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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000403729
Querying Taster for transcript #2: ENST00000404191
Querying Taster for transcript #3: ENST00000346652
Querying Taster for transcript #4: ENST00000307333
Querying Taster for transcript #5: ENST00000295465
MT speed 0 s - this script 5.546521 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ANTXR2disease_causing_automatic0.999981939190322simple_aaeaffected0G28Dsingle base exchangers137852902show file
ANTXR2disease_causing_automatic0.999999675755366simple_aaeaffected0G105Dsingle base exchangers137852902show file
ANTXR2disease_causing_automatic0.999999675755366simple_aaeaffected0G105Dsingle base exchangers137852902show file
ANTXR2disease_causing_automatic0.999999675755366simple_aaeaffected0G105Dsingle base exchangers137852902show file
ANTXR2disease_causing_automatic0.999999675755366simple_aaeaffected0G105Dsingle base exchangers137852902show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999981939190322 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033742)
  • known disease mutation: rs2600 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:80977150C>TN/A show variant in all transcripts   IGV
HGNC symbol ANTXR2
Ensembl transcript ID ENST00000404191
Genbank transcript ID N/A
UniProt peptide P58335
alteration type single base exchange
alteration region CDS
DNA changes c.83G>A
cDNA.240G>A
g.69459G>A
AA changes G28D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 28
frameshift no
known variant Reference ID: rs137852902
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2600 (pathogenic for Hyaline fibromatosis syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8480.733
4.8271
(flanking)4.8271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased69457wt: 0.76 / mu: 0.88wt: AGTAAAGGCTTGGAG
mu: AGTAAAGACTTGGAG		 TAAA|ggct
Donor marginally increased69452wt: 0.9993 / mu: 0.9993 (marginal change - not scored)wt: AAATCAGTAAAGGCT
mu: AAATCAGTAAAGACT		 ATCA|gtaa
Donor marginally increased69460wt: 0.2918 / mu: 0.3285 (marginal change - not scored)wt: AAAGGCTTGGAGGAT
mu: AAAGACTTGGAGGAT		 AGGC|ttgg
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      28PLTGDRGKISKGLEDLKRVSPVGE
mutated  not conserved    28PLTGDRGKISKDLEDLKRVSPVG
Ptroglodytes  all identical  ENSPTRG00000016207  105PLTGDRGKISKGLEDLKRVSPVG
Mmulatta  no alignment  ENSMMUG00000003333  n/a
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000029338  105PLTGDRYKIGKGLEDLKAVKPVG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060520  97PLTGDRSEINKGLKTLSEVNPAG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021531  103PLTGDRYEITKGLKDLSSVIPAG
protein features
start (aa)end (aa)featuredetails 
133SIGNALPotential.lost
34318TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
3939DISULFIDmight get lost (downstream of altered splice site)
4350STRANDmight get lost (downstream of altered splice site)
44213DOMAINVWFA.might get lost (downstream of altered splice site)
5252METALDivalent metal cation.might get lost (downstream of altered splice site)
5358HELIXmight get lost (downstream of altered splice site)
5454METALDivalent metal cation.might get lost (downstream of altered splice site)
5972HELIXmight get lost (downstream of altered splice site)
7896STRANDmight get lost (downstream of altered splice site)
99110HELIXmight get lost (downstream of altered splice site)
118118METALDivalent metal cation.might get lost (downstream of altered splice site)
120134HELIXmight get lost (downstream of altered splice site)
136138HELIXmight get lost (downstream of altered splice site)
141147STRANDmight get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
155168HELIXmight get lost (downstream of altered splice site)
172177STRANDmight get lost (downstream of altered splice site)
183189HELIXmight get lost (downstream of altered splice site)
190192STRANDmight get lost (downstream of altered splice site)
193195HELIXmight get lost (downstream of altered splice site)
196201STRANDmight get lost (downstream of altered splice site)
204215HELIXmight get lost (downstream of altered splice site)
218218DISULFIDmight get lost (downstream of altered splice site)
250250CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
260260CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
319341TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342489TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
352360COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
362366COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1236 / 1236
position (AA) of stopcodon in wt / mu AA sequence 412 / 412
position of stopcodon in wt / mu cDNA 1393 / 1393
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 158 / 158
chromosome 4
strand -1
last intron/exon boundary 1355
theoretical NMD boundary in CDS 1147
length of CDS 1236
coding sequence (CDS) position 83
cDNA position
(for ins/del: last normal base / first normal base)		 240
gDNA position
(for ins/del: last normal base / first normal base)		 69459
chromosomal position
(for ins/del: last normal base / first normal base)		 80977150
original gDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered gDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
original cDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered cDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
wildtype AA sequence MRLSFIVFSS QATIILPLTG DRGKISKGLE DLKRVSPVGE TYIHEGLKLA NEQIQKAGGL
KTSSIIIALT DGKLDGLVPS YAEKEAKISR SLGASVYCVG VLDFEQAQLE RIADSKEQVF
PVKGGFQALK GIINSILAQS CTEILELQPS SVCVGEEFQI VLSGRGFMLG SRNGSVLCTY
TVNETYTTSV KPVSVQLNSM LCPAPILNKA GETLDVSVSF NGGKSVISGS LIVTATECSN
GIAAIIVILV LLLLLGIGLM WWFWPLCCKV VIKDPPPPPA PAPKEEEEEP LPTKKWPTVD
ASYYGGRGVG GIKRMEVRWG DKGSTEEGAR LEKAKNAVVK IPEETEEPIR PRPPRPKPTH
QPPQTKWYTP IKGRLDALWA LLRRQYDRVS LMRPQEGDEG RCINFSRVPS Q*
mutated AA sequence MRLSFIVFSS QATIILPLTG DRGKISKDLE DLKRVSPVGE TYIHEGLKLA NEQIQKAGGL
KTSSIIIALT DGKLDGLVPS YAEKEAKISR SLGASVYCVG VLDFEQAQLE RIADSKEQVF
PVKGGFQALK GIINSILAQS CTEILELQPS SVCVGEEFQI VLSGRGFMLG SRNGSVLCTY
TVNETYTTSV KPVSVQLNSM LCPAPILNKA GETLDVSVSF NGGKSVISGS LIVTATECSN
GIAAIIVILV LLLLLGIGLM WWFWPLCCKV VIKDPPPPPA PAPKEEEEEP LPTKKWPTVD
ASYYGGRGVG GIKRMEVRWG DKGSTEEGAR LEKAKNAVVK IPEETEEPIR PRPPRPKPTH
QPPQTKWYTP IKGRLDALWA LLRRQYDRVS LMRPQEGDEG RCINFSRVPS Q*
speed 0.84 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: 0.999999675755366 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033742)
  • known disease mutation: rs2600 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:80977150C>TN/A show variant in all transcripts   IGV
HGNC symbol ANTXR2
Ensembl transcript ID ENST00000403729
Genbank transcript ID NM_058172
UniProt peptide P58335
alteration type single base exchange
alteration region CDS
DNA changes c.314G>A
cDNA.840G>A
g.69459G>A
AA changes G105D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 105
frameshift no
known variant Reference ID: rs137852902
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2600 (pathogenic for Hyaline fibromatosis syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8480.733
4.8271
(flanking)4.8271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased69457wt: 0.76 / mu: 0.88wt: AGTAAAGGCTTGGAG
mu: AGTAAAGACTTGGAG		 TAAA|ggct
Donor marginally increased69452wt: 0.9993 / mu: 0.9993 (marginal change - not scored)wt: AAATCAGTAAAGGCT
mu: AAATCAGTAAAGACT		 ATCA|gtaa
Donor marginally increased69460wt: 0.2918 / mu: 0.3285 (marginal change - not scored)wt: AAAGGCTTGGAGGAT
mu: AAAGACTTGGAGGAT		 AGGC|ttgg
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105PLTGDRGKISKGLEDLKRVSPVGE
mutated  not conserved    105PLTGDRGKISKDLEDLKRVSPVG
Ptroglodytes  all identical  ENSPTRG00000016207  105PLTGDRGKISKGLEDLKRVSPVG
Mmulatta  no alignment  ENSMMUG00000003333  n/a
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000029338  105PLTGDRYKIGKGLEDLKAVKPVG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060520  97LTGDRSEINKGLKTLSEVNPAG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021531  103LTGDRYEITKGLKDLSSVIPAG
protein features
start (aa)end (aa)featuredetails 
34318TOPO_DOMExtracellular (Potential).lost
44213DOMAINVWFA.lost
99110HELIXlost
118118METALDivalent metal cation.might get lost (downstream of altered splice site)
120134HELIXmight get lost (downstream of altered splice site)
136138HELIXmight get lost (downstream of altered splice site)
141147STRANDmight get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
155168HELIXmight get lost (downstream of altered splice site)
172177STRANDmight get lost (downstream of altered splice site)
183189HELIXmight get lost (downstream of altered splice site)
190192STRANDmight get lost (downstream of altered splice site)
193195HELIXmight get lost (downstream of altered splice site)
196201STRANDmight get lost (downstream of altered splice site)
204215HELIXmight get lost (downstream of altered splice site)
218218DISULFIDmight get lost (downstream of altered splice site)
250250CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
260260CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
319341TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342489TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
352360COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
362366COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1467 / 1467
position (AA) of stopcodon in wt / mu AA sequence 489 / 489
position of stopcodon in wt / mu cDNA 1993 / 1993
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 527 / 527
chromosome 4
strand -1
last intron/exon boundary 1955
theoretical NMD boundary in CDS 1378
length of CDS 1467
coding sequence (CDS) position 314
cDNA position
(for ins/del: last normal base / first normal base)		 840
gDNA position
(for ins/del: last normal base / first normal base)		 69459
chromosomal position
(for ins/del: last normal base / first normal base)		 80977150
original gDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered gDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
original cDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered cDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
wildtype AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGET LDVSVSFNGG
KSVISGSLIV TATECSNGIA AIIVILVLLL LLGIGLMWWF WPLCCKVVIK DPPPPPAPAP
KEEEEEPLPT KKWPTVDASY YGGRGVGGIK RMEVRWGDKG STEEGARLEK AKNAVVKIPE
ETEEPIRPRP PRPKPTHQPP QTKWYTPIKG RLDALWALLR RQYDRVSLMR PQEGDEGRCI
NFSRVPSQ*
mutated AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKDLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGET LDVSVSFNGG
KSVISGSLIV TATECSNGIA AIIVILVLLL LLGIGLMWWF WPLCCKVVIK DPPPPPAPAP
KEEEEEPLPT KKWPTVDASY YGGRGVGGIK RMEVRWGDKG STEEGARLEK AKNAVVKIPE
ETEEPIRPRP PRPKPTHQPP QTKWYTPIKG RLDALWALLR RQYDRVSLMR PQEGDEGRCI
NFSRVPSQ*
speed 1.12 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: 0.999999675755366 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033742)
  • known disease mutation: rs2600 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:80977150C>TN/A show variant in all transcripts   IGV
HGNC symbol ANTXR2
Ensembl transcript ID ENST00000346652
Genbank transcript ID N/A
UniProt peptide P58335
alteration type single base exchange
alteration region CDS
DNA changes c.314G>A
cDNA.454G>A
g.69459G>A
AA changes G105D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 105
frameshift no
known variant Reference ID: rs137852902
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2600 (pathogenic for Hyaline fibromatosis syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8480.733
4.8271
(flanking)4.8271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased69457wt: 0.76 / mu: 0.88wt: AGTAAAGGCTTGGAG
mu: AGTAAAGACTTGGAG		 TAAA|ggct
Donor marginally increased69452wt: 0.9993 / mu: 0.9993 (marginal change - not scored)wt: AAATCAGTAAAGGCT
mu: AAATCAGTAAAGACT		 ATCA|gtaa
Donor marginally increased69460wt: 0.2918 / mu: 0.3285 (marginal change - not scored)wt: AAAGGCTTGGAGGAT
mu: AAAGACTTGGAGGAT		 AGGC|ttgg
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105PLTGDRGKISKGLEDLKRVSPVGE
mutated  not conserved    105PLTGDRGKISKDLEDLKRVSPVG
Ptroglodytes  all identical  ENSPTRG00000016207  105PLTGDRGKISKGLEDLKRVSPVG
Mmulatta  no alignment  ENSMMUG00000003333  n/a
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000029338  105PLTGDRYKIGKGLEDLKAVKPVG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060520  97LTGDRSEINKGLKTLSEVNPAG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021531  103LTGDRYEITKGLKDLSSVIPAG
protein features
start (aa)end (aa)featuredetails 
34318TOPO_DOMExtracellular (Potential).lost
44213DOMAINVWFA.lost
99110HELIXlost
118118METALDivalent metal cation.might get lost (downstream of altered splice site)
120134HELIXmight get lost (downstream of altered splice site)
136138HELIXmight get lost (downstream of altered splice site)
141147STRANDmight get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
155168HELIXmight get lost (downstream of altered splice site)
172177STRANDmight get lost (downstream of altered splice site)
183189HELIXmight get lost (downstream of altered splice site)
190192STRANDmight get lost (downstream of altered splice site)
193195HELIXmight get lost (downstream of altered splice site)
196201STRANDmight get lost (downstream of altered splice site)
204215HELIXmight get lost (downstream of altered splice site)
218218DISULFIDmight get lost (downstream of altered splice site)
250250CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
260260CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
319341TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342489TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
352360COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
362366COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1161 / 1161
position (AA) of stopcodon in wt / mu AA sequence 387 / 387
position of stopcodon in wt / mu cDNA 1301 / 1301
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 141 / 141
chromosome 4
strand -1
last intron/exon boundary 1179
theoretical NMD boundary in CDS 988
length of CDS 1161
coding sequence (CDS) position 314
cDNA position
(for ins/del: last normal base / first normal base)		 454
gDNA position
(for ins/del: last normal base / first normal base)		 69459
chromosomal position
(for ins/del: last normal base / first normal base)		 80977150
original gDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered gDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
original cDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered cDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
wildtype AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSSNGIAAII VILVLLLLLG IGLMWWFWPL
CCKVVIKDPP PPPAPAPKEE EEEPLPTKKW PTVDASYYGG RGVGGIKRME VRWGDKGSTE
EGARLEKAKN AVVKIPEETE EPIRPRPPRP KPTHQPPQTK WYTPIKGRLD ALWALLRRQY
DRVSLMRPQE GDEVCIWECI EKELTA*
mutated AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKDLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSSNGIAAII VILVLLLLLG IGLMWWFWPL
CCKVVIKDPP PPPAPAPKEE EEEPLPTKKW PTVDASYYGG RGVGGIKRME VRWGDKGSTE
EGARLEKAKN AVVKIPEETE EPIRPRPPRP KPTHQPPQTK WYTPIKGRLD ALWALLRRQY
DRVSLMRPQE GDEVCIWECI EKELTA*
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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999675755366 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033742)
  • known disease mutation: rs2600 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:80977150C>TN/A show variant in all transcripts   IGV
HGNC symbol ANTXR2
Ensembl transcript ID ENST00000307333
Genbank transcript ID NM_001145794
UniProt peptide P58335
alteration type single base exchange
alteration region CDS
DNA changes c.314G>A
cDNA.317G>A
g.69459G>A
AA changes G105D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 105
frameshift no
known variant Reference ID: rs137852902
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2600 (pathogenic for Hyaline fibromatosis syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8480.733
4.8271
(flanking)4.8271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased69457wt: 0.76 / mu: 0.88wt: AGTAAAGGCTTGGAG
mu: AGTAAAGACTTGGAG		 TAAA|ggct
Donor marginally increased69452wt: 0.9993 / mu: 0.9993 (marginal change - not scored)wt: AAATCAGTAAAGGCT
mu: AAATCAGTAAAGACT		 ATCA|gtaa
Donor marginally increased69460wt: 0.2918 / mu: 0.3285 (marginal change - not scored)wt: AAAGGCTTGGAGGAT
mu: AAAGACTTGGAGGAT		 AGGC|ttgg
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105PLTGDRGKISKGLEDLKRVSPVGE
mutated  not conserved    105PLTGDRGKISKDLEDLKRVSPVG
Ptroglodytes  all identical  ENSPTRG00000016207  105PLTGDRGKISKGLEDLKRVSPVG
Mmulatta  no alignment  ENSMMUG00000003333  n/a
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000029338  105PLTGDRYKIGKGLEDLKAVKPVG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060520  97LTGDRSEINKGLKTLSEVNPAG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021531  103LTGDRYEITKGLKDLSSVIPAG
protein features
start (aa)end (aa)featuredetails 
34318TOPO_DOMExtracellular (Potential).lost
44213DOMAINVWFA.lost
99110HELIXlost
118118METALDivalent metal cation.might get lost (downstream of altered splice site)
120134HELIXmight get lost (downstream of altered splice site)
136138HELIXmight get lost (downstream of altered splice site)
141147STRANDmight get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
155168HELIXmight get lost (downstream of altered splice site)
172177STRANDmight get lost (downstream of altered splice site)
183189HELIXmight get lost (downstream of altered splice site)
190192STRANDmight get lost (downstream of altered splice site)
193195HELIXmight get lost (downstream of altered splice site)
196201STRANDmight get lost (downstream of altered splice site)
204215HELIXmight get lost (downstream of altered splice site)
218218DISULFIDmight get lost (downstream of altered splice site)
250250CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
260260CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
319341TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342489TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
352360COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
362366COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1470 / 1470
position (AA) of stopcodon in wt / mu AA sequence 490 / 490
position of stopcodon in wt / mu cDNA 1473 / 1473
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 4 / 4
chromosome 4
strand -1
last intron/exon boundary 1351
theoretical NMD boundary in CDS 1297
length of CDS 1470
coding sequence (CDS) position 314
cDNA position
(for ins/del: last normal base / first normal base)		 317
gDNA position
(for ins/del: last normal base / first normal base)		 69459
chromosomal position
(for ins/del: last normal base / first normal base)		 80977150
original gDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered gDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
original cDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered cDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
wildtype AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGET LDVSVSFNGG
KSVISGSLIV TATECSNGIA AIIVILVLLL LLGIGLMWWF WPLCCKVVIK DPPPPPAPAP
KEEEEEPLPT KKWPTVDASY YGGRGVGGIK RMEVRWGDKG STEEGARLEK AKNAVVKIPE
ETEEPIRPRP PRPKPTHQPP QTKWYTPIKG RLDALWALLR RQYDRVSLMR PQEGDEVCIW
ECIEKELTA*
mutated AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKDLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGET LDVSVSFNGG
KSVISGSLIV TATECSNGIA AIIVILVLLL LLGIGLMWWF WPLCCKVVIK DPPPPPAPAP
KEEEEEPLPT KKWPTVDASY YGGRGVGGIK RMEVRWGDKG STEEGARLEK AKNAVVKIPE
ETEEPIRPRP PRPKPTHQPP QTKWYTPIKG RLDALWALLR RQYDRVSLMR PQEGDEVCIW
ECIEKELTA*
speed 0.85 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: 0.999999675755366 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033742)
  • known disease mutation: rs2600 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:80977150C>TN/A show variant in all transcripts   IGV
HGNC symbol ANTXR2
Ensembl transcript ID ENST00000295465
Genbank transcript ID N/A
UniProt peptide P58335
alteration type single base exchange
alteration region CDS
DNA changes c.314G>A
cDNA.1077G>A
g.69459G>A
AA changes G105D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 105
frameshift no
known variant Reference ID: rs137852902
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2600 (pathogenic for Hyaline fibromatosis syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033742)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8480.733
4.8271
(flanking)4.8271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased69457wt: 0.76 / mu: 0.88wt: AGTAAAGGCTTGGAG
mu: AGTAAAGACTTGGAG		 TAAA|ggct
Donor marginally increased69452wt: 0.9993 / mu: 0.9993 (marginal change - not scored)wt: AAATCAGTAAAGGCT
mu: AAATCAGTAAAGACT		 ATCA|gtaa
Donor marginally increased69460wt: 0.2918 / mu: 0.3285 (marginal change - not scored)wt: AAAGGCTTGGAGGAT
mu: AAAGACTTGGAGGAT		 AGGC|ttgg
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      105PLTGDRGKISKGLEDLKRVSPVGE
mutated  not conserved    105PLTGDRGKISKDLEDLKRVSPVG
Ptroglodytes  all identical  ENSPTRG00000016207  105PLTGDRGKISKGLEDLKRVSPVG
Mmulatta  no alignment  ENSMMUG00000003333  n/a
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000029338  105PLTGDRYKIGKGLEDLKAVKPVG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060520  97LTGDRSEINKGLKTLSEVNPAG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021531  103LTGDRYEITKGLKDLSSVIPAG
protein features
start (aa)end (aa)featuredetails 
34318TOPO_DOMExtracellular (Potential).lost
44213DOMAINVWFA.lost
99110HELIXlost
118118METALDivalent metal cation.might get lost (downstream of altered splice site)
120134HELIXmight get lost (downstream of altered splice site)
136138HELIXmight get lost (downstream of altered splice site)
141147STRANDmight get lost (downstream of altered splice site)
147147MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
155168HELIXmight get lost (downstream of altered splice site)
172177STRANDmight get lost (downstream of altered splice site)
183189HELIXmight get lost (downstream of altered splice site)
190192STRANDmight get lost (downstream of altered splice site)
193195HELIXmight get lost (downstream of altered splice site)
196201STRANDmight get lost (downstream of altered splice site)
204215HELIXmight get lost (downstream of altered splice site)
218218DISULFIDmight get lost (downstream of altered splice site)
250250CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
260260CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
319341TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
342489TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
352360COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
362366COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 969 / 969
position (AA) of stopcodon in wt / mu AA sequence 323 / 323
position of stopcodon in wt / mu cDNA 1732 / 1732
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 764 / 764
chromosome 4
strand -1
last intron/exon boundary 1630
theoretical NMD boundary in CDS 816
length of CDS 969
coding sequence (CDS) position 314
cDNA position
(for ins/del: last normal base / first normal base)		 1077
gDNA position
(for ins/del: last normal base / first normal base)		 69459
chromosomal position
(for ins/del: last normal base / first normal base)		 80977150
original gDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered gDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
original cDNA sequence snippet CAGAGGCAAAATCAGTAAAGGCTTGGAGGATTTAAAACGTG
altered cDNA sequence snippet CAGAGGCAAAATCAGTAAAGACTTGGAGGATTTAAAACGTG
wildtype AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKGLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGEW GLTVTQAGVK
WHDLTHCTFG LSGSGDPPTS AS*
mutated AA sequence MVAERSPARS PGSWLFPGLW LLVLSGPGGL LRAQEQPSCR RAFDLYFVLD KSGSVANNWI
EIYNFVQQLA ERFVSPEMRL SFIVFSSQAT IILPLTGDRG KISKDLEDLK RVSPVGETYI
HEGLKLANEQ IQKAGGLKTS SIIIALTDGK LDGLVPSYAE KEAKISRSLG ASVYCVGVLD
FEQAQLERIA DSKEQVFPVK GGFQALKGII NSILAQSCTE ILELQPSSVC VGEEFQIVLS
GRGFMLGSRN GSVLCTYTVN ETYTTSVKPV SVQLNSMLCP APILNKAGEW GLTVTQAGVK
WHDLTHCTFG LSGSGDPPTS AS*
speed 1.13 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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