAERQLER EINRTIQMII RDFVLSWYRS
VSQEPAFEEE MEAAMKGLVQ ELRRRMSVMD SHAVAQSVLT LCGCHLQSYI QAKEATAGKN
GPVEPSHLWE AYCRATAPHP AVHSPSAEVT YTRGVVNLLL QGLVPKPHLE TRTGRHVVVE
LITCNVILPL ISRLSDPDWI HLVLVGIFSK ARDPAPCPAS APEQPSVPTS LPLIAEVEQL
PEGRASPVAA PVFLSYSEPE GSAGPSPEVE EGHEAVEGDL GGMCEERKVG NNSSHFLQPN
VRGPLFLCED SELESPLSEL GKETIMLMTP GSFLSDRIQD ALCALESSQA LEPKDGEASE
GAEAEEGPGT ETETGLPVST LNSCPEIHID TADKEIEQGD VTASVTALLE GPEKTCPSRP
SCLEKDLTND VSSLDPTLPP VLLSSSPPGP LSSATFSFEP LSSPDGPVII QNLRITGTIT
AREHSGTGFH PYTLYTVKYE TALDGENSSG LQQLAYHTVN RRYREFLNLQ TRLEEKPDLR
KFIKNVKGPK KLFPDLPLGN MDSDRVEARK SLLESFLKQL CAIPEIANSE EVQEFLALNT
DARIAFVKKP FMVSRIDKMV VSAIVDTLKT AFPRSEPQSP TEELSEAETE SKPQTEGKKA
SKSRLRFSSS KISPALSVTE AQDKILYCLQ EGNVTKLLEM QPTKAPEKDP EQPPKGRVDS
CVSDAAVPAQ DPSNSDPAEH AMC*
mutated AA sequence MKTETVPPFQ ETPAGSSCHL NNLLSSRKLM AVGVLLGWLL VIHLLVNVWL LCLLSALLVV
LGGWLGSSLA GVASGRLHLE RFIPLATCPP CPEAERQLER EINRTIQMII RDFVLSWYRS
VSQEPAFEEE MEAAMKGLVQ ELRRRMSVMD SHAVAQSVLT LCGCHLQSYI QAKEATAGKN
GPVEPSHLWE AYCRATAPHP AVHSPSAEVT YTRGVVNLLL QGLVPKPHLE TRTGRHVVVE
LITCNVILPL ISRLSDPDWI HLVLVGIFSK ARDPAPCPAS APEQPSVPTS LPLIAEVEQL
PEGRASPVAA PVFLSYSEPE GSAGPSPEVE EGHEAVEGDL GGMCEERKVG NNSSHFLQPN
LRGPLFLCED SELESPLSEL GKETIMLMTP GSFLSDRIQD ALCALESSQA LEPKDGEASE
GAEAEEGPGT ETETGLPVST LNSCPEIHID TADKEIEQGD VTASVTALLE GPEKTCPSRP
SCLEKDLTND VSSLDPTLPP VLLSSSPPGP LSSATFSFEP LSSPDGPVII QNLRITGTIT
AREHSGTGFH PYTLYTVKYE TALDGENSSG LQQLAYHTVN RRYREFLNLQ TRLEEKPDLR
KFIKNVKGPK KLFPDLPLGN MDSDRVEARK SLLESFLKQL CAIPEIANSE EVQEFLALNT
DARIAFVKKP FMVSRIDKMV VSAIVDTLKT AFPRSEPQSP TEELSEAETE SKPQTEGKKA
SKSRLRFSSS KISPALSVTE AQDKILYCLQ EGNVTKLLEM QPTKAPEKDP EQPPKGRVDS
CVSDAAVPAQ DPSNSDPAEH AMC*
speed 0.56 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: 0.99999989231099 (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) chr11:130784754C>GN/A show variant in all transcripts   IGV
HGNC symbol SNX19
Ensembl transcript ID ENST00000528555
Genbank transcript ID N/A
UniProt peptide Q92543
alteration type single base exchange
alteration region intron
DNA changes g.1651G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3751037
databasehomozygous (G/G)heterozygousallele carriers
1000G13459682313
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4610.02
-0.4970
(flanking)0.240
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -61) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased1642wt: 0.59 / mu: 0.69wt: ACAACTCATCTCATTTCCTACAGCCAAATGTTCGAGGTCCC
mu: ACAACTCATCTCATTTCCTACAGCCAAATCTTCGAGGTCCC		 ctac|AGCC
Donor increased1652wt: 0.66 / mu: 0.82wt: AAATGTTCGAGGTCC
mu: AAATCTTCGAGGTCC		 ATGT|tcga
Donor marginally increased1643wt: 0.9985 / mu: 0.9990 (marginal change - not scored)wt: CCTACAGCCAAATGT
mu: CCTACAGCCAAATCT		 TACA|gcca
distance from splice site 1421
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
95272DOMAINPXA.might get lost (downstream of altered splice site)
533663DOMAINPX.might get lost (downstream of altered splice site)
582582BINDINGPhosphatidylinositol 3-phosphate (By similarity).might get lost (downstream of altered splice site)
629629BINDINGPhosphatidylinositol 3-phosphate (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 359 / 359
chromosome 11
strand -1
last intron/exon boundary 1345
theoretical NMD boundary in CDS 936
length of CDS 1119
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)		 1651
chromosomal position
(for ins/del: last normal base / first normal base)		 130784754
original gDNA sequence snippet CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA
altered gDNA sequence snippet CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDSDRVEARK SLLESFLKQL CAIPEIANSE EVQEFLALNT DARIAFVKKP FMVSRIDKMV
VSAIVDTLKT AFPRSEPQSP TEELSEAETE SKPQTEGKKA SKSRLRFSSS KISPALSVTE
AQDKILYCLQ EGNVESETLS MSAMESFIEK QTKLLEMQPT KAPEKDPEQP PKGRVDSCVS
DAAVPAQDPS NSDPGTETEL ADTALDLLLL LLTEQWKWLC TENMQKFLRL IFGTLVQRWL
EVQVANLTSP QRWVQYLLLL QESIWPGGVL PKFPRPVRTQ EQKLAAEKQA LQSLMGVLPD
LVVEILGVNK CRLSWGLVLE SLQQPLINRH LIYCLGDIIL EFLDLSASVE ESAATTSASD
TPGNSKRMGV SS*
mutated AA sequence N/A
speed 0.75 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: 0.99999989231099 (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) chr11:130784754C>GN/A show variant in all transcripts   IGV
HGNC symbol SNX19
Ensembl transcript ID ENST00000530356
Genbank transcript ID N/A
UniProt peptide Q92543
alteration type single base exchange
alteration region intron
DNA changes g.1651G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3751037
databasehomozygous (G/G)heterozygousallele carriers
1000G13459682313
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4610.02
-0.4970
(flanking)0.240
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -80) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased1642wt: 0.59 / mu: 0.69wt: ACAACTCATCTCATTTCCTACAGCCAAATGTTCGAGGTCCC
mu: ACAACTCATCTCATTTCCTACAGCCAAATCTTCGAGGTCCC		 ctac|AGCC
Donor increased1652wt: 0.66 / mu: 0.82wt: AAATGTTCGAGGTCC
mu: AAATCTTCGAGGTCC		 ATGT|tcga
Donor marginally increased1643wt: 0.9985 / mu: 0.9990 (marginal change - not scored)wt: CCTACAGCCAAATGT
mu: CCTACAGCCAAATCT		 TACA|gcca
distance from splice site 110
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
95272DOMAINPXA.might get lost (downstream of altered splice site)
533663DOMAINPX.might get lost (downstream of altered splice site)
582582BINDINGPhosphatidylinositol 3-phosphate (By similarity).might get lost (downstream of altered splice site)
629629BINDINGPhosphatidylinositol 3-phosphate (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 415 / 415
chromosome 11
strand -1
last intron/exon boundary 1401
theoretical NMD boundary in CDS 936
length of CDS 1119
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)		 1651
chromosomal position
(for ins/del: last normal base / first normal base)		 130784754
original gDNA sequence snippet CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA
altered gDNA sequence snippet CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDSDRVEARK SLLESFLKQL CAIPEIANSE EVQEFLALNT DARIAFVKKP FMVSRIDKMV
VSAIVDTLKT AFPRSEPQSP TEELSEAETE SKPQTEGKKA SKSRLRFSSS KISPALSVTE
AQDKILYCLQ EGNVESETLS MSAMESFIEK QTKLLEMQPT KAPEKDPEQP PKGRVDSCVS
DAAVPAQDPS NSDPGTETEL ADTALDLLLL LLTEQWKWLC TENMQKFLRL IFGTLVQRWL
EVQVANLTSP QRWVQYLLLL QESIWPGGVL PKFPRPVRTQ EQKLAAEKQA LQSLMGVLPD
LVVEILGVNK CRLSWGLVLE SLQQPLINRH LIYCLGDIIL EFLDLSASVE ESAATTSASD
TPGNSKRMGV SS*
mutated AA sequence N/A
speed 0.60 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.99999989231099 (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) chr11:130784754C>GN/A show variant in all transcripts   IGV
HGNC symbol SNX19
Ensembl transcript ID ENST00000539184
Genbank transcript ID N/A
UniProt peptide Q92543
alteration type single base exchange
alteration region intron
DNA changes g.1651G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs3751037
databasehomozygous (G/G)heterozygousallele carriers
1000G13459682313
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4610.02
-0.4970
(flanking)0.240
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -17) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased1642wt: 0.59 / mu: 0.69wt: ACAACTCATCTCATTTCCTACAGCCAAATGTTCGAGGTCCC
mu: ACAACTCATCTCATTTCCTACAGCCAAATCTTCGAGGTCCC		 ctac|AGCC
Donor increased1652wt: 0.66 / mu: 0.82wt: AAATGTTCGAGGTCC
mu: AAATCTTCGAGGTCC		 ATGT|tcga
Donor marginally increased1643wt: 0.9985 / mu: 0.9990 (marginal change - not scored)wt: CCTACAGCCAAATGT
mu: CCTACAGCCAAATCT		 TACA|gcca
distance from splice site 110
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
95272DOMAINPXA.might get lost (downstream of altered splice site)
533663DOMAINPX.might get lost (downstream of altered splice site)
582582BINDINGPhosphatidylinositol 3-phosphate (By similarity).might get lost (downstream of altered splice site)
629629BINDINGPhosphatidylinositol 3-phosphate (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 226 / 226
chromosome 11
strand -1
last intron/exon boundary 1401
theoretical NMD boundary in CDS 1125
length of CDS 1308
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)		 1651
chromosomal position
(for ins/del: last normal base / first normal base)		 130784754
original gDNA sequence snippet CTCATTTCCTACAGCCAAATGTTCGAGGTCCCCTGTTCTTA
altered gDNA sequence snippet CTCATTTCCTACAGCCAAATCTTCGAGGTCCCCTGTTCTTA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MYETALDGEN SSGLQQLAYH TVNRRYREFL NLQTRLEEKP DLRKFIKNVK GPKKLFPDLP
LGNMDSDRVE ARKSLLESFL KQLCAIPEIA NSEEVQEFLA LNTDARIAFV KKPFMVSRID
KMVVSAIVDT LKTAFPRSEP QSPTEELSEA ETESKPQTEG KKASKSRLRF SSSKISPALS
VTEAQDKILY CLQEGNVESE TLSMSAMESF IEKQTKLLEM QPTKAPEKDP EQPPKGRVDS
CVSDAAVPAQ DPSNSDPGTE TELADTALDL LLLLLTEQWK WLCTENMQKF LRLIFGTLVQ
RWLEVQVANL TSPQRWVQYL LLLQESIWPG GVLPKFPRPV RTQEQKLAAE KQALQSLMGV
LPDLVVEILG VNKCRLSWGL VLESLQQPLI NRHLIYCLGD IILEFLDLSA SVEESAATTS
ASDTPGNSKR MGVSS*
mutated AA sequence N/A
speed 0.56 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
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Problems