Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999874 (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) chr5:140230370A>CN/A show variant in all transcripts   IGV
HGNC symbol PCDHA9
Ensembl transcript ID ENST00000378122
Genbank transcript ID NM_014005
UniProt peptide Q9Y5H5
alteration type single base exchange
alteration region CDS
DNA changes c.2290A>C
cDNA.3014A>C
g.3323A>C
AA changes K764Q Score: 53 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 764
frameshift no
known variant Reference ID: rs369636
databasehomozygous (C/C)heterozygousallele carriers
1000G10709962066
ExAC25467-181677300
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.740.001
-0.6730
(flanking)-0.0210
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased3327wt: 0.26 / mu: 0.56wt: TAAGCAGAAGACCGA
mu: TCAGCAGAAGACCGA		 AGCA|gaag
Donor marginally increased3324wt: 0.8948 / mu: 0.9022 (marginal change - not scored)wt: GGGTAAGCAGAAGAC
mu: GGGTCAGCAGAAGAC		 GTAA|gcag
Donor increased3314wt: 0.52 / mu: 0.77wt: GCTCTGGCGAGGGTA
mu: GCTCTGGCGAGGGTC		 TCTG|gcga
distance from splice site 3014
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      764QRRQRVCSGEGKQKTDLMAFSPGL
mutated  all conserved    764QRRQRVCSGEGQQKTDLMAFSPG
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  not conserved  ENSXETG00000032691  755QRQYKVHLNGTPLKNDLILFTPN
protein features
start (aa)end (aa)featuredetails 
719950TOPO_DOMCytoplasmic (Potential).lost
734894REGION5 X 4 AA repeats of P-X-X-P.lost
799802REPEATPXXP 2.might get lost (downstream of altered splice site)
832835REPEATPXXP 3.might get lost (downstream of altered splice site)
873876REPEATPXXP 4.might get lost (downstream of altered splice site)
891894REPEATPXXP 5.might get lost (downstream of altered splice site)
923930COMPBIASPoly-Lys.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2529 / 2529
position (AA) of stopcodon in wt / mu AA sequence 843 / 843
position of stopcodon in wt / mu cDNA 3253 / 3253
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 725 / 725
chromosome 5
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 2529
coding sequence (CDS) position 2290
cDNA position
(for ins/del: last normal base / first normal base)		 3014
gDNA position
(for ins/del: last normal base / first normal base)		 3323
chromosomal position
(for ins/del: last normal base / first normal base)		 140230370
original gDNA sequence snippet GGGTGTGCTCTGGCGAGGGTAAGCAGAAGACCGACCTCATG
altered gDNA sequence snippet GGGTGTGCTCTGGCGAGGGTCAGCAGAAGACCGACCTCATG
original cDNA sequence snippet GGGTGTGCTCTGGCGAGGGTAAGCAGAAGACCGACCTCATG
altered cDNA sequence snippet GGGTGTGCTCTGGCGAGGGTCAGCAGAAGACCGACCTCATG
wildtype AA sequence MLYSSRGDPE GQPLLLSLLI LAMWVVGSGQ LHYSVPEEAE HGTFVGRIAQ DLGLELAELV
PRLFQLDSKG RGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVKDINDNP PVFPATQKNL FIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFFL
DVPTSNQQVK PLGLVLRKLL DREETPELHL LLTATDGGKP ELTGTVQLLI TVLDNNDNAP
VFDRTLYTVK LPENVSIGTL VIHPNASDLD EGLNGDIIYS FSSDVSPDIK SKFHMDPLSG
AITVIGHMDF EESRAHKIPV EAVDKGFPPL AGHCTLLVEV VDVNDNAPQL TIKTLSVPVK
EDAQLGTVIA LISVIDLDAD ANGQVTCSLT PHVPFKLVST YKNYYSLVLD RALDRESVSA
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRLG ERSLSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLTPRM RGTDGAVSEM VLRSVGAGVV VGKVRAVDAD
SGYNAWLSYE LQPETASASI PFRVGLYTGE ISTTRALDET DAPRQRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKSSS RASVGATGPE VTLVDVNVYL IIAICAVSSL LVLTLLLYTV
LRCSAMPTEG ECAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEGKQKTDLM AFSPGLSPCA
GSTERTGEPS ASSDSTGKVG FSSILFIYII FFLERYYRLL PGAVQIVLFI FLEIQQIFFL
IK*
mutated AA sequence MLYSSRGDPE GQPLLLSLLI LAMWVVGSGQ LHYSVPEEAE HGTFVGRIAQ DLGLELAELV
PRLFQLDSKG RGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVKDINDNP PVFPATQKNL FIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFFL
DVPTSNQQVK PLGLVLRKLL DREETPELHL LLTATDGGKP ELTGTVQLLI TVLDNNDNAP
VFDRTLYTVK LPENVSIGTL VIHPNASDLD EGLNGDIIYS FSSDVSPDIK SKFHMDPLSG
AITVIGHMDF EESRAHKIPV EAVDKGFPPL AGHCTLLVEV VDVNDNAPQL TIKTLSVPVK
EDAQLGTVIA LISVIDLDAD ANGQVTCSLT PHVPFKLVST YKNYYSLVLD RALDRESVSA
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRLG ERSLSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLTPRM RGTDGAVSEM VLRSVGAGVV VGKVRAVDAD
SGYNAWLSYE LQPETASASI PFRVGLYTGE ISTTRALDET DAPRQRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKSSS RASVGATGPE VTLVDVNVYL IIAICAVSSL LVLTLLLYTV
LRCSAMPTEG ECAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEGQQKTDLM AFSPGLSPCA
GSTERTGEPS ASSDSTGKVG FSSILFIYII FFLERYYRLL PGAVQIVLFI FLEIQQIFFL
IK*
speed 0.95 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