Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.968021762817626 (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) chr5:140183058G>AN/A show variant in all transcripts   IGV
HGNC symbol PCDHA3
Ensembl transcript ID ENST00000522353
Genbank transcript ID NM_018906
UniProt peptide Q9Y5H8
alteration type single base exchange
alteration region CDS
DNA changes c.2276G>A
cDNA.2276G>A
g.2276G>A
AA changes C759Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 759
frameshift no
known variant Reference ID: rs2240694
databasehomozygous (A/A)heterozygousallele carriers
1000G71711971914
ExAC16867-96715900
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)1.040.922
3.2690.921
(flanking)-0.3550.194
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2278wt: 0.37 / mu: 0.73wt: TGTGCTCTGGAGAGG
mu: TGTACTCTGGAGAGG		 TGCT|ctgg
Donor marginally increased2268wt: 0.2619 / mu: 0.2827 (marginal change - not scored)wt: CAGCAGAGGGTGTGC
mu: CAGCAGAGGGTGTAC		 GCAG|aggg
Donor increased2281wt: 0.60 / mu: 0.77wt: GCTCTGGAGAGGGGT
mu: ACTCTGGAGAGGGGT		 TCTG|gaga
Donor marginally increased2280wt: 0.9168 / mu: 0.9607 (marginal change - not scored)wt: TGCTCTGGAGAGGGG
mu: TACTCTGGAGAGGGG		 CTCT|ggag
distance from splice site 119
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      759WSYSQQRQQRVCSGEGLPKTDLMA
mutated  not conserved    759WSYSQQRQQRVYSGEGLPKTDLM
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  750WTYSQQRQYKVHLNGTPLKNDLI
protein features
start (aa)end (aa)featuredetails 
719950TOPO_DOMCytoplasmic (Potential).lost
734894REGION6 X 4 AA repeats of P-X-X-P.lost
774777REPEATPXXP 2.might get lost (downstream of altered splice site)
799802REPEATPXXP 3.might get lost (downstream of altered splice site)
832835REPEATPXXP 4.might get lost (downstream of altered splice site)
873876REPEATPXXP 5.might get lost (downstream of altered splice site)
891894REPEATPXXP 6.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 2853 / 2853
position (AA) of stopcodon in wt / mu AA sequence 951 / 951
position of stopcodon in wt / mu cDNA 2853 / 2853
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 2543
theoretical NMD boundary in CDS 2492
length of CDS 2853
coding sequence (CDS) position 2276
cDNA position
(for ins/del: last normal base / first normal base)		 2276
gDNA position
(for ins/del: last normal base / first normal base)		 2276
chromosomal position
(for ins/del: last normal base / first normal base)		 140183058
original gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered gDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
original cDNA sequence snippet GCAGAGGCAGCAGAGGGTGTGCTCTGGAGAGGGGTTGCCCA
altered cDNA sequence snippet GCAGAGGCAGCAGAGGGTGTACTCTGGAGAGGGGTTGCCCA
wildtype AA sequence MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVCS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *
mutated AA sequence MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVYS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *
speed 0.68 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