mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 3.65108307097496e-22 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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

PCDHA2

Ensembl transcript ID

ENST00000526136

Genbank transcript ID

NM_018905

UniProt peptide

Q9Y5H9

alteration type

single base exchange

alteration region

intron

DNA changes

g.8615G>A

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

Reference ID: rs2240694

database	homozygous (A/A)	heterozygous	allele carriers
1000G	717	1197	1914
ExAC	16867	-967	15900

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

	PhyloP	PhastCons
(flanking)	1.04	0.922
	3.269	0.921
(flanking)	-0.355	0.194

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	8607	wt: 0.2619 / mu: 0.2827 (marginal change - not scored)	wt: CAGCAGAGGGTGTGC mu: CAGCAGAGGGTGTAC	GCAG\|aggg
Donor increased	8620	wt: 0.60 / mu: 0.77	wt: GCTCTGGAGAGGGGT mu: ACTCTGGAGAGGGGT	TCTG\|gaga
Donor increased	8617	wt: 0.37 / mu: 0.73	wt: TGTGCTCTGGAGAGG mu: TGTACTCTGGAGAGG	TGCT\|ctgg
Donor marginally increased	8619	wt: 0.9168 / mu: 0.9607 (marginal change - not scored)	wt: TGCTCTGGAGAGGGG mu: TACTCTGGAGAGGGG	CTCT\|ggag

distance from splice site

6121

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
719	948	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	892	REGION	5 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
797	800	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
830	833	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
871	874	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
889	892	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
921	928	COMPBIAS	Poly-Lys.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

position (AA) of stopcodon in wt / mu AA sequence

N/A

position of stopcodon in wt / mu cDNA

N/A

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

strand

last intron/exon boundary

2537

theoretical NMD boundary in CDS

2486

length of CDS

2847

coding sequence (CDS) position

N/A

cDNA position
(for ins/del: last normal base / first normal base)

N/A

gDNA position
(for ins/del: last normal base / first normal base)

8615

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

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MASSIRRGRG AWTRLLSLLL LAAWEVGSGQ LRYSVPEEAK HGTFVGRIAQ DLGLELEELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHVEVIV DRPLQVFHVE
VEVKDINDNP PIFPMTVKTI RFPESRLLDS RFPLEGASDA DIGVNALLSY KLSSSEFFFL
DIQANDELSE SLSLVLGKSL DREETAEVNL LLVATDGGKP ELTGTVQILI KVLDVNDNEP
TFAQSVYKVK LLENTANGTL VVKLNASDAD EGPNSEIVYS LGSDVSSTIQ TKFTIDPISG
EIRTKGKLDY EEAKSYEIQV TATDKGTPSM SGHCKISLKL VDINDNTPEV SITSLSLPIS
ENASLGTVIA LITVSDRDSG TNGHVTCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATTS VSIEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEEVEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRA GTAAGAVSEL VPWSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQLGTGSARI PFRVGLYTGE ISTTRALDEA DSPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RAWVGAAGSE ATLVDVNVYL IIAICAVSSL LVLTVLLYTA
LRCSVPPTEG ARAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEDPPKTDLM AFSPSLSQGP
DSAEEKQLSE SEYVGKPRQP NPDWRYSASL RAGMHSSVHL EEAGILRAGP GGPDQQWPTV
SSATPEPEAG EVSPPVGAGV NSNSWTFKYG PGNPKQSGPG ELPDKFIIPG SPAIISIRQE
PTNSQIDKSD FITFGKKEET KKKKKKKKGN KTQEKKEKGN STTDNSDQ*

mutated AA sequence

N/A

speed

1.05 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