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 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      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 1.01 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