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: ENST00000251921
Querying Taster for transcript #2: ENST00000536312
Querying Taster for transcript #3: ENST00000424269
MT speed 3.47 s - this script 7.422455 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
NXPE1polymorphism_automatic3.28959082196434e-13simple_aaeaffectedL40Ssingle base exchangers7944960show file
NXPE1polymorphism_automatic3.28959082196434e-13simple_aaeaffectedL40Ssingle base exchangers7944960show file
NXPE1polymorphism_automatic1.39042272495615e-06without_aaeaffectedsingle base exchangers7944960show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999671 (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) chr11:114401611A>GN/A show variant in all transcripts   IGV
HGNC symbol NXPE1
Ensembl transcript ID ENST00000536312
Genbank transcript ID N/A
UniProt peptide Q8N323
alteration type single base exchange
alteration region CDS
DNA changes c.119T>C
cDNA.1012T>C
g.29007T>C
AA changes L40S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS
40
frameshift no
known variant Reference ID: rs7944960
databasehomozygous (G/G)heterozygousallele carriers
1000G240716956
ExAC23281553217860
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0780.002
0.2310.001
(flanking)-1.5630
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased29002wt: 0.52 / mu: 0.58wt: TTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCA
mu: TTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCA
 tcta|AACT
Acc increased29001wt: 0.23 / mu: 0.29wt: ATTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCC
mu: ATTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCC
 ctct|AAAC
Donor gained289990.37mu: TCTGCTCTAAACTCA TGCT|ctaa
distance from splice site 20
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      40QNFTKLWSALNLSISVHYWNNSAK
mutated  not conserved    40QNFTKLWSALNSSISVHYWNNSA
Ptroglodytes  no alignment  ENSPTRG00000004307  n/a
Mmulatta  no alignment  ENSMMUG00000012268  n/a
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000003928  n/a
protein features
start (aa)end (aa)featuredetails 
3939CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
211211CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
491491CONFLICTG -> V (in Ref. 4; AAH29049).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 888 / 888
position (AA) of stopcodon in wt / mu AA sequence 296 / 296
position of stopcodon in wt / mu cDNA 1781 / 1781
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 894 / 894
chromosome 11
strand -1
last intron/exon boundary 1826
theoretical NMD boundary in CDS 882
length of CDS 888
coding sequence (CDS) position 119
cDNA position
(for ins/del: last normal base / first normal base)
1012
gDNA position
(for ins/del: last normal base / first normal base)
29007
chromosomal position
(for ins/del: last normal base / first normal base)
114401611
original gDNA sequence snippet GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT
altered gDNA sequence snippet GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT
original cDNA sequence snippet GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT
altered cDNA sequence snippet GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT
wildtype AA sequence MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNL SISVHYWNNS AKSLFPKTSL
IPLKPLTETE LRIKEIIEKL DQQIPPRPFT HVNTTTSATH STATILNPRD TYCRGDQLDI
LLEVRDHLGQ RKQYGGDFLR ARMSSPALTA GASGKVMDFN NGTYLVSFTL FWEGQVSLSL
LLIHPSEGAS ALWRARNQGY DKIIFKGKFV NGTSHVFTEC GLTLNSNAEL CEYLDDRDQE
AFYCMKPQHM PCEALTYMTT RNREVSYLTD KENSLFHRMA PGETSIAGNQ VQSGS*
mutated AA sequence MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNS SISVHYWNNS AKSLFPKTSL
IPLKPLTETE LRIKEIIEKL DQQIPPRPFT HVNTTTSATH STATILNPRD TYCRGDQLDI
LLEVRDHLGQ RKQYGGDFLR ARMSSPALTA GASGKVMDFN NGTYLVSFTL FWEGQVSLSL
LLIHPSEGAS ALWRARNQGY DKIIFKGKFV NGTSHVFTEC GLTLNSNAEL CEYLDDRDQE
AFYCMKPQHM PCEALTYMTT RNREVSYLTD KENSLFHRMA PGETSIAGNQ VQSGS*
speed 1.44 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: 0.999999999999671 (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) chr11:114401611A>GN/A show variant in all transcripts   IGV
HGNC symbol NXPE1
Ensembl transcript ID ENST00000424269
Genbank transcript ID N/A
UniProt peptide Q8N323
alteration type single base exchange
alteration region CDS
DNA changes c.119T>C
cDNA.119T>C
g.29007T>C
AA changes L40S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS
40
frameshift no
known variant Reference ID: rs7944960
databasehomozygous (G/G)heterozygousallele carriers
1000G240716956
ExAC23281553217860
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0780.002
0.2310.001
(flanking)-1.5630
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased29002wt: 0.52 / mu: 0.58wt: TTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCA
mu: TTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCA
 tcta|AACT
Acc increased29001wt: 0.23 / mu: 0.29wt: ATTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCC
mu: ATTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCC
 ctct|AAAC
Donor gained289990.37mu: TCTGCTCTAAACTCA TGCT|ctaa
distance from splice site 20
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      40QNFTKLWSALNLSISVHYWNNSAK
mutated  not conserved    40QNFTKLWSALNSSISVHYWNNSA
Ptroglodytes  no alignment  ENSPTRG00000004307  n/a
Mmulatta  no alignment  ENSMMUG00000012268  n/a
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000003928  n/a
protein features
start (aa)end (aa)featuredetails 
3939CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
211211CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
491491CONFLICTG -> V (in Ref. 4; AAH29049).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1644 / 1644
position (AA) of stopcodon in wt / mu AA sequence 548 / 548
position of stopcodon in wt / mu cDNA 1644 / 1644
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 1109
theoretical NMD boundary in CDS 1058
length of CDS 1644
coding sequence (CDS) position 119
cDNA position
(for ins/del: last normal base / first normal base)
119
gDNA position
(for ins/del: last normal base / first normal base)
29007
chromosomal position
(for ins/del: last normal base / first normal base)
114401611
original gDNA sequence snippet GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT
altered gDNA sequence snippet GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT
original cDNA sequence snippet GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT
altered cDNA sequence snippet GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT
wildtype AA sequence MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNL SISVHYWNNS AKSLFPKTSL
IPLKPLTETE LRIKEIIEKL DQQIPPRPFT HVNTTTSATH STATILNPRD TYCRGDQLDI
LLEVRDHLGQ RKQYGGDFLR ARMSSPALTA GASGKVMDFN NGTYLVSFTL FWEGQVSLSL
LLIHPSEGAS ALWRARNQGY DKIIFKGKFV NGTSHVFTEC GLTLNSNAEL CEYLDDRDQE
AFYCMKPQHM PCEALTYMTT RNREVSYLTD KENSLFHRSK VGVEMMKDRK HIDVTNCNKR
EKIEETCQVG MKPPVPGGYT LQGKWITTFC NQVQLDTIKI NGCLKGKLIY LLGDSTLRQW
IYYFPKVVKT LKFFDLHETG IFKKHLLLDA ERHTQIQWKK HSYPFVTFQL YSLIDHDYIP
REIDRLSGDK NTAIVITFGQ HFRPFPIDIF IRRAIGVQKA IERLFLRSPA TKVIIKTENI
REMHIETERF GDFHGYIHYL IMKDIFKDLN VGIIDAWDMT IAYGTDTIHP PDHVIGNQIN
MFLNYIC*
mutated AA sequence MSSNTMLQKT LLILISFSVV TWMIFIISQN FTKLWSALNS SISVHYWNNS AKSLFPKTSL
IPLKPLTETE LRIKEIIEKL DQQIPPRPFT HVNTTTSATH STATILNPRD TYCRGDQLDI
LLEVRDHLGQ RKQYGGDFLR ARMSSPALTA GASGKVMDFN NGTYLVSFTL FWEGQVSLSL
LLIHPSEGAS ALWRARNQGY DKIIFKGKFV NGTSHVFTEC GLTLNSNAEL CEYLDDRDQE
AFYCMKPQHM PCEALTYMTT RNREVSYLTD KENSLFHRSK VGVEMMKDRK HIDVTNCNKR
EKIEETCQVG MKPPVPGGYT LQGKWITTFC NQVQLDTIKI NGCLKGKLIY LLGDSTLRQW
IYYFPKVVKT LKFFDLHETG IFKKHLLLDA ERHTQIQWKK HSYPFVTFQL YSLIDHDYIP
REIDRLSGDK NTAIVITFGQ HFRPFPIDIF IRRAIGVQKA IERLFLRSPA TKVIIKTENI
REMHIETERF GDFHGYIHYL IMKDIFKDLN VGIIDAWDMT IAYGTDTIHP PDHVIGNQIN
MFLNYIC*
speed 1.22 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: 0.999998609577275 (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) chr11:114401611A>GN/A show variant in all transcripts   IGV
HGNC symbol NXPE1
Ensembl transcript ID ENST00000251921
Genbank transcript ID NM_152315
UniProt peptide Q8N323
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.110T>C
g.29007T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs7944960
databasehomozygous (G/G)heterozygousallele carriers
1000G240716956
ExAC23281553217860
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0780.002
0.2310.001
(flanking)-1.5630
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -104) | splice site change before start ATG (at aa -103) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased29002wt: 0.52 / mu: 0.58wt: TTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCA
mu: TTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCA
 tcta|AACT
Acc increased29001wt: 0.23 / mu: 0.29wt: ATTTCAGCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCC
mu: ATTTCAGCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCC
 ctct|AAAC
Donor gained289990.37mu: TCTGCTCTAAACTCA TGCT|ctaa
distance from splice site 20
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
121SIGNALPotential.might get lost (downstream of altered splice site)
3939CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
211211CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
491491CONFLICTG -> V (in Ref. 4; AAH29049).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 418 / 418
chromosome 11
strand -1
last intron/exon boundary 1100
theoretical NMD boundary in CDS 632
length of CDS 1218
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
110
gDNA position
(for ins/del: last normal base / first normal base)
29007
chromosomal position
(for ins/del: last normal base / first normal base)
114401611
original gDNA sequence snippet GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT
altered gDNA sequence snippet GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT
original cDNA sequence snippet GCTTTGGTCTGCTCTAAACTTATCCATCTCTGTCCATTACT
altered cDNA sequence snippet GCTTTGGTCTGCTCTAAACTCATCCATCTCTGTCCATTACT
wildtype AA sequence MSSPALTAGA SGKVMDFNNG TYLVSFTLFW EGQVSLSLLL IHPSEGASAL WRARNQGYDK
IIFKGKFVNG TSHVFTECGL TLNSNAELCE YLDDRDQEAF YCMKPQHMPC EALTYMTTRN
REVSYLTDKE NSLFHRSKVG VEMMKDRKHI DVTNCNKREK IEETCQVGMK PPVPGGYTLQ
GKWITTFCNQ VQLDTIKING CLKGKLIYLL GDSTLRQWIY YFPKVVKTLK FFDLHETGIF
KKHLLLDAER HTQIQWKKHS YPFVTFQLYS LIDHDYIPRE IDRLSGDKNT AIVITFGQHF
RPFPIDIFIR RAIGVQKAIE RLFLRSPATK VIIKTENIRE MHIETERFGD FHGYIHYLIM
KDIFKDLNVG IIDAWDMTIA YGTDTIHPPD HVIGNQINMF LNYIC*
mutated AA sequence N/A
speed 0.81 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