Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.895405030067638 (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) chr1:67288045C>TN/A show variant in all transcripts   IGV
HGNC symbol WDR78
Ensembl transcript ID ENST00000431318
Genbank transcript ID N/A
UniProt peptide Q5VTH9
alteration type single base exchange
alteration region CDS
DNA changes c.1634G>A
cDNA.2452G>A
g.102526G>A
AA changes R545Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 545
frameshift no
known variant Reference ID: rs482082
databasehomozygous (T/T)heterozygousallele carriers
1000G67912201899
ExAC15457185317310
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2091
1.1640.975
(flanking)1.3450.858
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost102527sequence motif lost- wt: CCGG|gtaa
 mu: CCAG.gtaa
Donor marginally increased102522wt: 0.9517 / mu: 0.9895 (marginal change - not scored)wt: AAACTGGCCGGGTAA
mu: AAACTGGCCAGGTAA		 ACTG|gccg
Donor marginally increased102526wt: 0.9888 / mu: 0.9968 (marginal change - not scored)wt: TGGCCGGGTAAGACT
mu: TGGCCAGGTAAGACT		 GCCG|ggta
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      545LRNMPTVLETGRGDIMDTLLGSKS
mutated  all conserved    545LETGQGDIMDTLLGSK
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000000641  826LRNMPTALESGRGDIIDTLLGSK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000035126  791LRNMPTASDTSRGDVINILLGPK
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000006622  770LKNLHG--KSSQVDVLDGIICS
Drerio  all conserved  ENSDARG00000044400  763LKNI-TAGGGSQGETLEDVIQS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000020368  783LRNVSSSKDSEVNALYDIIGATL
protein features
start (aa)end (aa)featuredetails 
534574REPEATWD 1.lost
583631REPEATWD 2.might get lost (downstream of altered splice site)
658698REPEATWD 3.might get lost (downstream of altered splice site)
702742REPEATWD 4.might get lost (downstream of altered splice site)
745784REPEATWD 5.might get lost (downstream of altered splice site)
790829REPEATWD 6.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1686 / 1686
position (AA) of stopcodon in wt / mu AA sequence 562 / 562
position of stopcodon in wt / mu cDNA 2504 / 2504
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 819 / 819
chromosome 1
strand -1
last intron/exon boundary 2454
theoretical NMD boundary in CDS 1585
length of CDS 1686
coding sequence (CDS) position 1634
cDNA position
(for ins/del: last normal base / first normal base)		 2452
gDNA position
(for ins/del: last normal base / first normal base)		 102526
chromosomal position
(for ins/del: last normal base / first normal base)		 67288045
original gDNA sequence snippet TACTGTTTTGGAAACTGGCCGGGTAAGACTCAAGAGTAAAA
altered gDNA sequence snippet TACTGTTTTGGAAACTGGCCAGGTAAGACTCAAGAGTAAAA
original cDNA sequence snippet TACTGTTTTGGAAACTGGCCGGGGAGATATAATGGATACTT
altered cDNA sequence snippet TACTGTTTTGGAAACTGGCCAGGGAGATATAATGGATACTT
wildtype AA sequence MVSVESEEAE KVTQRNKNYE VLCRNRLGND LYVERMMQTF NGAPKNKDVQ CDKIIMEDKG
IMSTAWDLYD SYNAMELVSL SVKQSVVESS SKANVLPKDQ DQRLPGSTTE KNSETSSLMD
IENVILAKIH EDEEDHSDAI LKSDKFHQDL FFMERVLMEN IFQPKLAAYR QLPVLKEPEP
EEPEDVLESA KHEEVEEESK KEEEEEIHAE ESTIPANLER LWSFSCDLTK GLNVSSLAWN
KTNPDLLAVG YGHFGFKEQK RGLACCWSIK NPMWPERIYQ SPYGVTAVDF SIGAPNLLAV
GYHNGTIAIY NVRSNSNVPV LDSSESPQKH LGPVWQLQWI EQDRGTTGDG KREILVSISA
DGRISKWVIR KGLDCYDLMR LKRTTAASNK KGGEKEKKDE ALISRQAPGM CFAFHPKGPV
YKVTWNPFCH DVFLSCSADW GVIIWQQENV KPSLSFYPAT SVVYDVAWSP KSSYIFAAAN
ENRVEIWDLH ISTLDPLIVN TANPGIKFTT ILFAKQTDCL LVGDSDGQVS VYELRNMPTV
LETGRGDIMD TLLGSKSNQS A*
mutated AA sequence MVSVESEEAE KVTQRNKNYE VLCRNRLGND LYVERMMQTF NGAPKNKDVQ CDKIIMEDKG
IMSTAWDLYD SYNAMELVSL SVKQSVVESS SKANVLPKDQ DQRLPGSTTE KNSETSSLMD
IENVILAKIH EDEEDHSDAI LKSDKFHQDL FFMERVLMEN IFQPKLAAYR QLPVLKEPEP
EEPEDVLESA KHEEVEEESK KEEEEEIHAE ESTIPANLER LWSFSCDLTK GLNVSSLAWN
KTNPDLLAVG YGHFGFKEQK RGLACCWSIK NPMWPERIYQ SPYGVTAVDF SIGAPNLLAV
GYHNGTIAIY NVRSNSNVPV LDSSESPQKH LGPVWQLQWI EQDRGTTGDG KREILVSISA
DGRISKWVIR KGLDCYDLMR LKRTTAASNK KGGEKEKKDE ALISRQAPGM CFAFHPKGPV
YKVTWNPFCH DVFLSCSADW GVIIWQQENV KPSLSFYPAT SVVYDVAWSP KSSYIFAAAN
ENRVEIWDLH ISTLDPLIVN TANPGIKFTT ILFAKQTDCL LVGDSDGQVS VYELRNMPTV
LETGQGDIMD TLLGSKSNQS A*
speed 0.83 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