Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999471928592284 (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) chr16:71660310G>AN/A show variant in all transcripts   IGV
HGNC symbol MARVELD3
Ensembl transcript ID ENST00000567566
Genbank transcript ID N/A
UniProt peptide Q96A59
alteration type single base exchange
alteration region CDS
DNA changes c.178G>A
cDNA.247G>A
g.247G>A
AA changes E60K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 60
frameshift no
known variant Reference ID: rs4788821
databasehomozygous (A/A)heterozygousallele carriers
1000G52910141543
ExAC125042135463
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9230.892
1.8820.904
(flanking)0.1250.882
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 increased250wt: 0.8869 / mu: 0.9265 (marginal change - not scored)wt: CGGAGAGAGACCAGG
mu: CGAAGAGAGACCAGG		 GAGA|gaga
Donor increased243wt: 0.41 / mu: 0.90wt: CGGGACCCGGAGAGA
mu: CGGGACCCGAAGAGA		 GGAC|ccgg
Donor increased248wt: 0.58 / mu: 0.84wt: CCCGGAGAGAGACCA
mu: CCCGAAGAGAGACCA		 CGGA|gaga
Donor marginally increased252wt: 0.9267 / mu: 0.9594 (marginal change - not scored)wt: GAGAGAGACCAGGAG
mu: AAGAGAGACCAGGAG		 GAGA|gacc
Donor marginally increased245wt: 0.9820 / mu: 0.9894 (marginal change - not scored)wt: GGACCCGGAGAGAGA
mu: GGACCCGAAGAGAGA		 ACCC|ggag
Donor increased247wt: 0.55 / mu: 0.96wt: ACCCGGAGAGAGACC
mu: ACCCGAAGAGAGACC		 CCGG|agag
distance from splice site 247
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      60GNRRRDGDRDPERDQERDGNRDRN
mutated  all conserved    60GNRRRDGDRDPKRDQERDGNRDR
Ptroglodytes  all identical  ENSPTRG00000008325  35GNRRRDRDRDPERDQERDRNRDR
Mmulatta  no alignment  ENSMMUG00000019204  n/a
Fcatus  no alignment  ENSFCAG00000011898  n/a
Mmusculus  not conserved  ENSMUSG00000001672  60------------RHRERNGDVRG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000037528  40GEKR---DRDPRSQQDRPSDRRP
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000031429  n/a
protein features
start (aa)end (aa)featuredetails 
1226TOPO_DOMCytoplasmic (Potential).lost
8120COMPBIASArg-rich.lost
129170COMPBIASPro-rich.might get lost (downstream of altered splice site)
193386DOMAINMARVEL.might get lost (downstream of altered splice site)
227247TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
248271TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
272292TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
293300TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
301321TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
322360TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
361381TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
382401TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 660 / 660
position (AA) of stopcodon in wt / mu AA sequence 220 / 220
position of stopcodon in wt / mu cDNA 729 / 729
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 70 / 70
chromosome 16
strand 1
last intron/exon boundary 537
theoretical NMD boundary in CDS 417
length of CDS 660
coding sequence (CDS) position 178
cDNA position
(for ins/del: last normal base / first normal base)		 247
gDNA position
(for ins/del: last normal base / first normal base)		 247
chromosomal position
(for ins/del: last normal base / first normal base)		 71660310
original gDNA sequence snippet GGGACGGGGACCGGGACCCGGAGAGAGACCAGGAGAGGGAC
altered gDNA sequence snippet GGGACGGGGACCGGGACCCGAAGAGAGACCAGGAGAGGGAC
original cDNA sequence snippet GGGACGGGGACCGGGACCCGGAGAGAGACCAGGAGAGGGAC
altered cDNA sequence snippet GGGACGGGGACCGGGACCCGAAGAGAGACCAGGAGAGGGAC
wildtype AA sequence MEDPSGAREP RARPRERDPG RRPHPDQGRT HDRPRDRPGD PRRKRSSDGN RRRDGDRDPE
RDQERDGNRD RNRDRERERE RERDPDRGPR RDTHRDAGPR AGEHGVWEKP RQSRTRDGAR
GLTWDAAAPP GPAPWEAPEP PQPQRKGDPG RRRPESEPPS ERYLPSTPRP GREEVEYYQS
EAEGLLECHK CKYLCTGRGE PFCRLFDHLL SLVVLEGMV*
mutated AA sequence MEDPSGAREP RARPRERDPG RRPHPDQGRT HDRPRDRPGD PRRKRSSDGN RRRDGDRDPK
RDQERDGNRD RNRDRERERE RERDPDRGPR RDTHRDAGPR AGEHGVWEKP RQSRTRDGAR
GLTWDAAAPP GPAPWEAPEP PQPQRKGDPG RRRPESEPPS ERYLPSTPRP GREEVEYYQS
EAEGLLECHK CKYLCTGRGE PFCRLFDHLL SLVVLEGMV*
speed 1.08 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