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: ENST00000559087
Querying Taster for transcript #2: ENST00000245451
Querying Taster for transcript #3: ENST00000558984
Querying Taster for transcript #4: ENST00000417573
MT speed 0 s - this script 5.079904 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BMP4disease_causing_automatic0.999999513635384simple_aaeaffected0E93Gsingle base exchangers121912765show file
BMP4disease_causing_automatic0.999999513635384simple_aaeaffected0E93Gsingle base exchangers121912765show file
BMP4disease_causing_automatic0.999999513635384simple_aaeaffected0E93Gsingle base exchangers121912765show file
BMP4disease_causing_automatic0.999999513635384simple_aaeaffected0E93Gsingle base exchangers121912765show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999513635384 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080109)
  • known disease mutation: rs17701 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:54418663T>CN/A show variant in all transcripts   IGV
HGNC symbol BMP4
Ensembl transcript ID ENST00000559087
Genbank transcript ID NM_130850
UniProt peptide P12644
alteration type single base exchange
alteration region CDS
DNA changes c.278A>G
cDNA.463A>G
g.6817A>G
AA changes E93G Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 93
frameshift no
known variant Reference ID: rs121912765
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs17701 (pathogenic for Microphthalmia with brain and digit anomalies) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9861
3.0471
(flanking)5.6951
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6809wt: 0.38 / mu: 0.46wt: CGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGA
mu: CGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGA		 tcag|TCTG
Acc marginally increased6812wt: 0.6443 / mu: 0.6748 (marginal change - not scored)wt: GATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCA
mu: GATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCA		 gtct|GGGG
Acc marginally increased6808wt: 0.7589 / mu: 0.7688 (marginal change - not scored)wt: GCGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAG
mu: GCGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAG		 ttca|GTCT
Donor increased6808wt: 0.21 / mu: 0.30wt: GCTTCAGTCTGGGGA
mu: GCTTCAGTCTGGGGG		 TTCA|gtct
distance from splice site 93
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      93YMRDLYRLQSGEEEEEQIHSTGLE
mutated  not conserved    93YMRDLYRLQSGGEEEEQIHSTGL
Ptroglodytes  all identical  ENSPTRG00000006358  93YMRDLYRLQSGEEEEEQIHSTGL
Mmulatta  all identical  ENSMMUG00000000429  93YMRDLYRLQSGEEEEEQIHSAGL
Fcatus  all identical  ENSFCAG00000004772  93YMRDLYRLQSGEEEEEEQTHSVGL
Mmusculus  all identical  ENSMUSG00000021835  93YMRDLYRLQSGEEEEEEQSQGTGL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014535  89YLLDLYRLQSGEAEEAEGQDIAF
Drerio  all identical  ENSDARG00000019995  86YLLDLYRLQSGELEEAGAQHVSF
Dmelanogaster  not conserved  FBgn0000490  262PMKKLYAEIMGHE----LDSVNI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008620  91YMRDLYRLQSAEEEDE-LHDISM
protein features
start (aa)end (aa)featuredetails 
20292PROPEP /FTId=PRO_0000033856.lost
143143CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
308308DISULFIDBy similarity.might get lost (downstream of altered splice site)
337337DISULFIDBy similarity.might get lost (downstream of altered splice site)
341341DISULFIDBy similarity.might get lost (downstream of altered splice site)
350350CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
365365CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
373373DISULFIDBy similarity.might get lost (downstream of altered splice site)
405405DISULFIDBy similarity.might get lost (downstream of altered splice site)
407407DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1227 / 1227
position (AA) of stopcodon in wt / mu AA sequence 409 / 409
position of stopcodon in wt / mu cDNA 1412 / 1412
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 186 / 186
chromosome 14
strand -1
last intron/exon boundary 556
theoretical NMD boundary in CDS 320
length of CDS 1227
coding sequence (CDS) position 278
cDNA position
(for ins/del: last normal base / first normal base)		 463
gDNA position
(for ins/del: last normal base / first normal base)		 6817
chromosomal position
(for ins/del: last normal base / first normal base)		 54418663
original gDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered gDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
original cDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered cDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
wildtype AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGEEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
mutated AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGGEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
speed 0.90 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

disease causing

 Model: simple_aae, prob: 0.999999513635384 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080109)
  • known disease mutation: rs17701 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:54418663T>CN/A show variant in all transcripts   IGV
HGNC symbol BMP4
Ensembl transcript ID ENST00000245451
Genbank transcript ID NM_001202
UniProt peptide P12644
alteration type single base exchange
alteration region CDS
DNA changes c.278A>G
cDNA.672A>G
g.6817A>G
AA changes E93G Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 93
frameshift no
known variant Reference ID: rs121912765
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs17701 (pathogenic for Microphthalmia with brain and digit anomalies) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9861
3.0471
(flanking)5.6951
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6809wt: 0.38 / mu: 0.46wt: CGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGA
mu: CGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGA		 tcag|TCTG
Acc marginally increased6812wt: 0.6443 / mu: 0.6748 (marginal change - not scored)wt: GATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCA
mu: GATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCA		 gtct|GGGG
Acc marginally increased6808wt: 0.7589 / mu: 0.7688 (marginal change - not scored)wt: GCGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAG
mu: GCGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAG		 ttca|GTCT
Donor increased6808wt: 0.21 / mu: 0.30wt: GCTTCAGTCTGGGGA
mu: GCTTCAGTCTGGGGG		 TTCA|gtct
distance from splice site 93
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      93YMRDLYRLQSGEEEEEQIHSTGLE
mutated  not conserved    93YMRDLYRLQSGGEEEEQIHSTGL
Ptroglodytes  all identical  ENSPTRG00000006358  93YMRDLYRLQSGEEEEEQIHSTGL
Mmulatta  all identical  ENSMMUG00000000429  93YMRDLYRLQSGEEEEEQIHSAGL
Fcatus  all identical  ENSFCAG00000004772  93YMRDLYRLQSGEEEEEEQTHSVGL
Mmusculus  all identical  ENSMUSG00000021835  93YMRDLYRLQSGEEEEEEQSQGTGL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014535  89YLLDLYRLQSGEAEEAEGQDIAF
Drerio  all identical  ENSDARG00000019995  86YLLDLYRLQSGELEEAGAQHVSF
Dmelanogaster  not conserved  FBgn0000490  262PMKKLYAEIMGHE----LDSVNI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008620  91YMRDLYRLQSAEEEDE-LHDISM
protein features
start (aa)end (aa)featuredetails 
20292PROPEP /FTId=PRO_0000033856.lost
143143CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
308308DISULFIDBy similarity.might get lost (downstream of altered splice site)
337337DISULFIDBy similarity.might get lost (downstream of altered splice site)
341341DISULFIDBy similarity.might get lost (downstream of altered splice site)
350350CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
365365CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
373373DISULFIDBy similarity.might get lost (downstream of altered splice site)
405405DISULFIDBy similarity.might get lost (downstream of altered splice site)
407407DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1227 / 1227
position (AA) of stopcodon in wt / mu AA sequence 409 / 409
position of stopcodon in wt / mu cDNA 1621 / 1621
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 395 / 395
chromosome 14
strand -1
last intron/exon boundary 765
theoretical NMD boundary in CDS 320
length of CDS 1227
coding sequence (CDS) position 278
cDNA position
(for ins/del: last normal base / first normal base)		 672
gDNA position
(for ins/del: last normal base / first normal base)		 6817
chromosomal position
(for ins/del: last normal base / first normal base)		 54418663
original gDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered gDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
original cDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered cDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
wildtype AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGEEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
mutated AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGGEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
speed 1.07 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999513635384 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080109)
  • known disease mutation: rs17701 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:54418663T>CN/A show variant in all transcripts   IGV
HGNC symbol BMP4
Ensembl transcript ID ENST00000558984
Genbank transcript ID N/A
UniProt peptide P12644
alteration type single base exchange
alteration region CDS
DNA changes c.278A>G
cDNA.465A>G
g.6817A>G
AA changes E93G Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 93
frameshift no
known variant Reference ID: rs121912765
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs17701 (pathogenic for Microphthalmia with brain and digit anomalies) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9861
3.0471
(flanking)5.6951
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6809wt: 0.38 / mu: 0.46wt: CGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGA
mu: CGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGA		 tcag|TCTG
Acc marginally increased6812wt: 0.6443 / mu: 0.6748 (marginal change - not scored)wt: GATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCA
mu: GATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCA		 gtct|GGGG
Acc marginally increased6808wt: 0.7589 / mu: 0.7688 (marginal change - not scored)wt: GCGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAG
mu: GCGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAG		 ttca|GTCT
Donor increased6808wt: 0.21 / mu: 0.30wt: GCTTCAGTCTGGGGA
mu: GCTTCAGTCTGGGGG		 TTCA|gtct
distance from splice site 93
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      93YMRDLYRLQSGEEEEEQIHSTGLE
mutated  not conserved    93YMRDLYRLQSGGEEEEQIHSTGL
Ptroglodytes  all identical  ENSPTRG00000006358  93YMRDLYRLQSGEEEEEQIHSTGL
Mmulatta  all identical  ENSMMUG00000000429  93YMRDLYRLQSGEEEEEQIHSAGL
Fcatus  all identical  ENSFCAG00000004772  93YMRDLYRLQSGEEEEEEQTHSVGL
Mmusculus  all identical  ENSMUSG00000021835  93YMRDLYRLQSGEEEEEEQSQGTGL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014535  89YLLDLYRLQSGEAEEAEGQDIAF
Drerio  all identical  ENSDARG00000019995  86YLLDLYRLQSGELEEAGAQHVSF
Dmelanogaster  not conserved  FBgn0000490  262PMKKLYAEIMGHE----LDSVNI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008620  91YMRDLYRLQSAEEEDE-LHDISM
protein features
start (aa)end (aa)featuredetails 
20292PROPEP /FTId=PRO_0000033856.lost
143143CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
308308DISULFIDBy similarity.might get lost (downstream of altered splice site)
337337DISULFIDBy similarity.might get lost (downstream of altered splice site)
341341DISULFIDBy similarity.might get lost (downstream of altered splice site)
350350CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
365365CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
373373DISULFIDBy similarity.might get lost (downstream of altered splice site)
405405DISULFIDBy similarity.might get lost (downstream of altered splice site)
407407DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1227 / 1227
position (AA) of stopcodon in wt / mu AA sequence 409 / 409
position of stopcodon in wt / mu cDNA 1414 / 1414
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 188 / 188
chromosome 14
strand -1
last intron/exon boundary 558
theoretical NMD boundary in CDS 320
length of CDS 1227
coding sequence (CDS) position 278
cDNA position
(for ins/del: last normal base / first normal base)		 465
gDNA position
(for ins/del: last normal base / first normal base)		 6817
chromosomal position
(for ins/del: last normal base / first normal base)		 54418663
original gDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered gDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
original cDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered cDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
wildtype AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGEEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
mutated AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGGEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
speed 0.89 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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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999513635384 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080109)
  • known disease mutation: rs17701 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:54418663T>CN/A show variant in all transcripts   IGV
HGNC symbol BMP4
Ensembl transcript ID ENST00000417573
Genbank transcript ID NM_130851
UniProt peptide P12644
alteration type single base exchange
alteration region CDS
DNA changes c.278A>G
cDNA.542A>G
g.6817A>G
AA changes E93G Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 93
frameshift no
known variant Reference ID: rs121912765
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs17701 (pathogenic for Microphthalmia with brain and digit anomalies) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080109)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9861
3.0471
(flanking)5.6951
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6809wt: 0.38 / mu: 0.46wt: CGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGA
mu: CGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGA		 tcag|TCTG
Acc marginally increased6812wt: 0.6443 / mu: 0.6748 (marginal change - not scored)wt: GATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCA
mu: GATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCA		 gtct|GGGG
Acc marginally increased6808wt: 0.7589 / mu: 0.7688 (marginal change - not scored)wt: GCGGGATCTTTACCGGCTTCAGTCTGGGGAGGAGGAGGAAG
mu: GCGGGATCTTTACCGGCTTCAGTCTGGGGGGGAGGAGGAAG		 ttca|GTCT
Donor increased6808wt: 0.21 / mu: 0.30wt: GCTTCAGTCTGGGGA
mu: GCTTCAGTCTGGGGG		 TTCA|gtct
distance from splice site 93
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      93YMRDLYRLQSGEEEEEQIHSTGLE
mutated  not conserved    93YMRDLYRLQSGGEEEEQIHSTGL
Ptroglodytes  all identical  ENSPTRG00000006358  93YMRDLYRLQSGEEEEEQIHSTGL
Mmulatta  all identical  ENSMMUG00000000429  93YMRDLYRLQSGEEEEEQIHSAGL
Fcatus  all identical  ENSFCAG00000004772  93YMRDLYRLQSGEEEEEEQTHSVGL
Mmusculus  all identical  ENSMUSG00000021835  93YMRDLYRLQSGEEEEEEQSQGTGL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014535  89YLLDLYRLQSGEAEEAEGQDIAF
Drerio  all identical  ENSDARG00000019995  86YLLDLYRLQSGELEEAGAQHVSF
Dmelanogaster  not conserved  FBgn0000490  262PMKKLYAEIMGHE----LDSVNI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000008620  91YMRDLYRLQSAEEEDE-LHDISM
protein features
start (aa)end (aa)featuredetails 
20292PROPEP /FTId=PRO_0000033856.lost
143143CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
308308DISULFIDBy similarity.might get lost (downstream of altered splice site)
337337DISULFIDBy similarity.might get lost (downstream of altered splice site)
341341DISULFIDBy similarity.might get lost (downstream of altered splice site)
350350CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
365365CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
372372DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
373373DISULFIDBy similarity.might get lost (downstream of altered splice site)
405405DISULFIDBy similarity.might get lost (downstream of altered splice site)
407407DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1227 / 1227
position (AA) of stopcodon in wt / mu AA sequence 409 / 409
position of stopcodon in wt / mu cDNA 1491 / 1491
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 265 / 265
chromosome 14
strand -1
last intron/exon boundary 635
theoretical NMD boundary in CDS 320
length of CDS 1227
coding sequence (CDS) position 278
cDNA position
(for ins/del: last normal base / first normal base)		 542
gDNA position
(for ins/del: last normal base / first normal base)		 6817
chromosomal position
(for ins/del: last normal base / first normal base)		 54418663
original gDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered gDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
original cDNA sequence snippet TTACCGGCTTCAGTCTGGGGAGGAGGAGGAAGAGCAGATCC
altered cDNA sequence snippet TTACCGGCTTCAGTCTGGGGGGGAGGAGGAAGAGCAGATCC
wildtype AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGEEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
mutated AA sequence MIPGNRMLMV VLLCQVLLGG ASHASLIPET GKKKVAEIQG HAGGRRSGQS HELLRDFEAT
LLQMFGLRRR PQPSKSAVIP DYMRDLYRLQ SGGEEEEQIH STGLEYPERP ASRANTVRSF
HHEEHLENIP GTSENSAFRF LFNLSSIPEN EVISSAELRL FREQVDQGPD WERGFHRINI
YEVMKPPAEV VPGHLITRLL DTRLVHHNVT RWETFDVSPA VLRWTREKQP NYGLAIEVTH
LHQTRTHQGQ HVRISRSLPQ GSGNWAQLRP LLVTFGHDGR GHALTRRRRA KRSPKHHSQR
ARKKNKNCRR HSLYVDFSDV GWNDWIVAPP GYQAFYCHGD CPFPLADHLN STNHAIVQTL
VNSVNSSIPK ACCVPTELSA ISMLYLDEYD KVVLKNYQEM VVEGCGCR*
speed 1.05 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