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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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000307522
MT speed 0 s - this script 7.380568 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CCDC8polymorphism_automatic2.85511464104271e-06simple_aaeaffectedH383Ysingle base exchangers34186470show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999997144885359 (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) chr19:46914921G>AN/A show variant in all transcripts   IGV
HGNC symbol CCDC8
Ensembl transcript ID ENST00000307522
Genbank transcript ID NM_032040
UniProt peptide Q9H0W5
alteration type single base exchange
alteration region CDS
DNA changes c.1147C>T
cDNA.1921C>T
g.1921C>T
AA changes H383Y Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS
383
frameshift no
known variant Reference ID: rs34186470
databasehomozygous (A/A)heterozygousallele carriers
1000G199760959
ExAC25131652419037
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4410.512
2.4690.563
(flanking)-0.3670
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased1924wt: 0.9987 / mu: 0.9990 (marginal change - not scored)wt: ACCACAGGGAAGAGG
mu: ACTACAGGGAAGAGG
 CACA|ggga
Donor marginally increased1914wt: 0.9866 / mu: 0.9973 (marginal change - not scored)wt: GGCACAGATAACCAC
mu: GGCACAGATAACTAC
 CACA|gata
Donor marginally increased1919wt: 0.3210 / mu: 0.3370 (marginal change - not scored)wt: AGATAACCACAGGGA
mu: AGATAACTACAGGGA
 ATAA|ccac
Donor gained19250.35mu: CTACAGGGAAGAGGC ACAG|ggaa
distance from splice site 1293
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      383PADQRSQGTDNHREEAADNQRAEA
mutated  all conserved    383PADQRSQGTDNYREEAADNQRAE
Ptroglodytes  all identical  ENSPTRG00000011182  383PADQRSQGADNHREEAADNQRVE
Mmulatta  not conserved  ENSMMUG00000003190  391PADHRPQGADNLREEAL------
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000041117  390AASLRAEAVASPRAEAAASPRAE
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 
514535COILEDPotential.might get lost (downstream of altered splice site)
515515CONFLICTA -> V (in Ref. 1; CAB66544).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1617 / 1617
position (AA) of stopcodon in wt / mu AA sequence 539 / 539
position of stopcodon in wt / mu cDNA 2391 / 2391
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 775 / 775
chromosome 19
strand -1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1617
coding sequence (CDS) position 1147
cDNA position
(for ins/del: last normal base / first normal base)
1921
gDNA position
(for ins/del: last normal base / first normal base)
1921
chromosomal position
(for ins/del: last normal base / first normal base)
46914921
original gDNA sequence snippet GGTCACAGGGCACAGATAACCACAGGGAAGAGGCTGCAGAT
altered gDNA sequence snippet GGTCACAGGGCACAGATAACTACAGGGAAGAGGCTGCAGAT
original cDNA sequence snippet GGTCACAGGGCACAGATAACCACAGGGAAGAGGCTGCAGAT
altered cDNA sequence snippet GGTCACAGGGCACAGATAACTACAGGGAAGAGGCTGCAGAT
wildtype AA sequence MLQIGEDVDY LLIPREVRLA GGVWRVISKP ATKEAEFRER LTQFLEEEGR TLEDVARIME
KSTPHPPQPP KKPKEPRVRR RVQQMVTPPP RLVVGTYDSS NASDSEFSDF ETSRDKSRQG
PRRGKKVRKM PVSYLGSKFL GSDLESEDDE ELVEAFLRRQ EKQPSAPPAR RRVNLPVPMF
EDNLGPQLSK ADRWREYVSQ VSWGKLKRRV KGWAPRAGPG VGEARLASTA VESAGVSSAP
EGTSPGDRLG NAGDVCVPQA SPRRWRPKIN WASFRRRRKE QTAPTGQGAD IEADQGGEAA
DSQREEAIAD QREGAAGNQR AGAPADQGAE AADNQREEAA DNQRAGAPAE EGAEAADNQR
EEAADNQRAE APADQRSQGT DNHREEAADN QRAEAPADQG SEVTDNQREE AVHDQRERAP
AVQGADNQRA QARAGQRAEA AHNQRAGAPG IQEAEVSAAQ GTTGTAPGAR ARKQVKTVRF
QTPGRFSWFC KRRRAFWHTP RLPTLPKRVP RAGEARNLRV LRAEARAEAE QGEQEDQL*
mutated AA sequence MLQIGEDVDY LLIPREVRLA GGVWRVISKP ATKEAEFRER LTQFLEEEGR TLEDVARIME
KSTPHPPQPP KKPKEPRVRR RVQQMVTPPP RLVVGTYDSS NASDSEFSDF ETSRDKSRQG
PRRGKKVRKM PVSYLGSKFL GSDLESEDDE ELVEAFLRRQ EKQPSAPPAR RRVNLPVPMF
EDNLGPQLSK ADRWREYVSQ VSWGKLKRRV KGWAPRAGPG VGEARLASTA VESAGVSSAP
EGTSPGDRLG NAGDVCVPQA SPRRWRPKIN WASFRRRRKE QTAPTGQGAD IEADQGGEAA
DSQREEAIAD QREGAAGNQR AGAPADQGAE AADNQREEAA DNQRAGAPAE EGAEAADNQR
EEAADNQRAE APADQRSQGT DNYREEAADN QRAEAPADQG SEVTDNQREE AVHDQRERAP
AVQGADNQRA QARAGQRAEA AHNQRAGAPG IQEAEVSAAQ GTTGTAPGAR ARKQVKTVRF
QTPGRFSWFC KRRRAFWHTP RLPTLPKRVP RAGEARNLRV LRAEARAEAE QGEQEDQL*
speed 2.07 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
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