Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000535621
Querying Taster for transcript #2: ENST00000287706
MT speed 0 s - this script 2.260543 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
NTAN1polymorphism_automatic0.000295150837472002simple_aaeaffectedS287Psingle base exchangers1135999show file
PDXDC1polymorphism_automatic1without_aaeaffectedsingle base exchangers1135999show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999704849162528 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:15131962A>GN/A show variant in all transcripts   IGV
HGNC symbol NTAN1
Ensembl transcript ID ENST00000287706
Genbank transcript ID NM_173474
UniProt peptide Q96AB6
alteration type single base exchange
alteration region CDS
DNA changes c.859T>C
cDNA.952T>C
g.17960T>C
AA changes S287P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 287
frameshift no
known variant Reference ID: rs1135999
databasehomozygous (G/G)heterozygousallele carriers
1000G33410551389
ExAC76091754925158
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3791
3.3931
(flanking)0.7761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased17952wt: 0.22 / mu: 0.27wt: ACACCCATCTCCAGCTCACACACTGTTTTCTGGAAATAAAG
mu: ACACCCATCTCCAGCTCACACACTGTTTCCTGGAAATAAAG		 acac|ACTG
Donor gained179610.41mu: GTTTCCTGGAAATAA TTCC|tgga
distance from splice site 106
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      287KKHPSPAHTLFSGNKALLYKKNED
mutated  not conserved    287KKHPSPAHTLFPGNKALLYKKNE
Ptroglodytes  not conserved  ENSPTRG00000007800  287KKHPSPANTLFPGNKALLYKKNE
Mmulatta  not conserved  ENSMMUG00000002989  287KKYPSPTNTLFPGNKALLYKKNE
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000022681  287KKFPSPENILFPGNKALLYKKNK
Ggallus  not conserved  ENSGALG00000002835  287KAHPFPSHSLFPDRKPRIYKKNE
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079495  262LEHPT-ADALFPDDQPQFYSRME
Dmelanogaster  not conserved  FBgn0034371  289QENQFPAVTVFRDNRPRYFRRDDA
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000033953  287KANPRPLRSLFPDNKPHVYTMDG
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 933 / 933
position (AA) of stopcodon in wt / mu AA sequence 311 / 311
position of stopcodon in wt / mu cDNA 1026 / 1026
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 94 / 94
chromosome 16
strand -1
last intron/exon boundary 847
theoretical NMD boundary in CDS 703
length of CDS 933
coding sequence (CDS) position 859
cDNA position
(for ins/del: last normal base / first normal base)		 952
gDNA position
(for ins/del: last normal base / first normal base)		 17960
chromosomal position
(for ins/del: last normal base / first normal base)		 15131962
original gDNA sequence snippet CTCCAGCTCACACACTGTTTTCTGGAAATAAAGCCCTACTC
altered gDNA sequence snippet CTCCAGCTCACACACTGTTTCCTGGAAATAAAGCCCTACTC
original cDNA sequence snippet CTCCAGCTCACACACTGTTTTCTGGAAATAAAGCCCTACTC
altered cDNA sequence snippet CTCCAGCTCACACACTGTTTCCTGGAAATAAAGCCCTACTC
wildtype AA sequence MPLLVEGRRV RLPQSAGDLV RAHPPLEERA RLLRGQSVQQ VGPQGLLYVQ QRELAVTSPK
DGSISILGSD DATTCHIVVL RHTGNGATCL THCDGTDTKA EVPLIMNSIK SFSDHAQCGR
LEVHLVGGFS DDRQLSQKLT HQLLSEFDRQ EDDIHLVTLC VTELNDREEN ENHFPVIYGI
AVNIKTAEIY RASFQDRGPE EQLRAARTLA GGPMISIYDA ETEQLRIGPY SWTPFPHVDF
WLHQDDKQIL ENLSTSPLAE PPHFVEHIRS TLMFLKKHPS PAHTLFSGNK ALLYKKNEDG
LWEKISSPGS *
mutated AA sequence MPLLVEGRRV RLPQSAGDLV RAHPPLEERA RLLRGQSVQQ VGPQGLLYVQ QRELAVTSPK
DGSISILGSD DATTCHIVVL RHTGNGATCL THCDGTDTKA EVPLIMNSIK SFSDHAQCGR
LEVHLVGGFS DDRQLSQKLT HQLLSEFDRQ EDDIHLVTLC VTELNDREEN ENHFPVIYGI
AVNIKTAEIY RASFQDRGPE EQLRAARTLA GGPMISIYDA ETEQLRIGPY SWTPFPHVDF
WLHQDDKQIL ENLSTSPLAE PPHFVEHIRS TLMFLKKHPS PAHTLFPGNK ALLYKKNEDG
LWEKISSPGS *
speed 0.21 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: 4.03644766828775e-30 (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) chr16:15131962A>GN/A show variant in all transcripts   IGV
HGNC symbol PDXDC1
Ensembl transcript ID ENST00000535621
Genbank transcript ID N/A
UniProt peptide Q6P996
alteration type single base exchange
alteration region intron
DNA changes g.63515A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs1135999
databasehomozygous (G/G)heterozygousallele carriers
1000G33410551389
ExAC76091754925158
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3791
3.3931
(flanking)0.7761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased63514wt: 0.53 / mu: 0.75wt: AGAGTAGGGCTTTATTTCCAGAAAACAGTGTGTGAGCTGGA
mu: AGAGTAGGGCTTTATTTCCAGGAAACAGTGTGTGAGCTGGA		 ccag|AAAA
Acc increased63513wt: 0.41 / mu: 0.52wt: TAGAGTAGGGCTTTATTTCCAGAAAACAGTGTGTGAGCTGG
mu: TAGAGTAGGGCTTTATTTCCAGGAAACAGTGTGTGAGCTGG		 tcca|GAAA
Donor gained635140.50mu: TTCCAGGAAACAGTG CCAG|gaaa
distance from splice site 8049
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
687687MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
691691MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
718718MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
720720MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
721721MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
722722MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
724724MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
737737MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
757757MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
779779MOD_RESPhosphoserine.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 189 / 189
chromosome 16
strand 1
last intron/exon boundary 1588
theoretical NMD boundary in CDS 1349
length of CDS 1497
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)		 63515
chromosomal position
(for ins/del: last normal base / first normal base)		 15131962
original gDNA sequence snippet GAGTAGGGCTTTATTTCCAGAAAACAGTGTGTGAGCTGGAG
altered gDNA sequence snippet GAGTAGGGCTTTATTTCCAGGAAACAGTGTGTGAGCTGGAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDASLEKIAD PTLAEMGKNL KEAVKMLEDS QRRTEEENGK KLISGDIPGP LQGSGQDMVS
ILQLVQNLMH GDEDEEPQSP RIQNIGEQGH MALLGHSLGA YISTLDKEKL RKLTTRILSD
TTLWLCRIFR YENGCAYFHE EEREGLAKIC RLAIHSRYED FVVDGFNVLY NKKPVIYLSA
AARPGLGQYL CNQLGLPFPC LCRVPCNTVF GSQHQMDVAF LEKLIKDDIE RGRLPLLLVA
NAGTAAVGHT DKIGRLKELC EQYGIWLHVE GVNLATLALG YVSSSVLAAA KCDSMTMTPG
PWLGLPAVPA VTLYKHDDPA LTLVAGLTSN KPTDKLRALP LWLSLQYLGL DGFVERIKHA
CQLSQRLQES LKKVNYIKIL VEDELSSPVV VFRFFQELPG SDPVFKAVPV PNMTPSGVGR
ERHSCDALNR WLGEQLKQLV PASGLTVMDL EAEGTCLRFS PLMTAAGWSH CGTTTRYDCV
RSRLTTRLPG STGEQAPP*
mutated AA sequence N/A
speed 0.19 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

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