mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.843723128784204 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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

ENST00000425673

Genbank transcript ID

N/A

UniProt peptide

Q9H7P9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3898C>G
cDNA.4223C>G
g.12534C>G

AA changes

P1300A Score: 27 explain score(s)

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

1300

frameshift

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

1386

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1300

mutated

not conserved

1300

Ptroglodytes

all identical

ENSPTRG00000010969

984

Mmulatta

all identical

ENSMMUG00000019369

1287

Fcatus

all identical

ENSFCAG00000010742

1274

Mmusculus

all identical

ENSMUSG00000037552

1312

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0050115

n/a

Celegans

no alignment

F32F2.1

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
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

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4074 / 4074

position (AA) of stopcodon in wt / mu AA sequence

1358 / 1358

position of stopcodon in wt / mu cDNA

4399 / 4399

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

2838

theoretical NMD boundary in CDS

2462

length of CDS

4074

coding sequence (CDS) position

3898

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

4223

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

AGCCCCAGCCACCACCTCCCCCAGCCAGGCGGCTCAGCTAT

altered cDNA sequence snippet

AGCCCCAGCCACCACCTCCCGCAGCCAGGCGGCTCAGCTAT

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 PGRRNTAKPG FKHAGSEGEL
YPPESQPPVS GSAPPEDLED AGPPTLDPSG TSITEEILEL LNQRGLRDPG PSTHDIPKFP
GDSQVPGDSE TLTFQALPSR DSSEEEEEEE EGLEMDERGP SPLHVLEGLE SSIAAEMPSI
PCLTKIPDVP NLPEIPSRCE IPEGSRLPSL SDISDVFEMP CLPAIPSVPN TPSLSSTPTL
SCDSWLQGPL QEPAEAPATR RELFSGSNPG KLGEPPSGGK AGPEEDEEGV SFTDFQPQDV
TQHQGFPDEL AFRSCSEIRS AWQALEQGQL ARPGFPEPLL ILEDSDLGGD SGSGKAGAPS
SERTASRVRE LARLYSERIQ QMQRAETRAS ANAPRRRPRV LAQPQPSPCL PQEQAEPGLL
PAFGHVLVCE LAFPLTCAQE SVPLGPAVWV QAAIPLSKQG GSPDGQGLHV SNLPKQDLPG
IHVSAATLLP EQGGSRHVQA PAATPLPKQE GPLHLQVPAL TTFSDQGHPE IQVPATTPLP
EHRSHMVIPA PSTAFCPEQG HCADIHVPTT PALPKEICSD FTVSVTTPVP KQEGHLDSES
PTNIPLTKQG GSRDVQGPDP VCSQPIQPLS WHGSSLDPQG PGDTLPPLPC HLPDLQIPGT
SPLPAHGSHL DHRIPANAPL SLSQELPDTQ VPATTPLPLP QVLTDIWVQA LPTSPKQGSL
PDIQGPAAAP PLPEPSLTDT QVQKLTPSLE QKSLIDAHVP AATPLPERGG SLDIQGLSPT
PVQTTMVLSK PGGSLASHVA RLESSDLTPP HSPPPSSRQL LGPNAAALSR YLAASYISQS
LARRQGPGGG APAASRGSWS SAPTSRASSP PPQPQPPPPP ARRLSYATTV NIHVGGGGRL
RPAKAQVRLN HPALLASTQE SMGLHRAQGA PDAPFHM*

mutated 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 PGRRNTAKPG FKHAGSEGEL
YPPESQPPVS GSAPPEDLED AGPPTLDPSG TSITEEILEL LNQRGLRDPG PSTHDIPKFP
GDSQVPGDSE TLTFQALPSR DSSEEEEEEE EGLEMDERGP SPLHVLEGLE SSIAAEMPSI
PCLTKIPDVP NLPEIPSRCE IPEGSRLPSL SDISDVFEMP CLPAIPSVPN TPSLSSTPTL
SCDSWLQGPL QEPAEAPATR RELFSGSNPG KLGEPPSGGK AGPEEDEEGV SFTDFQPQDV
TQHQGFPDEL AFRSCSEIRS AWQALEQGQL ARPGFPEPLL ILEDSDLGGD SGSGKAGAPS
SERTASRVRE LARLYSERIQ QMQRAETRAS ANAPRRRPRV LAQPQPSPCL PQEQAEPGLL
PAFGHVLVCE LAFPLTCAQE SVPLGPAVWV QAAIPLSKQG GSPDGQGLHV SNLPKQDLPG
IHVSAATLLP EQGGSRHVQA PAATPLPKQE GPLHLQVPAL TTFSDQGHPE IQVPATTPLP
EHRSHMVIPA PSTAFCPEQG HCADIHVPTT PALPKEICSD FTVSVTTPVP KQEGHLDSES
PTNIPLTKQG GSRDVQGPDP VCSQPIQPLS WHGSSLDPQG PGDTLPPLPC HLPDLQIPGT
SPLPAHGSHL DHRIPANAPL SLSQELPDTQ VPATTPLPLP QVLTDIWVQA LPTSPKQGSL
PDIQGPAAAP PLPEPSLTDT QVQKLTPSLE QKSLIDAHVP AATPLPERGG SLDIQGLSPT
PVQTTMVLSK PGGSLASHVA RLESSDLTPP HSPPPSSRQL LGPNAAALSR YLAASYISQS
LARRQGPGGG APAASRGSWS SAPTSRASSP PPQPQPPPPA ARRLSYATTV NIHVGGGGRL
RPAKAQVRLN HPALLASTQE SMGLHRAQGA PDAPFHM*

speed

1.33 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