Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.97432096367802 (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) chr5:140182101G>TN/A show variant in all transcripts   IGV
HGNC symbol PCDHA3
Ensembl transcript ID ENST00000532566
Genbank transcript ID NM_031497
UniProt peptide Q9Y5H8
alteration type single base exchange
alteration region CDS
DNA changes c.1319G>T
cDNA.1319G>T
g.1319G>T
AA changes S440I Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 440
frameshift no
known variant Reference ID: rs7701755
databasehomozygous (T/T)heterozygousallele carriers
1000G91011422052
ExAC18302-383714465
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.160.992
1.2080.987
(flanking)0.3230.959
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc gained13300.42mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC gtgg|AGGT
distance from splice site 1157
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      440DGGSPSLWATASVSVEVADVNDNA
mutated  not conserved    440DGGSPSLWATAIVSVEVADVNDN
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  all identical  ENSXETG00000032691  439SLSVTKSIKIQISDVNDN
protein features
start (aa)end (aa)featuredetails 
30697TOPO_DOMExtracellular (Potential).lost
351455DOMAINCadherin 4.lost
456565DOMAINCadherin 5.might get lost (downstream of altered splice site)
548548CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
581678DOMAINCadherin 6.might get lost (downstream of altered splice site)
698718TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
719950TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
734737REPEATPXXP 1.might get lost (downstream of altered splice site)
734894REGION6 X 4 AA repeats of P-X-X-P.might get lost (downstream of altered splice site)
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 2475 / 2475
position (AA) of stopcodon in wt / mu AA sequence 825 / 825
position of stopcodon in wt / mu cDNA 2475 / 2475
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 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 2475
coding sequence (CDS) position 1319
cDNA position
(for ins/del: last normal base / first normal base)		 1319
gDNA position
(for ins/del: last normal base / first normal base)		 1319
chromosomal position
(for ins/del: last normal base / first normal base)		 140182101
original gDNA sequence snippet TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG
altered gDNA sequence snippet TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG
original cDNA sequence snippet TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG
altered cDNA sequence snippet TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG
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 VDVDLSAKVS NFYLFFPKCL CFSFLNVSTP LEIH*
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 GSPSLWATAI 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 VDVDLSAKVS NFYLFFPKCL CFSFLNVSTP LEIH*
speed 0.62 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