mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 9.21994670376815e-12 (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)

chr5:140793007A>GN/A show variant in all transcripts IGV

HGNC symbol

PCDHGA4

Ensembl transcript ID

ENST00000571252

Genbank transcript ID

NM_018917

UniProt peptide

Q9Y5G9

alteration type

single base exchange

alteration region

intron

DNA changes

g.58240A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs4912751

database	homozygous (G/G)	heterozygous	allele carriers
1000G	919	947	1866
ExAC	14948	2871	17819

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2AZ, Histone, Histone 2A variant Z
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.342	0.998
	0.243	0.986
(flanking)	2.96	0.987

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
Acc gained	58249	0.30	mu: GCGGCAGCTTGGTCACCGCGGGCAGGATAGACCGGGAGGAG	gcgg\|GCAG
Donor gained	58234	0.49	mu: GCGGCAGCTTGGTCA	GGCA\|gctt

distance from splice site

55819

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
714	931	TOPO_DOM	Cytoplasmic (Potential).	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

2570

theoretical NMD boundary in CDS

2519

length of CDS

2796

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)

58240

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

140793007

original gDNA sequence snippet

ACCCGCGCAGCGGCAGCTTGATCACCGCGGGCAGGATAGAC

altered gDNA sequence snippet

ACCCGCGCAGCGGCAGCTTGGTCACCGCGGGCAGGATAGAC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAAPPARPDH TRLLQICLLL GVLVEIRAEQ ILYSVFEEQE EGSVVGNIAK DLGLAPRELA
ERGVRIVSRG RTQLFALNPR SGTLVTAGRI DREELCDRSP NCVTNLEILL EDTVKILRVE
VEIIDVNDNP PSFGTEQREI KVAENENPGA RFPLPEAFDP DVGVNSLQGY QLNSNGYFSL
DVQSGADGIK YPELVLERAL DREEEAVHHL VLTAFDGGDP VRSGTARILI ILVDTNDNAP
VFTQPEYHVS VRENVPVGTR LLTVKATDPD EGANGDVTYS FRKVRDKISQ LFQLNSLSGD
ITILGGLDYE DSGFYDIDVE AHDGPGLRAR SKVLVTVLDE NDNAPEVTVT SLTSSVQESS
SPGTVIALFN VHDSDSGGNG LVTCSIPDNL PFTLEKTYGN YYRLLTHRTL DREEVSEYNI
TVTATDQGTP PLSTETHISL QVMDINDNPP TFPHASYSAY IPENNPRGAS ILSMTAQDPD
SGDNARITYS LAEDTFQGAP LSSYVSINSN TGILYALCSF DYEQFRDLQL LMTASDSGDP
PLSSNVSLSL FVLDQNDNVP EILYPTFPTD GSTGVELAPR SADSGYLVTK VVAVDRDSGQ
NAWLSYSLLK SSEPGLFAVG LHTGEVRTAR ALLDRDALKQ RLVVVVQDHG QPPLSATVTL
TVAVADSIPD VLADLGSLKP SADPDDSGLT LYLVVAVAAV SCVFLAFVTV LLALKLRRWH
KSRLLHAEGS RLAGVPASHF VGVDGVRAFL QTYSHEVSLT ADSRKSHLIF SQPSYADTLI
SRESCEKSEP LLITQDLLET KGDPNLQQAP PNTDWRFSQA QRPGTSGSQN GDDTGTWPNN
QFDTEMLQAM ILASASEAAD GSSTLGGGAG TMGLSARYGP QFTLQHVPDY RQNVYIPGSN
ATLTNAAGKR DGKAPAGGNG NKKKSGKKEK K*

mutated AA sequence

N/A

speed

0.93 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