mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 3.89362792581957e-14 (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)

chr1:38397369C>TN/A show variant in all transcripts IGV

HGNC symbol

INPP5B

Ensembl transcript ID

ENST00000373024

Genbank transcript ID

NM_005540

UniProt peptide

P32019

alteration type

single base exchange

alteration region

intron

DNA changes

g.15361G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs35267671

database	homozygous (T/T)	heterozygous	allele carriers
1000G	397	985	1382
ExAC	3718	6258	9976

regulatory features

Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Egr1, Transcription Factor, Egr1 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Pbx3, Transcription Factor, Pbx3 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SP1, Transcription Factor, SP1 Transcription Factor Binding
SP2, Transcription Factor, SP2 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.604	0.999
	-0.183	0.953
(flanking)	1.193	0.957

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	15361	wt: 0.6960 / mu: 0.7328 (marginal change - not scored)	wt: GGGAAATGTCTGCCGCCGCCGGCTCTCGGGAGCGCAACACT mu: GGGAAATGTCTGCCGCCGCCAGCTCTCGGGAGCGCAACACT	gccg\|GCTC
Donor increased	15366	wt: 0.32 / mu: 0.53	wt: GGCTCTCGGGAGCGC mu: AGCTCTCGGGAGCGC	CTCT\|cggg

distance from splice site

216

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
340	353	STRAND		might get lost (downstream of altered splice site)
342	668	REGION	5-phosphatase (By similarity).	might get lost (downstream of altered splice site)
355	355	METAL	Magnesium.	might get lost (downstream of altered splice site)
364	367	HELIX		might get lost (downstream of altered splice site)
368	370	STRAND		might get lost (downstream of altered splice site)
375	382	STRAND		might get lost (downstream of altered splice site)
383	383	BINDING	Substrate.	might get lost (downstream of altered splice site)
383	383	METAL	Magnesium.	might get lost (downstream of altered splice site)
388	391	HELIX		might get lost (downstream of altered splice site)
398	409	HELIX		might get lost (downstream of altered splice site)
416	424	STRAND		might get lost (downstream of altered splice site)
427	434	STRAND		might get lost (downstream of altered splice site)
435	440	HELIX		might get lost (downstream of altered splice site)
441	450	STRAND		might get lost (downstream of altered splice site)
453	455	HELIX		might get lost (downstream of altered splice site)
459	460	REGION	Substrate binding.	might get lost (downstream of altered splice site)
460	469	STRAND		might get lost (downstream of altered splice site)
472	480	STRAND		might get lost (downstream of altered splice site)
485	487	HELIX		might get lost (downstream of altered splice site)
488	501	HELIX		might get lost (downstream of altered splice site)
509	511	STRAND		might get lost (downstream of altered splice site)
518	527	STRAND		might get lost (downstream of altered splice site)
537	545	HELIX		might get lost (downstream of altered splice site)
549	553	HELIX		might get lost (downstream of altered splice site)
557	563	HELIX		might get lost (downstream of altered splice site)
582	583	REGION	Substrate binding.	might get lost (downstream of altered splice site)
587	606	CONFLICT	GSDDWDTSEKCRAPAWCDRI -> RALTTGIPVRSAVLLPG VIGF (in Ref. 5; AA sequence).	might get lost (downstream of altered splice site)
588	591	STRAND		might get lost (downstream of altered splice site)
596	598	REGION	Substrate binding.	might get lost (downstream of altered splice site)
604	620	STRAND		might get lost (downstream of altered splice site)
626	629	STRAND		might get lost (downstream of altered splice site)
632	643	STRAND		might get lost (downstream of altered splice site)
669	782	REGION	ASH (By similarity).	might get lost (downstream of altered splice site)
821	993	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)
911	911	CONFLICT	G -> P (in Ref. 5; AA sequence).	might get lost (downstream of altered splice site)
990	990	MUTAGEN	C->S: Loss of prenylation and membrane localization.	might get lost (downstream of altered splice site)
990	990	LIPID	S-farnesyl cysteine (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

89 / 89

chromosome

strand

-1

last intron/exon boundary

2715

theoretical NMD boundary in CDS

2576

length of CDS

2742

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)

15361

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

38397369

original gDNA sequence snippet

GGGAAATGTCTGCCGCCGCCGGCTCTCGGGAGCGCAACACT

altered gDNA sequence snippet

GGGAAATGTCTGCCGCCGCCAGCTCTCGGGAGCGCAACACT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MDQSVAIQET LAEGEYCVIA VQGVLCEGDS RQSRLLGLVR YRLEHGGQEH ALFLYTHRRM
AITGDDVSLD QIVPVSRDFT LEEVSPDGEL YILGSDVTVQ LDTAELSLVF QLPFGSQTRM
FLHEVARACP GFDSATRDPE FLWLSRYRCA ELELEMPTPR GCNSALVTWP GYATIGGGGS
NFDGLRPNGK GVPMDQSSRG QDKPESLQPR QNKSKSEITD MVRSSTITVS DKAHILSMQK
FGLRDTIVKS HLLQKEEDYT YIQNFRFFAG TYNVNGQSPK ECLRLWLSNG IQAPDVYCVG
FQELDLSKEA FFFHDTPKEE EWFKAVSEGL HPDAKYAKVK LIRLVGIMLL LYVKQEHAAY
ISEVEAETVG TGIMGRMGNK GGVAIRFQFH NTSICVVNSH LAAHIEEYER RNQDYKDICS
RMQFCQPDPS LPPLTISNHD VILWLGDLNY RIEELDVEKV KKLIEEKDFQ MLYAYDQLKI
QVAAKTVFEG FTEGELTFQP TYKYDTGSDD WDTSEKCRAP AWCDRILWKG KNITQLSYQS
HMALKTSDHK PVSSVFDIGV RVVNDELYRK TLEEIVRSLD KMENANIPSV SLSKREFCFQ
NVKYMQLKVE SFTIHNGQVP CHFEFINKPD EESYCKQWLN ANPSRGFLLP DSDVEIDLEL
FVNKMTATKL NSGEDKIEDI LVLHLDRGKD YFLSVSGNYL PSCFGSPIHT LCYMREPILD
LPLETISELT LMPVWTGDDG SQLDSPMEIP KELWMMVDYL YRNAVQQEDL FQQPGLRSEF
EHIRDCLDTG MIDNLSASNH SVAEALLLFL ESLPEPVICY STYHNCLECS GNYTASKQVI
STLPIFHKNV FHYLMAFLRE LLKNSAKNHL DENILASIFG SLLLRNPAGH QKLDMTEKKK
AQEFIHQFLC NPL*

mutated AA sequence

N/A

speed

0.87 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