Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999822516804176 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:140793007A>GN/A show variant in all transcripts   IGV
HGNC symbol PCDHGA10
Ensembl transcript ID ENST00000398610
Genbank transcript ID NM_018913
UniProt peptide Q9Y5H3
alteration type single base exchange
alteration region CDS
DNA changes c.265A>G
cDNA.265A>G
g.265A>G
AA changes I89V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 89
frameshift no
known variant Reference ID: rs4912751
databasehomozygous (G/G)heterozygousallele carriers
1000G9199471866
ExAC14948287117819
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2AZ, Histone, Histone 2A variant Z
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3420.998
0.2430.986
(flanking)2.960.987
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc gained2740.30mu: GCGGCAGCTTGGTCACCGCGGGCAGGATAGACCGGGAGGAG gcgg|GCAG
Donor gained2590.49mu: GCGGCAGCTTGGTCA GGCA|gctt
distance from splice site 265
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      89LFSLNPRSGSLITAGRIDREELCA
mutated  all conserved    89LFSLNPRSGSLVTAGRIDREELC
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
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 
33137DOMAINCadherin 1.lost
33696TOPO_DOMExtracellular (Potential).lost
138246DOMAINCadherin 2.might get lost (downstream of altered splice site)
247351DOMAINCadherin 3.might get lost (downstream of altered splice site)
352456DOMAINCadherin 4.might get lost (downstream of altered splice site)
423423CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
457566DOMAINCadherin 5.might get lost (downstream of altered splice site)
549549CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
574687DOMAINCadherin 6.might get lost (downstream of altered splice site)
697717TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
718936TOPO_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 2811 / 2811
position (AA) of stopcodon in wt / mu AA sequence 937 / 937
position of stopcodon in wt / mu cDNA 2811 / 2811
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 5
strand 1
last intron/exon boundary 2585
theoretical NMD boundary in CDS 2534
length of CDS 2811
coding sequence (CDS) position 265
cDNA position
(for ins/del: last normal base / first normal base)		 265
gDNA position
(for ins/del: last normal base / first normal base)		 265
chromosomal position
(for ins/del: last normal base / first normal base)		 140793007
original gDNA sequence snippet ACCCGCGCAGCGGCAGCTTGATCACCGCGGGCAGGATAGAC
altered gDNA sequence snippet ACCCGCGCAGCGGCAGCTTGGTCACCGCGGGCAGGATAGAC
original cDNA sequence snippet ACCCGCGCAGCGGCAGCTTGATCACCGCGGGCAGGATAGAC
altered cDNA sequence snippet ACCCGCGCAGCGGCAGCTTGGTCACCGCGGGCAGGATAGAC
wildtype AA sequence MAAQRNRSKE SKDCSGLVLL CLFFGIPWEA GARQISYSIP EELEKGSFVG NISKDLGLAP
RELAERGVRI VSRGRTQLFS LNPRSGSLIT AGRIDREELC AQSARCVVSF NILVEDRVKL
FGIEIEVTDI NDNAPKFQAE NLDVKINENV AAGMRFPLPE AIDPDVGVNS LQSYQLSPNK
HFSLRVQSRA NGVKYPELVL EHSLDREEEA IHHLVLTASD GGDPLRSGTV LVSVTVFDAN
DNAPVFTLPE YRVSVPENLP VGTQLLTVTA TDRDEGANGE VTYSFRKLPD TQLLKFQLNK
YTGEIKISEN LDYEETGFYE IEIQAEDGGA YLATAKVLIT VEDVNDNSPE LTITSLFSPV
TEDSPLGTVV ALLNVHDLDS EQNGQVTCSI LAYLPFKLEK SIDSYYRLVI HRALDREQVS
SYNITVTATD GGSPPLSTEA HFMLQVADIN DNPPTFSQVS YFTYIPENNA RGASIFSVTA
LDPDSKENAQ IIYSLAEDTI QGVPLSSYIS INSDTGVLYA LRSFDYEQFH ELQMQVTASD
SGDPPLSSNV SLSLFVLDQN DNAPEILYPA LPTDGSTGVE LAPRSAEPGY LVTKVVAVDR
DSGQNAWLSY RLLKASEPGL FAVGEHTGEV RTARALLDRD ALKQSLVVAV QDHGQPPLSA
TVTLTVAVAD SIPQVLADLG SFESPANSET SDLTLYLVVA VAAVSCVFLA FVIVLLAHRL
RRWHKSRLLQ ASGGGLTGVS GSHFVGVDGV RAFLQTYSHE VSLTADSRKS HLIFPQPNYA
DTLISQESCE KNDPLSLLDD SKFPIEDTPL VPQAPPNTDW RFSQAQRPGT SGSQNGDDTG
TWPNNQFDTE MLQAMILASA SEAADGSSTL GGGAGTMGLS ARYGPQFTLQ HVPDYRQNVY
IPGSNATLTN AAGKRDGKAP AGGNGNKKKS GKKEKK*
mutated AA sequence MAAQRNRSKE SKDCSGLVLL CLFFGIPWEA GARQISYSIP EELEKGSFVG NISKDLGLAP
RELAERGVRI VSRGRTQLFS LNPRSGSLVT AGRIDREELC AQSARCVVSF NILVEDRVKL
FGIEIEVTDI NDNAPKFQAE NLDVKINENV AAGMRFPLPE AIDPDVGVNS LQSYQLSPNK
HFSLRVQSRA NGVKYPELVL EHSLDREEEA IHHLVLTASD GGDPLRSGTV LVSVTVFDAN
DNAPVFTLPE YRVSVPENLP VGTQLLTVTA TDRDEGANGE VTYSFRKLPD TQLLKFQLNK
YTGEIKISEN LDYEETGFYE IEIQAEDGGA YLATAKVLIT VEDVNDNSPE LTITSLFSPV
TEDSPLGTVV ALLNVHDLDS EQNGQVTCSI LAYLPFKLEK SIDSYYRLVI HRALDREQVS
SYNITVTATD GGSPPLSTEA HFMLQVADIN DNPPTFSQVS YFTYIPENNA RGASIFSVTA
LDPDSKENAQ IIYSLAEDTI QGVPLSSYIS INSDTGVLYA LRSFDYEQFH ELQMQVTASD
SGDPPLSSNV SLSLFVLDQN DNAPEILYPA LPTDGSTGVE LAPRSAEPGY LVTKVVAVDR
DSGQNAWLSY RLLKASEPGL FAVGEHTGEV RTARALLDRD ALKQSLVVAV QDHGQPPLSA
TVTLTVAVAD SIPQVLADLG SFESPANSET SDLTLYLVVA VAAVSCVFLA FVIVLLAHRL
RRWHKSRLLQ ASGGGLTGVS GSHFVGVDGV RAFLQTYSHE VSLTADSRKS HLIFPQPNYA
DTLISQESCE KNDPLSLLDD SKFPIEDTPL VPQAPPNTDW RFSQAQRPGT SGSQNGDDTG
TWPNNQFDTE MLQAMILASA SEAADGSSTL GGGAGTMGLS ARYGPQFTLQ HVPDYRQNVY
IPGSNATLTN AAGKRDGKAP AGGNGNKKKS GKKEKK*
speed 1.28 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