mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999999923898413 (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)

chr5:140230370A>CN/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

intron

DNA changes

g.49588A>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs369636

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1070	996	2066
ExAC	25467	-18167	7300

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)	-0.74	0.001
	-0.673	0
(flanking)	-0.021	0

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	49589	wt: 0.8948 / mu: 0.9022 (marginal change - not scored)	wt: GGGTAAGCAGAAGAC mu: GGGTCAGCAGAAGAC	GTAA\|gcag
Donor increased	49579	wt: 0.52 / mu: 0.77	wt: GCTCTGGCGAGGGTA mu: GCTCTGGCGAGGGTC	TCTG\|gcga
Donor increased	49592	wt: 0.26 / mu: 0.56	wt: TAAGCAGAAGACCGA mu: TCAGCAGAAGACCGA	AGCA\|gaag

distance from splice site

47194

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
719	950	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	894	REGION	6 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
799	802	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 6.	might get lost (downstream of altered splice site)
923	930	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

2543

theoretical NMD boundary in CDS

2492

length of CDS

2853

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)

49588

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

N/A

altered cDNA sequence snippet

N/A

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

N/A

speed

0.80 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