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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000588790
Querying Taster for transcript #2: ENST00000458408
MT speed 2.65 s - this script 5.832065 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CCDC159polymorphism_automatic2.30038210702332e-13simple_aaeaffectedC278Ssingle base exchangers6887show file
CCDC159polymorphism_automatic2.30038210702332e-13simple_aaeaffectedC278Ssingle base exchangers6887show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999999977 (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) chr19:11465316G>CN/A show variant in all transcripts   IGV
HGNC symbol CCDC159
Ensembl transcript ID ENST00000588790
Genbank transcript ID NM_001080503
UniProt peptide P0C7I6
alteration type single base exchange
alteration region CDS
DNA changes c.833G>C
cDNA.1280G>C
g.9957G>C
AA changes C278S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS
278
frameshift no
known variant Reference ID: rs6887
databasehomozygous (C/C)heterozygousallele carriers
1000G37511361511
ExAC87241531924043
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0570.001
-0.0460
(flanking)-2.9720
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased9958wt: 0.43 / mu: 0.75wt: GACTGTGACCAGGAC
mu: GACTCTGACCAGGAC
 CTGT|gacc
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      278PPLPSWDSDSDCDQDLSQPPFSKS
mutated  not conserved    278PPLPSWDSDSDSDQDLSQPPFSK
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000006241  398SQCPSWDSDSDWER-----PFSK
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 
262298COILEDPotential.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 894 / 894
position (AA) of stopcodon in wt / mu AA sequence 298 / 298
position of stopcodon in wt / mu cDNA 1341 / 1341
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 448 / 448
chromosome 19
strand 1
last intron/exon boundary 1337
theoretical NMD boundary in CDS 839
length of CDS 894
coding sequence (CDS) position 833
cDNA position
(for ins/del: last normal base / first normal base)
1280
gDNA position
(for ins/del: last normal base / first normal base)
9957
chromosomal position
(for ins/del: last normal base / first normal base)
11465316
original gDNA sequence snippet CTGGGACTCTGACTCCGACTGTGACCAGGACCTCTCCCAGC
altered gDNA sequence snippet CTGGGACTCTGACTCCGACTCTGACCAGGACCTCTCCCAGC
original cDNA sequence snippet CTGGGACTCTGACTCCGACTGTGACCAGGACCTCTCCCAGC
altered cDNA sequence snippet CTGGGACTCTGACTCCGACTCTGACCAGGACCTCTCCCAGC
wildtype AA sequence MGEHEQVKPL ETSSSKVKAK TIVMIPDSQK LLRCELESLK SQLQAQTKAF EFLNHSVTML
EKESCLQQIK IQQLEEVLSP TGRQGEKEEH KWGMEQGRQE LYGALTQGLQ GLEKTLRDSE
EMQRARTTRC LQLLAQEIRD SKKFLWEELE LVREEVTFIY QKLQAQEDEI SENLVNIQKM
QKTQVKCRKI LTKMKQQGHE TAACPETEEI PQGASGCWKD DLQKELSDIW SAVHVLQNSI
DSLTLCSGAC PKASSLRGHK GHQCLSPPLP SWDSDSDCDQ DLSQPPFSKS GRSFPPA*
mutated AA sequence MGEHEQVKPL ETSSSKVKAK TIVMIPDSQK LLRCELESLK SQLQAQTKAF EFLNHSVTML
EKESCLQQIK IQQLEEVLSP TGRQGEKEEH KWGMEQGRQE LYGALTQGLQ GLEKTLRDSE
EMQRARTTRC LQLLAQEIRD SKKFLWEELE LVREEVTFIY QKLQAQEDEI SENLVNIQKM
QKTQVKCRKI LTKMKQQGHE TAACPETEEI PQGASGCWKD DLQKELSDIW SAVHVLQNSI
DSLTLCSGAC PKASSLRGHK GHQCLSPPLP SWDSDSDSDQ DLSQPPFSKS GRSFPPA*
speed 1.48 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: 0.99999999999977 (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) chr19:11465316G>CN/A show variant in all transcripts   IGV
HGNC symbol CCDC159
Ensembl transcript ID ENST00000458408
Genbank transcript ID N/A
UniProt peptide P0C7I6
alteration type single base exchange
alteration region CDS
DNA changes c.833G>C
cDNA.935G>C
g.9957G>C
AA changes C278S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS
278
frameshift no
known variant Reference ID: rs6887
databasehomozygous (C/C)heterozygousallele carriers
1000G37511361511
ExAC87241531924043
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0570.001
-0.0460
(flanking)-2.9720
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased9958wt: 0.43 / mu: 0.75wt: GACTGTGACCAGGAC
mu: GACTCTGACCAGGAC
 CTGT|gacc
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      278PPLPSWDSDSDCDQDLSQPPFSKS
mutated  not conserved    278PPLPSWDSDSDSDQDLSQPPFSK
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000006241  398SQCPSWDSDSDWER-----PFSK
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 
262298COILEDPotential.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 894 / 894
position (AA) of stopcodon in wt / mu AA sequence 298 / 298
position of stopcodon in wt / mu cDNA 996 / 996
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 103 / 103
chromosome 19
strand 1
last intron/exon boundary 992
theoretical NMD boundary in CDS 839
length of CDS 894
coding sequence (CDS) position 833
cDNA position
(for ins/del: last normal base / first normal base)
935
gDNA position
(for ins/del: last normal base / first normal base)
9957
chromosomal position
(for ins/del: last normal base / first normal base)
11465316
original gDNA sequence snippet CTGGGACTCTGACTCCGACTGTGACCAGGACCTCTCCCAGC
altered gDNA sequence snippet CTGGGACTCTGACTCCGACTCTGACCAGGACCTCTCCCAGC
original cDNA sequence snippet CTGGGACTCTGACTCCGACTGTGACCAGGACCTCTCCCAGC
altered cDNA sequence snippet CTGGGACTCTGACTCCGACTCTGACCAGGACCTCTCCCAGC
wildtype AA sequence MGEHEQVKPL ETSSSKVKAK TIVMIPDSQK LLRCELESLK SQLQAQTKAF EFLNHSVTML
EKESCLQQIK IQQLEEVLSP TGRQGEKEEH KWGMEQGRQE LYGALTQGLQ GLEKTLRDSE
EMQRARTTRC LQLLAQEIRD SKKFLWEELE LVREEVTFIY QKLQAQEDEI SENLVNIQKM
QKTQVKCRKI LTKMKQQGHE TAACPETEEI PQGASGCWKD DLQKELSDIW SAVHVLQNSI
DSLTLCSGAC PKASSLRGHK GHQCLSPPLP SWDSDSDCDQ DLSQPPFSKS GRSFPPA*
mutated AA sequence MGEHEQVKPL ETSSSKVKAK TIVMIPDSQK LLRCELESLK SQLQAQTKAF EFLNHSVTML
EKESCLQQIK IQQLEEVLSP TGRQGEKEEH KWGMEQGRQE LYGALTQGLQ GLEKTLRDSE
EMQRARTTRC LQLLAQEIRD SKKFLWEELE LVREEVTFIY QKLQAQEDEI SENLVNIQKM
QKTQVKCRKI LTKMKQQGHE TAACPETEEI PQGASGCWKD DLQKELSDIW SAVHVLQNSI
DSLTLCSGAC PKASSLRGHK GHQCLSPPLP SWDSDSDSDQ DLSQPPFSKS GRSFPPA*
speed 1.17 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