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: ENST00000269586
Querying Taster for transcript #2: ENST00000444555
MT speed 0 s - this script 3.451513 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ARL5Cpolymorphism_automatic0.905553361090873simple_aaeaffectedN39Ssingle base exchangers657723show file
ARL5Cpolymorphism_automatic0.905553361090873simple_aaeaffectedN39Ssingle base exchangers657723show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0944466389091274 (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) chr17:37319103T>CN/A show variant in all transcripts   IGV
HGNC symbol ARL5C
Ensembl transcript ID ENST00000444555
Genbank transcript ID N/A
UniProt peptide A6NH57
alteration type single base exchange
alteration region CDS
DNA changes c.116A>G
cDNA.456A>G
g.5000A>G
AA changes N39S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs657723
databasehomozygous (C/C)heterozygousallele carriers
1000G3809081288
ExAC78135294310
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2920.975
2.6990.992
(flanking)1.8070.987
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased4994wt: 0.9587 / mu: 0.9591 (marginal change - not scored)wt: CCACTCCTACCTCCCCAGCTTGACCAATGAGGTGGTCCATA
mu: CCACTCCTACCTCCCCAGCTTGACCAGTGAGGTGGTCCATA		 gctt|GACC
Acc increased4999wt: 0.46 / mu: 0.72wt: CCTACCTCCCCAGCTTGACCAATGAGGTGGTCCATATGTGT
mu: CCTACCTCCCCAGCTTGACCAGTGAGGTGGTCCATATGTGT		 acca|ATGA
Acc increased4991wt: 0.62 / mu: 0.71wt: TGCCCACTCCTACCTCCCCAGCTTGACCAATGAGGTGGTCC
mu: TGCCCACTCCTACCTCCCCAGCTTGACCAGTGAGGTGGTCC		 ccag|CTTG
Donor marginally increased4999wt: 0.9244 / mu: 0.9970 (marginal change - not scored)wt: TGACCAATGAGGTGG
mu: TGACCAGTGAGGTGG		 ACCA|atga
Donor gained49940.89mu: CAGCTTGACCAGTGA GCTT|gacc
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39GKTTILYRFLTNEVVHMCPTIGSN
mutated  all conserved    39GKTTILYRFLTSEVVHMCPTIGS
Ptroglodytes  all identical  ENSPTRG00000009084  39GKTTILYRFLINEVVHMCPTIGS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038352  39GKTTILYQFLTNEVVHTCSTIGS
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000016508  40GKTTILYQFLTKEAVHTSPTIGS
Drerio  not conserved  ENSDARG00000035719  39GKTTILYQFLTKEAVQTSPTIGS
Dmelanogaster  all identical  FBgn0035866  39GKTTILYQFLMNEVVHTSPTIGS
Celegans  not conserved  ZK632.8  39GKTTILYNYVTKDQVETKPTIGS
Xtropicalis  all identical  ENSXETG00000023713  54GKTTILYQFLMNEVVHTAPTIGS
protein features
start (aa)end (aa)featuredetails 
6670NP_BINDGTP (By similarity).might get lost (downstream of altered splice site)
125128NP_BINDGTP (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 540 / 540
position (AA) of stopcodon in wt / mu AA sequence 180 / 180
position of stopcodon in wt / mu cDNA 880 / 880
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 341 / 341
chromosome 17
strand -1
last intron/exon boundary 832
theoretical NMD boundary in CDS 441
length of CDS 540
coding sequence (CDS) position 116
cDNA position
(for ins/del: last normal base / first normal base)		 456
gDNA position
(for ins/del: last normal base / first normal base)		 5000
chromosomal position
(for ins/del: last normal base / first normal base)		 37319103
original gDNA sequence snippet CTACCTCCCCAGCTTGACCAATGAGGTGGTCCATATGTGTC
altered gDNA sequence snippet CTACCTCCCCAGCTTGACCAGTGAGGTGGTCCATATGTGTC
original cDNA sequence snippet TCTCTACCGGTTCTTGACCAATGAGGTGGTCCATATGTGTC
altered cDNA sequence snippet TCTCTACCGGTTCTTGACCAGTGAGGTGGTCCATATGTGTC
wildtype AA sequence MGQLIAKLMS IFGNQEHTVI IVGLDNEGKT TILYRFLTNE VVHMCPTIGS NVEEIILPKT
HFFMWDIVRP EALSFIWNTY YSNTEFIILV IDSTDRDRLL TTREELYKML AHEALQDASV
LIFANKQDVK DSMRMVEISH FLTLSTIKDH SWHIQGCCAL TREGLPARLQ WMESQAAAN*
mutated AA sequence MGQLIAKLMS IFGNQEHTVI IVGLDNEGKT TILYRFLTSE VVHMCPTIGS NVEEIILPKT
HFFMWDIVRP EALSFIWNTY YSNTEFIILV IDSTDRDRLL TTREELYKML AHEALQDASV
LIFANKQDVK DSMRMVEISH FLTLSTIKDH SWHIQGCCAL TREGLPARLQ WMESQAAAN*
speed 0.97 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: 0.0944466389091273 (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) chr17:37319103T>CN/A show variant in all transcripts   IGV
HGNC symbol ARL5C
Ensembl transcript ID ENST00000269586
Genbank transcript ID N/A
UniProt peptide A6NH57
alteration type single base exchange
alteration region CDS
DNA changes c.116A>G
cDNA.116A>G
g.5000A>G
AA changes N39S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs657723
databasehomozygous (C/C)heterozygousallele carriers
1000G3809081288
ExAC78135294310
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2920.975
2.6990.992
(flanking)1.8070.987
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased4994wt: 0.9587 / mu: 0.9591 (marginal change - not scored)wt: CCACTCCTACCTCCCCAGCTTGACCAATGAGGTGGTCCATA
mu: CCACTCCTACCTCCCCAGCTTGACCAGTGAGGTGGTCCATA		 gctt|GACC
Acc increased4999wt: 0.46 / mu: 0.72wt: CCTACCTCCCCAGCTTGACCAATGAGGTGGTCCATATGTGT
mu: CCTACCTCCCCAGCTTGACCAGTGAGGTGGTCCATATGTGT		 acca|ATGA
Acc increased4991wt: 0.62 / mu: 0.71wt: TGCCCACTCCTACCTCCCCAGCTTGACCAATGAGGTGGTCC
mu: TGCCCACTCCTACCTCCCCAGCTTGACCAGTGAGGTGGTCC		 ccag|CTTG
Donor marginally increased4999wt: 0.9244 / mu: 0.9970 (marginal change - not scored)wt: TGACCAATGAGGTGG
mu: TGACCAGTGAGGTGG		 ACCA|atga
Donor gained49940.89mu: CAGCTTGACCAGTGA GCTT|gacc
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39GKTTILYRFLTNEVVHMCPTIGSN
mutated  all conserved    39GKTTILYRFLTSEVVHMCPTIGS
Ptroglodytes  all identical  ENSPTRG00000009084  39GKTTILYRFLINEVVHMCPTIGS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038352  39GKTTILYQFLTNEVVHTCSTIGS
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000016508  40GKTTILYQFLTKEAVHTSPTIGS
Drerio  not conserved  ENSDARG00000035719  39GKTTILYQFLTKEAVQTSPTIGS
Dmelanogaster  all identical  FBgn0035866  39GKTTILYQFLMNEVVHTSPTIGS
Celegans  not conserved  ZK632.8  39GKTTILYNYVTKDQVETKPTIGS
Xtropicalis  all identical  ENSXETG00000023713  54GKTTILYQFLMNEVVHTAPTIGS
protein features
start (aa)end (aa)featuredetails 
6670NP_BINDGTP (By similarity).might get lost (downstream of altered splice site)
125128NP_BINDGTP (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 540 / 540
position (AA) of stopcodon in wt / mu AA sequence 180 / 180
position of stopcodon in wt / mu cDNA 540 / 540
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 17
strand -1
last intron/exon boundary 492
theoretical NMD boundary in CDS 441
length of CDS 540
coding sequence (CDS) position 116
cDNA position
(for ins/del: last normal base / first normal base)		 116
gDNA position
(for ins/del: last normal base / first normal base)		 5000
chromosomal position
(for ins/del: last normal base / first normal base)		 37319103
original gDNA sequence snippet CTACCTCCCCAGCTTGACCAATGAGGTGGTCCATATGTGTC
altered gDNA sequence snippet CTACCTCCCCAGCTTGACCAGTGAGGTGGTCCATATGTGTC
original cDNA sequence snippet TCTCTACCGGTTCTTGACCAATGAGGTGGTCCATATGTGTC
altered cDNA sequence snippet TCTCTACCGGTTCTTGACCAGTGAGGTGGTCCATATGTGTC
wildtype AA sequence MGQLIAKLMS IFGNQEHTVI IVGLDNEGKT TILYRFLTNE VVHMCPTIGS NVEEIILPKT
HFFMWDIVRP EALSFIWNTY YSNTEFIILV IDSTDRDRLL TTREELYKML AHEALQDASV
LIFANKQDVK DSMRMVEISH FLTLSTIKDH SWHIQGCCAL TREGLPARLQ WMESQAAAN*
mutated AA sequence MGQLIAKLMS IFGNQEHTVI IVGLDNEGKT TILYRFLTSE VVHMCPTIGS NVEEIILPKT
HFFMWDIVRP EALSFIWNTY YSNTEFIILV IDSTDRDRLL TTREELYKML AHEALQDASV
LIFANKQDVK DSMRMVEISH FLTLSTIKDH SWHIQGCCAL TREGLPARLQ WMESQAAAN*
speed 0.53 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