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

PCDHA1

Ensembl transcript ID

ENST00000504120

Genbank transcript ID

NM_018900

UniProt peptide

Q9Y5I3

alteration type

single base exchange

alteration region

intron

DNA changes

g.17183G>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 increased	17188	wt: 0.60 / mu: 0.77	wt: GCTCTGGAGAGGGGT mu: ACTCTGGAGAGGGGT	TCTG\|gaga
Donor marginally increased	17175	wt: 0.2619 / mu: 0.2827 (marginal change - not scored)	wt: CAGCAGAGGGTGTGC mu: CAGCAGAGGGTGTAC	GCAG\|aggg
Donor marginally increased	17187	wt: 0.9168 / mu: 0.9607 (marginal change - not scored)	wt: TGCTCTGGAGAGGGG mu: TACTCTGGAGAGGGG	CTCT\|ggag
Donor increased	17185	wt: 0.37 / mu: 0.73	wt: TGTGCTCTGGAGAGG mu: TGTACTCTGGAGAGG	TGCT\|ctgg

distance from splice site

14789

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	5 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
799	802	REPEAT	PXXP 2.	might get lost (downstream of altered splice site)
832	835	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
873	876	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
891	894	REPEAT	PXXP 5.	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)

17183

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

MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSVPPTEG AYVPGKPTLV CSSALGSWSN SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL
NTSERNEQPE ANLDLSGNPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

mutated AA sequence

N/A

speed

0.63 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