Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999860600049 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM051019)
  • known disease mutation: rs17640 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:68714968A>TN/A show variant in all transcripts   IGV
HGNC symbol CDH3
Ensembl transcript ID ENST00000264012
Genbank transcript ID NM_001793
UniProt peptide P22223
alteration type single base exchange
alteration region CDS
DNA changes c.965A>T
cDNA.1509A>T
g.44877A>T
AA changes N322I Score: 149 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 322
frameshift no
known variant Reference ID: rs121434543
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17640 (pathogenic for EEM syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051019)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9451
3.9451
(flanking)0.2751
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 increased44879wt: 0.2055 / mu: 0.2096 (marginal change - not scored)wt: CCAATGACAATGCTC
mu: CCATTGACAATGCTC		 AATG|acaa
distance from splice site 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      322TAVAVVEILDANDNAPMFDPQKYE
mutated  not conserved    322TAVAVVEILDAIDNAPMFDPQKY
Ptroglodytes  all identical  ENSPTRG00000008269  322TAVAVVEILDANDNAPVFDPQKY
Mmulatta  all identical  ENSMMUG00000010393  270TAVAVVEILDANDNAPVFDPQKY
Fcatus  all identical  ENSFCAG00000001062  261TAVAIVEILDANDNAPVFDPQKY
Mmusculus  all identical  ENSMUSG00000061048  314TAEAVVQILDANDNAPEFEPQKY
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002439  256VAKVILTVTDSNDNAPAFTQSSY
Drerio  all identical  ENSDARG00000024371  355TGTAVITVTDSNDNAPLFEQSSY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000025992  371EGKAIIEITDANDNAPI
protein features
start (aa)end (aa)featuredetails 
108654TOPO_DOMExtracellular (Potential).lost
216328DOMAINCadherin 2.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2490 / 2490
position (AA) of stopcodon in wt / mu AA sequence 830 / 830
position of stopcodon in wt / mu cDNA 3034 / 3034
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 545 / 545
chromosome 16
strand 1
last intron/exon boundary 2825
theoretical NMD boundary in CDS 2230
length of CDS 2490
coding sequence (CDS) position 965
cDNA position
(for ins/del: last normal base / first normal base)		 1509
gDNA position
(for ins/del: last normal base / first normal base)		 44877
chromosomal position
(for ins/del: last normal base / first normal base)		 68714968
original gDNA sequence snippet AGTGGAGATCCTTGATGCCAATGACAATGCTCCCATGTTTG
altered gDNA sequence snippet AGTGGAGATCCTTGATGCCATTGACAATGCTCCCATGTTTG
original cDNA sequence snippet AGTGGAGATCCTTGATGCCAATGACAATGCTCCCATGTTTG
altered cDNA sequence snippet AGTGGAGATCCTTGATGCCATTGACAATGCTCCCATGTTTG
wildtype AA sequence MGLPRGPLAS LLLLQVCWLQ CAASEPCRAV FREAEVTLEA GGAEQEPGQA LGKVFMGCPG
QEPALFSTDN DDFTVRNGET VQERRSLKER NPLKIFPSKR ILRRHKRDWV VAPISVPENG
KGPFPQRLNQ LKSNKDRDTK IFYSITGPGA DSPPEGVFAV EKETGWLLLN KPLDREEIAK
YELFGHAVSE NGASVEDPMN ISIIVTDQND HKPKFTQDTF RGSVLEGVLP GTSVMQVTAT
DEDDAIYTYN GVVAYSIHSQ EPKDPHDLMF TIHRSTGTIS VISSGLDREK VPEYTLTIQA
TDMDGDGSTT TAVAVVEILD ANDNAPMFDP QKYEAHVPEN AVGHEVQRLT VTDLDAPNSP
AWRATYLIMG GDDGDHFTIT THPESNQGIL TTRKGLDFEA KNQHTLYVEV TNEAPFVLKL
PTSTATIVVH VEDVNEAPVF VPPSKVVEVQ EGIPTGEPVC VYTAEDPDKE NQKISYRILR
DPAGWLAMDP DSGQVTAVGT LDREDEQFVR NNIYEVMVLA MDNGSPPTTG TGTLLLTLID
VNDHGPVPEP RQITICNQSP VRQVLNITDK DLSPHTSPFQ AQLTDDSDIY WTAEVNEEGD
TVVLSLKKFL KQDTYDVHLS LSDHGNKEQL TVIRATVCDC HGHVETCPGP WKGGFILPVL
GAVLALLFLL LVLLLLVRKK RKIKEPLLLP EDDTRDNVFY YGEEGGGEED QDYDITQLHR
GLEARPEVVL RNDVAPTIIP TPMYRPRPAN PDEIGNFIIE NLKAANTDPT APPYDTLLVF
DYEGSGSDAA SLSSLTSSAS DQDQDYDYLN EWGSRFKKLA DMYGGGEDD*
mutated AA sequence MGLPRGPLAS LLLLQVCWLQ CAASEPCRAV FREAEVTLEA GGAEQEPGQA LGKVFMGCPG
QEPALFSTDN DDFTVRNGET VQERRSLKER NPLKIFPSKR ILRRHKRDWV VAPISVPENG
KGPFPQRLNQ LKSNKDRDTK IFYSITGPGA DSPPEGVFAV EKETGWLLLN KPLDREEIAK
YELFGHAVSE NGASVEDPMN ISIIVTDQND HKPKFTQDTF RGSVLEGVLP GTSVMQVTAT
DEDDAIYTYN GVVAYSIHSQ EPKDPHDLMF TIHRSTGTIS VISSGLDREK VPEYTLTIQA
TDMDGDGSTT TAVAVVEILD AIDNAPMFDP QKYEAHVPEN AVGHEVQRLT VTDLDAPNSP
AWRATYLIMG GDDGDHFTIT THPESNQGIL TTRKGLDFEA KNQHTLYVEV TNEAPFVLKL
PTSTATIVVH VEDVNEAPVF VPPSKVVEVQ EGIPTGEPVC VYTAEDPDKE NQKISYRILR
DPAGWLAMDP DSGQVTAVGT LDREDEQFVR NNIYEVMVLA MDNGSPPTTG TGTLLLTLID
VNDHGPVPEP RQITICNQSP VRQVLNITDK DLSPHTSPFQ AQLTDDSDIY WTAEVNEEGD
TVVLSLKKFL KQDTYDVHLS LSDHGNKEQL TVIRATVCDC HGHVETCPGP WKGGFILPVL
GAVLALLFLL LVLLLLVRKK RKIKEPLLLP EDDTRDNVFY YGEEGGGEED QDYDITQLHR
GLEARPEVVL RNDVAPTIIP TPMYRPRPAN PDEIGNFIIE NLKAANTDPT APPYDTLLVF
DYEGSGSDAA SLSSLTSSAS DQDQDYDYLN EWGSRFKKLA DMYGGGEDD*
speed 0.40 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