Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.0107045291831511 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM016199)
  • known disease mutation: rs8629 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:53823691G>AN/A show variant in all transcripts   IGV
HGNC symbol AMHR2
Ensembl transcript ID ENST00000550311
Genbank transcript ID NM_001164690
UniProt peptide Q16671
alteration type single base exchange
alteration region CDS
DNA changes c.1217G>A
cDNA.1286G>A
g.6053G>A
AA changes R406Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 406
frameshift no
known variant Reference ID: rs137853104
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs8629 (pathogenic for Persistent mullerian duct syndrome, type II) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM016199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM016199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM016199)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0120.989
0.2110.985
(flanking)0.5660.99
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased6050wt: 0.39 / mu: 0.47wt: GGCCCTCCGACGAGC
mu: GGCCCTCCAACGAGC		 CCCT|ccga
distance from splice site 72
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      406TLDLQDWGMALRRADIYSLALLLW
mutated  all conserved    406TLDLQDWGMALQRADIYSLALLL
Ptroglodytes  all identical  ENSPTRG00000005015  406TLDLQDWGMALRRADIYSLALLL
Mmulatta  all identical  ENSMMUG00000020037  406TLDLQDWGMALRRADIYSLALLL
Fcatus  all identical  ENSFCAG00000005894  411TLDLQDWGTALRQADVYSLAL
Mmusculus  all conserved  ENSMUSG00000023047  402TLDLQDWGTALQRADVYSLALLL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
171573TOPO_DOMCytoplasmic (Potential).lost
203518DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1437 / 1437
position (AA) of stopcodon in wt / mu AA sequence 479 / 479
position of stopcodon in wt / mu cDNA 1506 / 1506
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 70 / 70
chromosome 12
strand 1
last intron/exon boundary 1491
theoretical NMD boundary in CDS 1371
length of CDS 1437
coding sequence (CDS) position 1217
cDNA position
(for ins/del: last normal base / first normal base)		 1286
gDNA position
(for ins/del: last normal base / first normal base)		 6053
chromosomal position
(for ins/del: last normal base / first normal base)		 53823691
original gDNA sequence snippet GGATTGGGGCATGGCCCTCCGACGAGCTGATATTTACTCTT
altered gDNA sequence snippet GGATTGGGGCATGGCCCTCCAACGAGCTGATATTTACTCTT
original cDNA sequence snippet GGATTGGGGCATGGCCCTCCGACGAGCTGATATTTACTCTT
altered cDNA sequence snippet GGATTGGGGCATGGCCCTCCAACGAGCTGATATTTACTCTT
wildtype AA sequence MLGSLGLWAL LPTAVEAPPN RRTCVFFEAP GVRGSTKTLG ELLDTGTELP RAIRCLYSRC
CFGIWNLTQD RAQVEMQGCR DSDEPGCESL HCDPSPRAHP SPGSTLFTCS CGTDFCNANY
SHLPPPGSPG TPGSQGPQAA PGESIWMALV LLGLFLLLLL LLGSIILALL QRKNYRVRGE
PVPEPRPDSG RDWSVELQEL PELCFSQVIR EGGHAVVWAG QLQGKLVAIK AFPPRSVAQF
QAERALYELP GLQHDHIVRF ITASRGGPGR LLSGPLLVLE LHPKGSLCHY LTQYTSDWGS
SLRMALSLAQ GLAFLHEERW QNGQYKPGIA HRDLSSQNVL IREDGSCAIG DLGLALVLPG
LTQPPAWTPT QPQGPAAIME AGTQRYMAPE LLDKTLDLQD WGMALRRADI YSLALLLWEI
LSRCPDLRPA VHHPSNWPMR QNWAIPLPLM SYGPWQCRRG GVPTSHPPGA ALPQTLMG*
mutated AA sequence MLGSLGLWAL LPTAVEAPPN RRTCVFFEAP GVRGSTKTLG ELLDTGTELP RAIRCLYSRC
CFGIWNLTQD RAQVEMQGCR DSDEPGCESL HCDPSPRAHP SPGSTLFTCS CGTDFCNANY
SHLPPPGSPG TPGSQGPQAA PGESIWMALV LLGLFLLLLL LLGSIILALL QRKNYRVRGE
PVPEPRPDSG RDWSVELQEL PELCFSQVIR EGGHAVVWAG QLQGKLVAIK AFPPRSVAQF
QAERALYELP GLQHDHIVRF ITASRGGPGR LLSGPLLVLE LHPKGSLCHY LTQYTSDWGS
SLRMALSLAQ GLAFLHEERW QNGQYKPGIA HRDLSSQNVL IREDGSCAIG DLGLALVLPG
LTQPPAWTPT QPQGPAAIME AGTQRYMAPE LLDKTLDLQD WGMALQRADI YSLALLLWEI
LSRCPDLRPA VHHPSNWPMR QNWAIPLPLM SYGPWQCRRG GVPTSHPPGA ALPQTLMG*
speed 0.22 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