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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000567566
Querying Taster for transcript #2: ENST00000565261
Querying Taster for transcript #3: ENST00000268485
Querying Taster for transcript #4: ENST00000299952
MT speed 4.17 s - this script 6.349819 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MARVELD3polymorphism_automatic0.000172168886911961simple_aaeaffectedE60Ksingle base exchangers4788821show file
MARVELD3polymorphism_automatic0.000528071407716046simple_aaeaffectedE60Ksingle base exchangers4788821show file
MARVELD3polymorphism_automatic0.000528071407716046simple_aaeaffectedE60Ksingle base exchangers4788821show file
MARVELD3polymorphism_automatic0.000528071407716046simple_aaeaffectedE60Ksingle base exchangers4788821show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999827831113088 (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 ENST00000565261
Genbank transcript ID N/A
UniProt peptide Q96A59
alteration type single base exchange
alteration region CDS
DNA changes c.178G>A
cDNA.224G>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 increased243wt: 0.41 / mu: 0.90wt: CGGGACCCGGAGAGA
mu: CGGGACCCGAAGAGA		 GGAC|ccgg
Donor marginally increased252wt: 0.9267 / mu: 0.9594 (marginal change - not scored)wt: GAGAGAGACCAGGAG
mu: AAGAGAGACCAGGAG		 GAGA|gacc
Donor increased247wt: 0.55 / mu: 0.96wt: ACCCGGAGAGAGACC
mu: ACCCGAAGAGAGACC		 CCGG|agag
Donor increased248wt: 0.58 / mu: 0.84wt: CCCGGAGAGAGACCA
mu: CCCGAAGAGAGACCA		 CGGA|gaga
Donor marginally increased250wt: 0.8869 / mu: 0.9265 (marginal change - not scored)wt: CGGAGAGAGACCAGG
mu: CGAAGAGAGACCAGG		 GAGA|gaga
Donor marginally increased245wt: 0.9820 / mu: 0.9894 (marginal change - not scored)wt: GGACCCGGAGAGAGA
mu: GGACCCGAAGAGAGA		 ACCC|ggag
distance from splice site 127
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  not conserved  ENSMMUG00000019204  18RERKRDPDRGPRRDRHRDAGPRA
Fcatus  no alignment  ENSFCAG00000011898  n/a
Mmusculus  all conserved  ENSMUSG00000001672  64QRTDRDQRQDRHRDAGHRASE
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 447 / 447
position (AA) of stopcodon in wt / mu AA sequence 149 / 149
position of stopcodon in wt / mu cDNA 493 / 493
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 47 / 47
chromosome 16
strand 1
last intron/exon boundary 479
theoretical NMD boundary in CDS 382
length of CDS 447
coding sequence (CDS) position 178
cDNA position
(for ins/del: last normal base / first normal base)		 224
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 AVNPLRRDIC PRPPGLDERR
WNITSQRRKD SWNATNANTC ALGEVWCR*
mutated AA sequence MEDPSGAREP RARPRERDPG RRPHPDQGRT HDRPRDRPGD PRRKRSSDGN RRRDGDRDPK
RDQERDGNRD RNRDRERERE RERDPDRGPR RDTHRDAGPR AVNPLRRDIC PRPPGLDERR
WNITSQRRKD SWNATNANTC ALGEVWCR*
speed 1.29 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: 0.999471928592284 (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 increased243wt: 0.41 / mu: 0.90wt: CGGGACCCGGAGAGA
mu: CGGGACCCGAAGAGA		 GGAC|ccgg
Donor marginally increased252wt: 0.9267 / mu: 0.9594 (marginal change - not scored)wt: GAGAGAGACCAGGAG
mu: AAGAGAGACCAGGAG		 GAGA|gacc
Donor increased247wt: 0.55 / mu: 0.96wt: ACCCGGAGAGAGACC
mu: ACCCGAAGAGAGACC		 CCGG|agag
Donor increased248wt: 0.58 / mu: 0.84wt: CCCGGAGAGAGACCA
mu: CCCGAAGAGAGACCA		 CGGA|gaga
Donor marginally increased250wt: 0.8869 / mu: 0.9265 (marginal change - not scored)wt: CGGAGAGAGACCAGG
mu: CGAAGAGAGACCAGG		 GAGA|gaga
Donor marginally increased245wt: 0.9820 / mu: 0.9894 (marginal change - not scored)wt: GGACCCGGAGAGAGA
mu: GGACCCGAAGAGAGA		 ACCC|ggag
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 0.58 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: 0.999471928592284 (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 ENST00000268485
Genbank transcript ID NM_052858
UniProt peptide Q96A59
alteration type single base exchange
alteration region CDS
DNA changes c.178G>A
cDNA.222G>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 increased243wt: 0.41 / mu: 0.90wt: CGGGACCCGGAGAGA
mu: CGGGACCCGAAGAGA		 GGAC|ccgg
Donor marginally increased252wt: 0.9267 / mu: 0.9594 (marginal change - not scored)wt: GAGAGAGACCAGGAG
mu: AAGAGAGACCAGGAG		 GAGA|gacc
Donor increased247wt: 0.55 / mu: 0.96wt: ACCCGGAGAGAGACC
mu: ACCCGAAGAGAGACC		 CCGG|agag
Donor increased248wt: 0.58 / mu: 0.84wt: CCCGGAGAGAGACCA
mu: CCCGAAGAGAGACCA		 CGGA|gaga
Donor marginally increased250wt: 0.8869 / mu: 0.9265 (marginal change - not scored)wt: CGGAGAGAGACCAGG
mu: CGAAGAGAGACCAGG		 GAGA|gaga
Donor marginally increased245wt: 0.9820 / mu: 0.9894 (marginal change - not scored)wt: GGACCCGGAGAGAGA
mu: GGACCCGAAGAGAGA		 ACCC|ggag
distance from splice site 222
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 1206 / 1206
position (AA) of stopcodon in wt / mu AA sequence 402 / 402
position of stopcodon in wt / mu cDNA 1250 / 1250
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 45 / 45
chromosome 16
strand 1
last intron/exon boundary 640
theoretical NMD boundary in CDS 545
length of CDS 1206
coding sequence (CDS) position 178
cDNA position
(for ins/del: last normal base / first normal base)		 222
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 CKYLCTGRAC CQMLEVLLNL LILACSSVSY SSTGGYTGIT SLGGIYYYQF
GGAYSGFDGA DGEKAQQLDV QFYQLKLPMV TVAMACSGAL TALCCLFVAM GVLRVPWHCP
LLLVTEGLLD MLIAGGYIPA LYFYFHYLSA AYGSPVCKER QALYQSKGYS GFGCSFHGAD
IGAGIFAALG IVVFALGAVL AIKGYRKVRK LKEKPAEMFE F*
mutated AA sequence MEDPSGAREP RARPRERDPG RRPHPDQGRT HDRPRDRPGD PRRKRSSDGN RRRDGDRDPK
RDQERDGNRD RNRDRERERE RERDPDRGPR RDTHRDAGPR AGEHGVWEKP RQSRTRDGAR
GLTWDAAAPP GPAPWEAPEP PQPQRKGDPG RRRPESEPPS ERYLPSTPRP GREEVEYYQS
EAEGLLECHK CKYLCTGRAC CQMLEVLLNL LILACSSVSY SSTGGYTGIT SLGGIYYYQF
GGAYSGFDGA DGEKAQQLDV QFYQLKLPMV TVAMACSGAL TALCCLFVAM GVLRVPWHCP
LLLVTEGLLD MLIAGGYIPA LYFYFHYLSA AYGSPVCKER QALYQSKGYS GFGCSFHGAD
IGAGIFAALG IVVFALGAVL AIKGYRKVRK LKEKPAEMFE F*
speed 1.69 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: 0.999471928592284 (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 ENST00000299952
Genbank transcript ID NM_001017967
UniProt peptide Q96A59
alteration type single base exchange
alteration region CDS
DNA changes c.178G>A
cDNA.221G>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 increased243wt: 0.41 / mu: 0.90wt: CGGGACCCGGAGAGA
mu: CGGGACCCGAAGAGA		 GGAC|ccgg
Donor marginally increased252wt: 0.9267 / mu: 0.9594 (marginal change - not scored)wt: GAGAGAGACCAGGAG
mu: AAGAGAGACCAGGAG		 GAGA|gacc
Donor increased247wt: 0.55 / mu: 0.96wt: ACCCGGAGAGAGACC
mu: ACCCGAAGAGAGACC		 CCGG|agag
Donor increased248wt: 0.58 / mu: 0.84wt: CCCGGAGAGAGACCA
mu: CCCGAAGAGAGACCA		 CGGA|gaga
Donor marginally increased250wt: 0.8869 / mu: 0.9265 (marginal change - not scored)wt: CGGAGAGAGACCAGG
mu: CGAAGAGAGACCAGG		 GAGA|gaga
Donor marginally increased245wt: 0.9820 / mu: 0.9894 (marginal change - not scored)wt: GGACCCGGAGAGAGA
mu: GGACCCGAAGAGAGA		 ACCC|ggag
distance from splice site 221
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 1233 / 1233
position (AA) of stopcodon in wt / mu AA sequence 411 / 411
position of stopcodon in wt / mu cDNA 1276 / 1276
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 44 / 44
chromosome 16
strand 1
last intron/exon boundary 639
theoretical NMD boundary in CDS 545
length of CDS 1233
coding sequence (CDS) position 178
cDNA position
(for ins/del: last normal base / first normal base)		 221
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 CKYLCTGRGV VQIVEVVLNG MVLICIVASY FVLAGFSASF SSGGGFGNNY
YSPFEGTELE QVRQLDQQYT ILRSPLIYGG VAVSLGLGVL TMGVLLQGAK SRTMLSGKWL
LTEAAFSLLA AVGYCTGIGV YLHVALQINS TDTCKTRERL YARKGLTWMD CQLAGTDGAA
ATFACLLVIM YGASVVLALR SYREQKRYKG SREQPGSYSD APEYLWSGTL *
mutated AA sequence MEDPSGAREP RARPRERDPG RRPHPDQGRT HDRPRDRPGD PRRKRSSDGN RRRDGDRDPK
RDQERDGNRD RNRDRERERE RERDPDRGPR RDTHRDAGPR AGEHGVWEKP RQSRTRDGAR
GLTWDAAAPP GPAPWEAPEP PQPQRKGDPG RRRPESEPPS ERYLPSTPRP GREEVEYYQS
EAEGLLECHK CKYLCTGRGV VQIVEVVLNG MVLICIVASY FVLAGFSASF SSGGGFGNNY
YSPFEGTELE QVRQLDQQYT ILRSPLIYGG VAVSLGLGVL TMGVLLQGAK SRTMLSGKWL
LTEAAFSLLA AVGYCTGIGV YLHVALQINS TDTCKTRERL YARKGLTWMD CQLAGTDGAA
ATFACLLVIM YGASVVLALR SYREQKRYKG SREQPGSYSD APEYLWSGTL *
speed 0.61 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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Problems