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 marginally increased69452wt: 0.9993 / mu: 0.9993 (marginal change - not scored)wt: AAATCAGTAAAGGCT
mu: AAATCAGTAAAGACT		 ATCA|gtaa
Donor increased69457wt: 0.76 / mu: 0.88wt: AGTAAAGGCTTGGAG
mu: AGTAAAGACTTGGAG		 TAAA|ggct
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 0.35 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