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

PCDHA4

Ensembl transcript ID

ENST00000530339

Genbank transcript ID

NM_018907

UniProt peptide

Q9UN74

alteration type

single base exchange

alteration region

intron

DNA changes

g.43712A>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 increased	43716	wt: 0.26 / mu: 0.56	wt: TAAGCAGAAGACCGA mu: TCAGCAGAAGACCGA	AGCA\|gaag
Donor increased	43703	wt: 0.52 / mu: 0.77	wt: GCTCTGGCGAGGGTA mu: GCTCTGGCGAGGGTC	TCTG\|gcga
Donor marginally increased	43713	wt: 0.8948 / mu: 0.9022 (marginal change - not scored)	wt: GGGTAAGCAGAAGAC mu: GGGTCAGCAGAAGAC	GTAA\|gcag

distance from splice site

41213

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
719	947	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
734	891	REGION	6 X 4 AA repeats of P-X-X-P.	might get lost (downstream of altered splice site)
796	799	REPEAT	PXXP 3.	might get lost (downstream of altered splice site)
829	832	REPEAT	PXXP 4.	might get lost (downstream of altered splice site)
870	873	REPEAT	PXXP 5.	might get lost (downstream of altered splice site)
888	891	REPEAT	PXXP 6.	might get lost (downstream of altered splice site)
920	927	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

2534

theoretical NMD boundary in CDS

2483

length of CDS

2844

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)

43712

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

MEFSWGSGQE SRRLLLLLLL LAAWEAGNGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKG RGGLLEVNLQ NGILFVNSRI DREELCRRSA ECSIHLEVIV DRPLQVFHVD
VEVRDINDNP PVFPATQKNL SIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFSL
EKPPDDELVK GLGLILRKSL DREEAPEIFL VLTATDGGKP ELTGTVQLLI TVLDANDNAP
AFDRTIYKVR LLENVPNGTL VIKLNASDLD EGLNGDIVYS FSNDISPNVK SKFHIDPITG
QIIVKGYIDF EESKSYEIIV EGIDKGQLPL SGHCRVIVEV EDNNDNVPDL EFKSLSLPIR
EDAPLGTVIA LISVSDKDMG VNGLVTCSLT SHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVTARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRA GGTGGAVSEL VPWSVGVGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDET DAPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RALVGAVGPD AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSALPTEG ACAPGKPTLV CSSAVGSWSY SQQRRPRVCS GEGPPKTDLM AFSPSLPDSR
DREDQLQTTE ESFAKPRQPN PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS
SATPEPEAGE VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP
TNSQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ*

mutated AA sequence

N/A

speed

0.88 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