Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999991477788163 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM023041)
  • known disease mutation: rs17639 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:68719191G>AN/A show variant in all transcripts   IGV
HGNC symbol CDH3
Ensembl transcript ID ENST00000429102
Genbank transcript ID N/A
UniProt peptide P22223
alteration type single base exchange
alteration region CDS
DNA changes c.1508G>A
cDNA.1895G>A
g.49100G>A
AA changes R503H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 503
frameshift no
known variant Reference ID: rs121434542
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17639 (pathogenic for Congenital hypotrichosis with juvenile macular dystrophy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023041)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023041)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023041)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5330.995
3.6270.992
(flanking)-2.0570.057
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased49103wt: 0.42 / mu: 0.59wt: TGTGGGCACCCTCGACCGTGAGGATGAGCAGTTTGTGAGGA
mu: TGTGGGCACCCTCGACCATGAGGATGAGCAGTTTGTGAGGA		 gtga|GGAT
Donor marginally increased49104wt: 0.9747 / mu: 0.9885 (marginal change - not scored)wt: CGTGAGGATGAGCAG
mu: CATGAGGATGAGCAG		 TGAG|gatg
Donor gained490980.36mu: CTCGACCATGAGGAT CGAC|catg
Donor gained491010.30mu: GACCATGAGGATGAG CCAT|gagg
distance from splice site 63
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      503SGQVTAVGTLDREDEQFVRNNIYE
mutated  not conserved    503SGQVTAVGTLDHEDEQFVRNNIY
Ptroglodytes  all identical  ENSPTRG00000008269  503SGQVTAVGTLDREDEQFVRNNIY
Mmulatta  all identical  ENSMMUG00000010393  451SGQVTVAGTLDREDERFVRNNIY
Fcatus  all identical  ENSFCAG00000001062  442SGQVTATGVLDREDERFVKNNVY
Mmusculus  all identical  ENSMUSG00000061048  495SGQITAAGILDREDEQFVKNNVY
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000002439  437TGLIKVKNAMDRE-STFVKDDKY
Drerio  all identical  ENSDARG00000024371  537SGQIQVKNALDRESSN-VKDGKY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000025992  551TGIVTGNGNLDRESE
protein features
start (aa)end (aa)featuredetails 
108654TOPO_DOMExtracellular (Potential).lost
441546DOMAINCadherin 4.lost
547650DOMAINCadherin 5.might get lost (downstream of altered splice site)
566566CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
655677TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
678829TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
713713MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
785800COMPBIASSer-rich.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2355 / 2355
position (AA) of stopcodon in wt / mu AA sequence 785 / 785
position of stopcodon in wt / mu cDNA 2742 / 2742
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 388 / 388
chromosome 16
strand 1
last intron/exon boundary 2668
theoretical NMD boundary in CDS 2230
length of CDS 2355
coding sequence (CDS) position 1508
cDNA position
(for ins/del: last normal base / first normal base)		 1895
gDNA position
(for ins/del: last normal base / first normal base)		 49100
chromosomal position
(for ins/del: last normal base / first normal base)		 68719191
original gDNA sequence snippet AGCTGTGGGCACCCTCGACCGTGAGGATGAGCAGTTTGTGA
altered gDNA sequence snippet AGCTGTGGGCACCCTCGACCATGAGGATGAGCAGTTTGTGA
original cDNA sequence snippet AGCTGTGGGCACCCTCGACCGTGAGGATGAGCAGTTTGTGA
altered cDNA sequence snippet AGCTGTGGGCACCCTCGACCATGAGGATGAGCAGTTTGTGA
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 GRGERGSQRG NGGLQLARGR
TRRS*
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 ANDNAPMFDP QKYEAHVPEN AVGHEVQRLT VTDLDAPNSP
AWRATYLIMG GDDGDHFTIT THPESNQGIL TTRKGLDFEA KNQHTLYVEV TNEAPFVLKL
PTSTATIVVH VEDVNEAPVF VPPSKVVEVQ EGIPTGEPVC VYTAEDPDKE NQKISYRILR
DPAGWLAMDP DSGQVTAVGT LDHEDEQFVR 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 GRGERGSQRG NGGLQLARGR
TRRS*
speed 1.25 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