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

PCDHA6

Ensembl transcript ID

ENST00000529310

Genbank transcript ID

NM_018909

UniProt peptide

Q9UN73

alteration type

single base exchange

alteration region

intron

DNA changes

g.22808A>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	22809	wt: 0.8948 / mu: 0.9022 (marginal change - not scored)	wt: GGGTAAGCAGAAGAC mu: GGGTCAGCAGAAGAC	GTAA\|gcag
Donor increased	22812	wt: 0.26 / mu: 0.56	wt: TAAGCAGAAGACCGA mu: TCAGCAGAAGACCGA	AGCA\|gaag
Donor increased	22799	wt: 0.52 / mu: 0.77	wt: GCTCTGGCGAGGGTA mu: GCTCTGGCGAGGGTC	TCTG\|gcga

distance from splice site

20300

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)
799	802	REPEAT	PXXP 1.	might get lost (downstream of altered splice site)
799	894	REGION	4 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 4.	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

115 / 115

chromosome

strand

last intron/exon boundary

2657

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)

22808

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

MVFTPEDRLG KQCLLLPLLL LAAWKVGSGQ LHYSVPEEAK HGTFVGRIAQ DLGLELAELV
PRLFRMASKD REDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVRDINDNP PLFPVEEQRV LIYESRLPDS VFPLEGASDA DVGSNSILTY KLSSSEYFGL
DVKINSDDNK QIGLLLKKSL DREEAPAHNL FLTATDGGKP ELTGTVQLLV TVLDVNDNAP
TFEQSEYEVR IFENADNGTT VIRLNASDRD EGANGAISYS FNSLVAAMVI DHFSIDRNTG
EIVIRGNLDF EQENLYKILI DATDKGHPPM AGHCTVLVRI LDKNDNVPEI ALTSLSLPVR
EDAQFGTVIA LISVNDLDSG ANGQVNCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS LSVEVADMND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYISV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTGGAVSEL VPRSLGAGQV VAKVRAVDAD
SGYNAWLSYE LQPPASSARF PFRVGLYTGE ISTTRVLDEA DSPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RASVGAAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSAPPTEG ACTADKPTLV CSSAVGSWSY SQQRRQRVCS GEGPPKMDLM AFSPSLSPCP
IMMGKAENQD LNEDHDAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

mutated AA sequence

N/A

speed

0.76 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