Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000289746
MT speed 1.21 s - this script 3.312386 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CDH15disease_causing0.999994319024929simple_aaeaffectedA122Vsingle base exchangers121434541show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999994319024929      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM086800)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:89249963C>TN/A show variant in all transcripts   IGV
HGNC symbol CDH15
Ensembl transcript ID ENST00000289746
Genbank transcript ID NM_004933
UniProt peptide P55291
alteration type single base exchange
alteration region CDS
DNA changes c.365C>T
cDNA.430C>T
g.11789C>T
AA changes A122V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 122
frameshift no
known variant Reference ID: rs121434541
databasehomozygous (T/T)heterozygousallele carriers
1000G112
ExAC13233

known disease mutation at this position, please check HGMD for details (HGMD ID CM086800)

known disease mutation at this position, please check HGMD for details (HGMD ID CM086800)
known disease mutation at this position, please check HGMD for details (HGMD ID CM086800)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0551
3.4861
(flanking)0.2160.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased11782wt: 0.62 / mu: 0.97wt: AACAGCTAAGAGCGT
mu: AACAGCTAAGAGTGT		 CAGC|taag
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      122DREKTDRFRLRAFALDLGGSTLED
mutated  not conserved    122RVFALDLGGSTLE
Ptroglodytes  all identical  ENSPTRG00000008473  108DREKTDRFRLRAFALDLGGSTLE
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031962  121RAFALDLGGSTLE
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000017254  97DREKHRSFTLKAFALSPSGERLE
Drerio  all identical  ENSDARG00000068191  118DREKHKSFKLKAFALSPSGERLE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011269  123KLQAFAVDEVGLTLE
protein features
start (aa)end (aa)featuredetails 
61152DOMAINCadherin 1.lost
61606TOPO_DOMExtracellular (Potential).lost
153260DOMAINCadherin 2.might get lost (downstream of altered splice site)
227227CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
261375DOMAINCadherin 3.might get lost (downstream of altered splice site)
376481DOMAINCadherin 4.might get lost (downstream of altered splice site)
482590DOMAINCadherin 5.might get lost (downstream of altered splice site)
531531CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
538538CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
576576CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
607626TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
627814TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2445 / 2445
position (AA) of stopcodon in wt / mu AA sequence 815 / 815
position of stopcodon in wt / mu cDNA 2510 / 2510
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 66 / 66
chromosome 16
strand 1
last intron/exon boundary 2217
theoretical NMD boundary in CDS 2101
length of CDS 2445
coding sequence (CDS) position 365
cDNA position
(for ins/del: last normal base / first normal base)		 430
gDNA position
(for ins/del: last normal base / first normal base)		 11789
chromosomal position
(for ins/del: last normal base / first normal base)		 89249963
original gDNA sequence snippet TATGTTTGAACAGCTAAGAGCGTTTGCCCTGGACCTGGGAG
altered gDNA sequence snippet TATGTTTGAACAGCTAAGAGTGTTTGCCCTGGACCTGGGAG
original cDNA sequence snippet TGATCGCTTCAGGCTAAGAGCGTTTGCCCTGGACCTGGGAG
altered cDNA sequence snippet TGATCGCTTCAGGCTAAGAGTGTTTGCCCTGGACCTGGGAG
wildtype AA sequence MDAAFLLVLG LLAQSLCLSL GVPGWRRPTT LYPWRRAPAL SRVRRAWVIP PISVSENHKR
LPYPLVQIKS DKQQLGSVIY SIQGPGVDEE PRGVFSIDKF TGKVFLNAML DREKTDRFRL
RAFALDLGGS TLEDPTDLEI VVVDQNDNRP AFLQEAFTGR VLEGAVPGTY VTRAEATDAD
DPETDNAALR FSILQQGSPE LFSIDELTGE IRTVQVGLDR EVVAVYNLTL QVADMSGDGL
TATASAIITL DDINDNAPEF TRDEFFMEAI EAVSGVDVGR LEVEDRDLPG SPNWVARFTI
LEGDPDGQFT IRTDPKTNEG VLSIVKALDY ESCEHYELKV SVQNEAPLQA AALRAERGQA
KVRVHVQDTN EPPVFQENPL RTSLAEGAPP GTLVATFSAR DPDTEQLQRL SYSKDYDPED
WLQVDAATGR IQTQHVLSPA SPFLKGGWYR AIVLAQDDAS QPRTATGTLS IEILEVNDHA
PVLAPPPPGS LCSEPHQGPG LLLGATDEDL PPHGAPFHFQ LSPRLPELGR NWSLSQVNVS
HARLRPRHQV PEGLHRLSLL LRDSGQPPQQ REQPLNVTVC RCGKDGVCLP GAAALLAGGT
GLSLGALVIV LASALLLLVL VLLVALRARF WKQSRGKGLL HGPQDDLRDN VLNYDEQGGG
EEDQDAYDIS QLRHPTALSL PLGPPPLRRD APQGRLHPQP PRVLPTSPLD IADFINDGLE
AADSDPSVPP YDTALIYDYE GDGSVAGTLS SILSSQGDED QDYDYLRDWG PRFARLADMY
GHPCGLEYGA RWDHQAREGL SPGALLPRHR GRTA*
mutated AA sequence MDAAFLLVLG LLAQSLCLSL GVPGWRRPTT LYPWRRAPAL SRVRRAWVIP PISVSENHKR
LPYPLVQIKS DKQQLGSVIY SIQGPGVDEE PRGVFSIDKF TGKVFLNAML DREKTDRFRL
RVFALDLGGS TLEDPTDLEI VVVDQNDNRP AFLQEAFTGR VLEGAVPGTY VTRAEATDAD
DPETDNAALR FSILQQGSPE LFSIDELTGE IRTVQVGLDR EVVAVYNLTL QVADMSGDGL
TATASAIITL DDINDNAPEF TRDEFFMEAI EAVSGVDVGR LEVEDRDLPG SPNWVARFTI
LEGDPDGQFT IRTDPKTNEG VLSIVKALDY ESCEHYELKV SVQNEAPLQA AALRAERGQA
KVRVHVQDTN EPPVFQENPL RTSLAEGAPP GTLVATFSAR DPDTEQLQRL SYSKDYDPED
WLQVDAATGR IQTQHVLSPA SPFLKGGWYR AIVLAQDDAS QPRTATGTLS IEILEVNDHA
PVLAPPPPGS LCSEPHQGPG LLLGATDEDL PPHGAPFHFQ LSPRLPELGR NWSLSQVNVS
HARLRPRHQV PEGLHRLSLL LRDSGQPPQQ REQPLNVTVC RCGKDGVCLP GAAALLAGGT
GLSLGALVIV LASALLLLVL VLLVALRARF WKQSRGKGLL HGPQDDLRDN VLNYDEQGGG
EEDQDAYDIS QLRHPTALSL PLGPPPLRRD APQGRLHPQP PRVLPTSPLD IADFINDGLE
AADSDPSVPP YDTALIYDYE GDGSVAGTLS SILSSQGDED QDYDYLRDWG PRFARLADMY
GHPCGLEYGA RWDHQAREGL SPGALLPRHR GRTA*
speed 1.21 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
back to results table

Problems