mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 5.50095036227114e-11 (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)

chr19:39915758C>GN/A show variant in all transcripts IGV

HGNC symbol

PLEKHG2

Ensembl transcript ID

ENST00000378550

Genbank transcript ID

N/A

UniProt peptide

Q9H7P9

alteration type

single base exchange

alteration region

intron

DNA changes

g.12534C>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs31728

database	homozygous (G/G)	heterozygous	allele carriers
1000G	873	1220	2093
ExAC	15219	2329	17548

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.594	0.095
	1.341	0.99
(flanking)	1.567	0.999

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 marginally increased	12537	wt: 0.4300 / mu: 0.4337 (marginal change - not scored)	wt: CCCAGCCACCACCTCCCCCAGCCAGGCGGCTCAGCTATGCC mu: CCCAGCCACCACCTCCCGCAGCCAGGCGGCTCAGCTATGCC	ccag\|CCAG
Acc gained	12533	0.54	mu: CAGCCCCAGCCACCACCTCCCGCAGCCAGGCGGCTCAGCTA	tccc\|GCAG

distance from splice site

120

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
593	600	COMPBIAS	Poly-Glu.	might get lost (downstream of altered splice site)
610	610	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1067	1184	COMPBIAS	Pro-rich.	might get lost (downstream of altered splice site)
1257	1257	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1261	1261	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1319	1328	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1344	1347	COMPBIAS	Poly-Gly.	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

326 / 326

chromosome

strand

last intron/exon boundary

2003

theoretical NMD boundary in CDS

1627

length of CDS

1734

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)

12534

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

39915758

original gDNA sequence snippet

AGCCCCAGCCACCACCTCCCCCAGCCAGGCGGCTCAGCTAT

altered gDNA sequence snippet

AGCCCCAGCCACCACCTCCCGCAGCCAGGCGGCTCAGCTAT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MPEGAQGLSL SKPSPSLGCG RRGEVCDCGT VCETRTAPAA PTMASPRGSG SSTSLSTVGS
EGDPAPGPTP ACSASRPEPL PGPPIRLHLS PVGIPGSARP SRLERVAREI VETERAYVRD
LRSIVEDYLG PLLDGGVLGL SVEQVGTLFA NIEDIYEFSS ELLEDLENSS SAGGIAECFV
QRSEDFDIYT LYCMNYPSSL ALLRELSLSP PAALWLQERQ AQLRHSLPLQ SFLLKPVQRI
LKYHLLLQEL GKHWAEGPGT GGREMVEEAI VSMTAVAWYI NDMKRKQEHA ARLQEVQRRL
GGWTGPELSA FGELVLEGAF RGGGGGGPRL RGGERLLFLF SRMLLVAKRR GLEYTYKGHI
FCCNLSVSES PRDPLGFKVS DLTIPKHRHL LQAKNQEEKR LWIHCLQRLF FENHPASIPA
KAKQVLLENS LHCAPKSKPV LEPLTPPLGS PRPRDARSFT PGRRNTAPSP GPSVIRRGRR
QSEPVKDPYV MFPQNAKPGF KHAGSEGELY PPESQPPVSG SAPPEDLEDA GPPTLDPSGT
SITEEILELL NQRGLRDPGE SMGLHRAQGA PDAPFHM*

mutated AA sequence

N/A

speed

0.99 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