Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999986046858 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM092881)
  • known disease mutation: rs4643 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:110604172T>CN/A show variant in all transcripts   IGV
HGNC symbol ALX3
Ensembl transcript ID ENST00000369792
Genbank transcript ID NM_006492
UniProt peptide O95076
alteration type single base exchange
alteration region CDS
DNA changes c.608A>G
cDNA.608A>G
g.9063A>G
AA changes N203S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 203
frameshift no
known variant Reference ID: rs121908166
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4643 (pathogenic for Frontonasal dysplasia 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM092881)

known disease mutation at this position, please check HGMD for details (HGMD ID CM092881)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092881)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.311
4.5541
(flanking)4.5541
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased9054wt: 0.3350 / mu: 0.3468 (marginal change - not scored)wt: CACAACCTGCCCCCAGGTCTGGTTCCAGAACCGCAGAGCCA
mu: CACAACCTGCCCCCAGGTCTGGTTCCAGAGCCGCAGAGCCA		 tctg|GTTC
Acc increased9053wt: 0.41 / mu: 0.49wt: CCACAACCTGCCCCCAGGTCTGGTTCCAGAACCGCAGAGCC
mu: CCACAACCTGCCCCCAGGTCTGGTTCCAGAGCCGCAGAGCC		 gtct|GGTT
Donor gained90620.56mu: TCCAGAGCCGCAGAG CAGA|gccg
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      203LTEARVQVWFQNRRAKWRKRERYG
mutated  all conserved    203LTEARVQVWFQSRRAKWRKRERY
Ptroglodytes  all identical  ENSPTRG00000001070  203LTEARVQVWFQNRRAKWRKRERY
Mmulatta  all identical  ENSMMUG00000031857  203LTEARVQVWFQNRRAKWRKRERY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000014603  203LTEARVQVWFQNRRAKWRKRERY
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000003032  63WFQNRRAKWRKRERY
Drerio  all identical  ENSDARG00000091086  205LTEARVQVWFQNRRAKWRKRERY
Dmelanogaster  all identical  FBgn0053980  280LPEDRIQVWFQNRRAK
Celegans  all identical  W03A3.1  186LQEDRIQVWFQNRRAKW
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
153212DNA_BINDHomeobox.lost
249249CONFLICTS -> G (in Ref. 1; AAD01418).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1032 / 1032
position (AA) of stopcodon in wt / mu AA sequence 344 / 344
position of stopcodon in wt / mu cDNA 1032 / 1032
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 1 / 1
chromosome 1
strand -1
last intron/exon boundary 724
theoretical NMD boundary in CDS 673
length of CDS 1032
coding sequence (CDS) position 608
cDNA position
(for ins/del: last normal base / first normal base)		 608
gDNA position
(for ins/del: last normal base / first normal base)		 9063
chromosomal position
(for ins/del: last normal base / first normal base)		 110604172
original gDNA sequence snippet CCCCCAGGTCTGGTTCCAGAACCGCAGAGCCAAGTGGCGGA
altered gDNA sequence snippet CCCCCAGGTCTGGTTCCAGAGCCGCAGAGCCAAGTGGCGGA
original cDNA sequence snippet GGTACAGGTCTGGTTCCAGAACCGCAGAGCCAAGTGGCGGA
altered cDNA sequence snippet GGTACAGGTCTGGTTCCAGAGCCGCAGAGCCAAGTGGCGGA
wildtype AA sequence MDPEHCAPFR VGPAPGPYVA SGDEPPGPQG TPAAAPHLHP APPRGPRLTR FPACGPLEPY
LPEPAKPPAK YLQDLGPGPA LNGGHFYEGP AEAEEKTSKA ASFPQLPLDC RGGPRDGPSN
LQGSPGPCLA SLHLPLSPGL PDSMELAKNK SKKRRNRTTF STFQLEELEK VFQKTHYPDV
YAREQLALRT DLTEARVQVW FQNRRAKWRK RERYGKIQEG RNPFTAAYDI SVLPRTDSHP
QLQNSLWASP GSGSPGGPCL VSPEGIPSPC MSPYSHPHGS VAGFMGVPAP SAAHPGIYSI
HGFPPTLGGH SFEPSSDGDY KSPSLVSLRV KPKEPPGLLN WTT*
mutated AA sequence MDPEHCAPFR VGPAPGPYVA SGDEPPGPQG TPAAAPHLHP APPRGPRLTR FPACGPLEPY
LPEPAKPPAK YLQDLGPGPA LNGGHFYEGP AEAEEKTSKA ASFPQLPLDC RGGPRDGPSN
LQGSPGPCLA SLHLPLSPGL PDSMELAKNK SKKRRNRTTF STFQLEELEK VFQKTHYPDV
YAREQLALRT DLTEARVQVW FQSRRAKWRK RERYGKIQEG RNPFTAAYDI SVLPRTDSHP
QLQNSLWASP GSGSPGGPCL VSPEGIPSPC MSPYSHPHGS VAGFMGVPAP SAAHPGIYSI
HGFPPTLGGH SFEPSSDGDY KSPSLVSLRV KPKEPPGLLN WTT*
speed 0.56 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