mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.953375779667687 (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)

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

HGNC symbol

INPP5B

Ensembl transcript ID

ENST00000373027

Genbank transcript ID

N/A

UniProt peptide

P32019

alteration type

single base exchange

alteration region

CDS

DNA changes

c.16G>A
cDNA.53G>A
g.15361G>A

AA changes

G6S Score: 56 explain score(s)

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

frameshift

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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000030681

250

Mmulatta

no alignment

ENSMMUG00000023277

n/a

Fcatus

no alignment

ENSFCAG00000011021

n/a

Mmusculus

all identical

ENSMUSG00000028894

250

Ggallus

no alignment

ENSGALG00000001606

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000042111

n/a

Dmelanogaster

no alignment

FBgn0023508

n/a

Celegans

no alignment

C16C2.3

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
22	148	DOMAIN	PH.	might get lost (downstream of altered splice site)
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	METAL	Magnesium.	might get lost (downstream of altered splice site)
383	383	BINDING	Substrate.	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	LIPID	S-farnesyl cysteine (Potential).	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)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2250 / 2250

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

750 / 750

position of stopcodon in wt / mu cDNA

2287 / 2287

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

38 / 38

chromosome

strand

-1

last intron/exon boundary

2172

theoretical NMD boundary in CDS

2084

length of CDS

2250

coding sequence (CDS) position

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

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

GGGAAATGTCTGCCGCCGCCGGCTCTCGGGAGCGCAACACT

altered cDNA sequence snippet

GGGAAATGTCTGCCGCCGCCAGCTCTCGGGAGCGCAACACT

wildtype AA sequence

MSAAAGSRER NTAGGSNFDG LRPNGKGVPM DQSSRGQDKP ESLQPRQNKS KSEITDMVRS
STITVSDKAH ILSMQKFGLR DTIVKSHLLQ KEEDYTYIQN FRFFAGTYNV NGQSPKECLR
LWLSNGIQAP DVYCVGFQEL DLSKEAFFFH DTPKEEEWFK AVSEGLHPDA KYAKVKLIRL
VGIMLLLYVK QEHAAYISEV EAETVGTGIM GRMGNKGGVA IRFQFHNTSI CVVNSHLAAH
IEEYERRNQD YKDICSRMQF CQPDPSLPPL TISNHDVILW LGDLNYRIEE LDVEKVKKLI
EEKDFQMLYA YDQLKIQVAA KTVFEGFTEG ELTFQPTYKY DTGSDDWDTS EKCRAPAWCD
RILWKGKNIT QLSYQSHMAL KTSDHKPVSS VFDIGVRVVN DELYRKTLEE IVRSLDKMEN
ANIPSVSLSK REFCFQNVKY MQLKVESFTI HNGQVPCHFE FINKPDEESY CKQWLNANPS
RGFLLPDSDV EIDLELFVNK MTATKLNSGE DKIEDILVLH LDRGKDYFLS VSGNYLPSCF
GSPIHTLCYM REPILDLPLE TISELTLMPV WTGDDGSQLD SPMEIPKELW MMVDYLYRNA
VQQEDLFQQP GLRSEFEHIR DCLDTGMIDN LSASNHSVAE ALLLFLESLP EPVICYSTYH
NCLECSGNYT ASKQVISTLP IFHKNVFHYL MAFLRELLKN SAKNHLDENI LASIFGSLLL
RNPAGHQKLD MTEKKKAQEF IHQFLCNPL*

mutated AA sequence

MSAAASSRER NTAGGSNFDG LRPNGKGVPM DQSSRGQDKP ESLQPRQNKS KSEITDMVRS
STITVSDKAH ILSMQKFGLR DTIVKSHLLQ KEEDYTYIQN FRFFAGTYNV NGQSPKECLR
LWLSNGIQAP DVYCVGFQEL DLSKEAFFFH DTPKEEEWFK AVSEGLHPDA KYAKVKLIRL
VGIMLLLYVK QEHAAYISEV EAETVGTGIM GRMGNKGGVA IRFQFHNTSI CVVNSHLAAH
IEEYERRNQD YKDICSRMQF CQPDPSLPPL TISNHDVILW LGDLNYRIEE LDVEKVKKLI
EEKDFQMLYA YDQLKIQVAA KTVFEGFTEG ELTFQPTYKY DTGSDDWDTS EKCRAPAWCD
RILWKGKNIT QLSYQSHMAL KTSDHKPVSS VFDIGVRVVN DELYRKTLEE IVRSLDKMEN
ANIPSVSLSK REFCFQNVKY MQLKVESFTI HNGQVPCHFE FINKPDEESY CKQWLNANPS
RGFLLPDSDV EIDLELFVNK MTATKLNSGE DKIEDILVLH LDRGKDYFLS VSGNYLPSCF
GSPIHTLCYM REPILDLPLE TISELTLMPV WTGDDGSQLD SPMEIPKELW MMVDYLYRNA
VQQEDLFQQP GLRSEFEHIR DCLDTGMIDN LSASNHSVAE ALLLFLESLP EPVICYSTYH
NCLECSGNYT ASKQVISTLP IFHKNVFHYL MAFLRELLKN SAKNHLDENI LASIFGSLLL
RNPAGHQKLD MTEKKKAQEF IHQFLCNPL*

speed

0.76 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