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: ENST00000344642
Querying Taster for transcript #2: ENST00000543870
MT speed 0 s - this script 4.052356 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
LDLRAD2polymorphism_automatic0.000554939816327038simple_aaeN134Tsingle base exchangers10917051show file
LDLRAD2polymorphism_automatic0.000554939816327038simple_aaeN134Tsingle base exchangers10917051show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999445060183673 (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
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:22141206A>CN/A show variant in all transcripts   IGV
HGNC symbol LDLRAD2
Ensembl transcript ID ENST00000344642
Genbank transcript ID NM_001013693
UniProt peptide Q5SZI1
alteration type single base exchange
alteration region CDS
DNA changes c.401A>C
cDNA.588A>C
g.2449A>C
AA changes N134T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 134
frameshift no
known variant Reference ID: rs10917051
databasehomozygous (C/C)heterozygousallele carriers
1000G97511192094
ExAC7254721114465
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.4731
1.4311
(flanking)2.0861
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 111
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      134PRPLGSPLCGLNIPVPVASSGPFL
mutated  not conserved    134PRPLGSPLCGLTIPVPVASSGPF
Ptroglodytes  not conserved  ENSPTRG00000000306  134PRPLGSPLCGLTIPVPVASSGPF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000094035  n/a
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000090297  158APLIGPPLCGKSPPRPVLSTGKF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
26233TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 819 / 819
position (AA) of stopcodon in wt / mu AA sequence 273 / 273
position of stopcodon in wt / mu cDNA 1006 / 1006
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 188 / 188
chromosome 1
strand 1
last intron/exon boundary 993
theoretical NMD boundary in CDS 755
length of CDS 819
coding sequence (CDS) position 401
cDNA position
(for ins/del: last normal base / first normal base)		 588
gDNA position
(for ins/del: last normal base / first normal base)		 2449
chromosomal position
(for ins/del: last normal base / first normal base)		 22141206
original gDNA sequence snippet GTCCCCACTGTGCGGCCTGAACATCCCGGTGCCTGTGGCAT
altered gDNA sequence snippet GTCCCCACTGTGCGGCCTGACCATCCCGGTGCCTGTGGCAT
original cDNA sequence snippet GTCCCCACTGTGCGGCCTGAACATCCCGGTGCCTGTGGCAT
altered cDNA sequence snippet GTCCCCACTGTGCGGCCTGACCATCCCGGTGCCTGTGGCAT
wildtype AA sequence MEACCLLQLP QRLLLLGAAA LTATALETAD LAELCGQTWQ GDGLLLRSHA ASRRFYFVAP
DTDCGLWVQA AAPGDRIRFQ FRFFLVYSLT PAPPALNTSS PAPADPCAPG SYLQFYEGPP
GAPRPLGSPL CGLNIPVPVA SSGPFLGLRL VTRGRQPRVD FVGEVTSFRL GPCGAYFRCQ
NGRCIPSSLV CDPWGMDNCG DGSDQGSWSP ADCRGPSPVP SQTGSTDAHT SRSLTPSPAL
GSAGSLWIAA ERSSPAGRDP TRQDAALEGS TE*
mutated AA sequence MEACCLLQLP QRLLLLGAAA LTATALETAD LAELCGQTWQ GDGLLLRSHA ASRRFYFVAP
DTDCGLWVQA AAPGDRIRFQ FRFFLVYSLT PAPPALNTSS PAPADPCAPG SYLQFYEGPP
GAPRPLGSPL CGLTIPVPVA SSGPFLGLRL VTRGRQPRVD FVGEVTSFRL GPCGAYFRCQ
NGRCIPSSLV CDPWGMDNCG DGSDQGSWSP ADCRGPSPVP SQTGSTDAHT SRSLTPSPAL
GSAGSLWIAA ERSSPAGRDP TRQDAALEGS TE*
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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999445060183673 (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
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:22141206A>CN/A show variant in all transcripts   IGV
HGNC symbol LDLRAD2
Ensembl transcript ID ENST00000543870
Genbank transcript ID N/A
UniProt peptide Q5SZI1
alteration type single base exchange
alteration region CDS
DNA changes c.401A>C
cDNA.490A>C
g.2449A>C
AA changes N134T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 134
frameshift no
known variant Reference ID: rs10917051
databasehomozygous (C/C)heterozygousallele carriers
1000G97511192094
ExAC7254721114465
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.4731
1.4311
(flanking)2.0861
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 111
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      134PRPLGSPLCGLNIPVPVASSGPFL
mutated  not conserved    134PRPLGSPLCGLTIPVPVASSGPF
Ptroglodytes  not conserved  ENSPTRG00000000306  134PRPLGSPLCGLTIPVPVASSGPF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000094035  n/a
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000090297  158APLIGPPLCGKSPPRPVLSTGKF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
26233TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 819 / 819
position (AA) of stopcodon in wt / mu AA sequence 273 / 273
position of stopcodon in wt / mu cDNA 908 / 908
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 90 / 90
chromosome 1
strand 1
last intron/exon boundary 1127
theoretical NMD boundary in CDS 987
length of CDS 819
coding sequence (CDS) position 401
cDNA position
(for ins/del: last normal base / first normal base)		 490
gDNA position
(for ins/del: last normal base / first normal base)		 2449
chromosomal position
(for ins/del: last normal base / first normal base)		 22141206
original gDNA sequence snippet GTCCCCACTGTGCGGCCTGAACATCCCGGTGCCTGTGGCAT
altered gDNA sequence snippet GTCCCCACTGTGCGGCCTGACCATCCCGGTGCCTGTGGCAT
original cDNA sequence snippet GTCCCCACTGTGCGGCCTGAACATCCCGGTGCCTGTGGCAT
altered cDNA sequence snippet GTCCCCACTGTGCGGCCTGACCATCCCGGTGCCTGTGGCAT
wildtype AA sequence MEACCLLQLP QRLLLLGAAA LTATALETAD LAELCGQTWQ GDGLLLRSHA ASRRFYFVAP
DTDCGLWVQA AAPGDRIRFQ FRFFLVYSLT PAPPALNTSS PAPADPCAPG SYLQFYEGPP
GAPRPLGSPL CGLNIPVPVA SSGPFLGLRL VTRGRQPRVD FVGEVTSFRL GPCGAYFRCQ
NGRCIPSSLV CDPWGMDNCG DGSDQGSWSP ADCRGPSPVP SQTGSTDAHT SRSLTPSPAL
GSAGSLWIAA ERSSPAGRDP TRQDAALEGS TE*
mutated AA sequence MEACCLLQLP QRLLLLGAAA LTATALETAD LAELCGQTWQ GDGLLLRSHA ASRRFYFVAP
DTDCGLWVQA AAPGDRIRFQ FRFFLVYSLT PAPPALNTSS PAPADPCAPG SYLQFYEGPP
GAPRPLGSPL CGLTIPVPVA SSGPFLGLRL VTRGRQPRVD FVGEVTSFRL GPCGAYFRCQ
NGRCIPSSLV CDPWGMDNCG DGSDQGSWSP ADCRGPSPVP SQTGSTDAHT SRSLTPSPAL
GSAGSLWIAA ERSSPAGRDP TRQDAALEGS TE*
speed 1.04 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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