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: ENST00000367341
Querying Taster for transcript #2: ENST00000286380
MT speed 2.62 s - this script 4.838669 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
RAET1Lpolymorphism_automatic2.06945571790129e-13simple_aaeaffectedR26Gsingle base exchangers1543547show file
RAET1Lpolymorphism_automatic2.06945571790129e-13simple_aaeaffectedR26Gsingle base exchangers1543547show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999793 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM0910659)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:150346532T>CN/A show variant in all transcripts   IGV
HGNC symbol RAET1L
Ensembl transcript ID ENST00000367341
Genbank transcript ID N/A
UniProt peptide Q5VY80
alteration type single base exchange
alteration region CDS
DNA changes c.76A>G
cDNA.76A>G
g.137A>G
AA changes R26G Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 26
frameshift no
known variant Reference ID: rs1543547
databasehomozygous (C/C)heterozygousallele carriers
1000G43511591594
ExAC111221052321645

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910659)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5860.001
-0.3890.001
(flanking)-0.6540.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased131wt: 0.28 / mu: 0.35wt: TCCTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAG
mu: TCCTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAG		 tccc|GGGC
Acc marginally increased127wt: 0.3046 / mu: 0.3288 (marginal change - not scored)wt: CTGTTCCTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGG
mu: CTGTTCCTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGG		 ctgg|TCCC
Acc marginally increased133wt: 0.7541 / mu: 0.8413 (marginal change - not scored)wt: CTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAGCT
mu: CTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAGCT		 ccgg|GCTA
Acc marginally increased132wt: 0.5275 / mu: 0.5304 (marginal change - not scored)wt: CCTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAGC
mu: CCTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAGC		 cccg|GGCT
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      26LLFLLFGWSRARRDDPHSLCYDIT
mutated  not conserved    26LLFLLFGWSRAGRDDPHSLCYDI
Ptroglodytes  not conserved  ENSPTRG00000033979  26LLFLLFGWSRAGQDHPHSLCYDI
Mmulatta  not conserved  ENSMMUG00000029466  26LLFLLSGWFGAGRADPHSLCYDI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000079685  27LLCLLSVCLCPRIEETASLC-NI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
125SIGNALPotential.might get lost (downstream of altered splice site)
29117REGIONMHC class I alpha-1 like (By similarity).might get lost (downstream of altered splice site)
5050DISULFIDBy similarity.might get lost (downstream of altered splice site)
6666DISULFIDBy similarity.might get lost (downstream of altered splice site)
6868CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8282CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
118210REGIONMHC class I alpha-2 like (By similarity).might get lost (downstream of altered splice site)
127127DISULFIDBy similarity.might get lost (downstream of altered splice site)
190190DISULFIDBy similarity.might get lost (downstream of altered splice site)
218218LIPIDGPI-anchor amidated glycine (By similarity).might get lost (downstream of altered splice site)
219246PROPEPRemoved in mature form (By similarity). /FTId=PRO_0000320325.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 741 / 741
position (AA) of stopcodon in wt / mu AA sequence 247 / 247
position of stopcodon in wt / mu cDNA 741 / 741
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 6
strand -1
last intron/exon boundary 764
theoretical NMD boundary in CDS 713
length of CDS 741
coding sequence (CDS) position 76
cDNA position
(for ins/del: last normal base / first normal base)		 76
gDNA position
(for ins/del: last normal base / first normal base)		 137
chromosomal position
(for ins/del: last normal base / first normal base)		 150346532
original gDNA sequence snippet TGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAGCTGGTG
altered gDNA sequence snippet TGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAGCTGGTG
original cDNA sequence snippet TGTTCGGCTGGTCCCGGGCTAGGCGAGACGACCCTCACTCT
altered cDNA sequence snippet TGTTCGGCTGGTCCCGGGCTGGGCGAGACGACCCTCACTCT
wildtype AA sequence MAAAAIPALL LCLPLLFLLF GWSRARRDDP HSLCYDITVI PKFRPGPRWC AVQGQVDEKT
FLHYDCGNKT VTPVSPLGKK LNVTMAWKAQ NPVLREVVDI LTEQLLDIQL ENYTPKEPLT
LQARMSCEQK AEGHSSGSWQ FSIDGQTFLL FDSEKRMWTT VHPGARKMKE KWENDKDVAM
SFHYISMGDC IGWLEDFLMG MDSTLEPSAG APLAMSSGTT QLRATATTLI LCCLLIILPC
FILPGI*
mutated AA sequence MAAAAIPALL LCLPLLFLLF GWSRAGRDDP HSLCYDITVI PKFRPGPRWC AVQGQVDEKT
FLHYDCGNKT VTPVSPLGKK LNVTMAWKAQ NPVLREVVDI LTEQLLDIQL ENYTPKEPLT
LQARMSCEQK AEGHSSGSWQ FSIDGQTFLL FDSEKRMWTT VHPGARKMKE KWENDKDVAM
SFHYISMGDC IGWLEDFLMG MDSTLEPSAG APLAMSSGTT QLRATATTLI LCCLLIILPC
FILPGI*
speed 1.24 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: 0.999999999999793 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM0910659)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:150346532T>CN/A show variant in all transcripts   IGV
HGNC symbol RAET1L
Ensembl transcript ID ENST00000286380
Genbank transcript ID NM_130900
UniProt peptide Q5VY80
alteration type single base exchange
alteration region CDS
DNA changes c.76A>G
cDNA.137A>G
g.137A>G
AA changes R26G Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 26
frameshift no
known variant Reference ID: rs1543547
databasehomozygous (C/C)heterozygousallele carriers
1000G43511591594
ExAC111221052321645

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910659)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5860.001
-0.3890.001
(flanking)-0.6540.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased131wt: 0.28 / mu: 0.35wt: TCCTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAG
mu: TCCTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAG		 tccc|GGGC
Acc marginally increased127wt: 0.3046 / mu: 0.3288 (marginal change - not scored)wt: CTGTTCCTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGG
mu: CTGTTCCTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGG		 ctgg|TCCC
Acc marginally increased133wt: 0.7541 / mu: 0.8413 (marginal change - not scored)wt: CTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAGCT
mu: CTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAGCT		 ccgg|GCTA
Acc marginally increased132wt: 0.5275 / mu: 0.5304 (marginal change - not scored)wt: CCTGCTGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAGC
mu: CCTGCTGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAGC		 cccg|GGCT
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      26LLFLLFGWSRARRDDPHSLCYDIT
mutated  not conserved    26LLFLLFGWSRAGRDDPHSLCYDI
Ptroglodytes  not conserved  ENSPTRG00000033979  26LLFLLFGWSRAGQDHPHSLCYDI
Mmulatta  not conserved  ENSMMUG00000029466  26LLFLLSGWFGAGRADPHSLCYDI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000079685  27LLCLLSVCLCPRIEETASLC-NI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
125SIGNALPotential.might get lost (downstream of altered splice site)
29117REGIONMHC class I alpha-1 like (By similarity).might get lost (downstream of altered splice site)
5050DISULFIDBy similarity.might get lost (downstream of altered splice site)
6666DISULFIDBy similarity.might get lost (downstream of altered splice site)
6868CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
8282CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
118210REGIONMHC class I alpha-2 like (By similarity).might get lost (downstream of altered splice site)
127127DISULFIDBy similarity.might get lost (downstream of altered splice site)
190190DISULFIDBy similarity.might get lost (downstream of altered splice site)
218218LIPIDGPI-anchor amidated glycine (By similarity).might get lost (downstream of altered splice site)
219246PROPEPRemoved in mature form (By similarity). /FTId=PRO_0000320325.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 741 / 741
position (AA) of stopcodon in wt / mu AA sequence 247 / 247
position of stopcodon in wt / mu cDNA 802 / 802
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 62 / 62
chromosome 6
strand -1
last intron/exon boundary 693
theoretical NMD boundary in CDS 581
length of CDS 741
coding sequence (CDS) position 76
cDNA position
(for ins/del: last normal base / first normal base)		 137
gDNA position
(for ins/del: last normal base / first normal base)		 137
chromosomal position
(for ins/del: last normal base / first normal base)		 150346532
original gDNA sequence snippet TGTTCGGCTGGTCCCGGGCTAGGCGAGACGGTGAGCTGGTG
altered gDNA sequence snippet TGTTCGGCTGGTCCCGGGCTGGGCGAGACGGTGAGCTGGTG
original cDNA sequence snippet TGTTCGGCTGGTCCCGGGCTAGGCGAGACGACCCTCACTCT
altered cDNA sequence snippet TGTTCGGCTGGTCCCGGGCTGGGCGAGACGACCCTCACTCT
wildtype AA sequence MAAAAIPALL LCLPLLFLLF GWSRARRDDP HSLCYDITVI PKFRPGPRWC AVQGQVDEKT
FLHYDCGNKT VTPVSPLGKK LNVTMAWKAQ NPVLREVVDI LTEQLLDIQL ENYTPKEPLT
LQARMSCEQK AEGHSSGSWQ FSIDGQTFLL FDSEKRMWTT VHPGARKMKE KWENDKDVAM
SFHYISMGDC IGWLEDFLMG MDSTLEPSAG APLAMSSGTT QLRATATTLI LCCLLIILPC
FILPGI*
mutated AA sequence MAAAAIPALL LCLPLLFLLF GWSRAGRDDP HSLCYDITVI PKFRPGPRWC AVQGQVDEKT
FLHYDCGNKT VTPVSPLGKK LNVTMAWKAQ NPVLREVVDI LTEQLLDIQL ENYTPKEPLT
LQARMSCEQK AEGHSSGSWQ FSIDGQTFLL FDSEKRMWTT VHPGARKMKE KWENDKDVAM
SFHYISMGDC IGWLEDFLMG MDSTLEPSAG APLAMSSGTT QLRATATTLI LCCLLIILPC
FILPGI*
speed 1.38 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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