INPP5B

inositol polyphosphate-5-phosphatase B, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 1:37860697-37947053

Links

ENSG00000204084

∙ NCBI:3633 ∙ OMIM:147264 ∙ HGNC:6077 ∙ Uniprot:P32019 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INPP5B gene.

not_specified (112 variants)
not_provided (11 variants)
INPP5B-related_disorder (10 variants)
Dent_disease_type_2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INPP5B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005540.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar		5
missense		1 clinvar	109 clinvar	5 clinvar	2 clinvar	117
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	1	109	11	2

Highest pathogenic variant AF is 0.0000173643

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INPP5B	protein_coding	protein_coding	ENST00000373024	23	86361

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.05e-16	0.979	124241	1	557	124799	0.00224

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	436	507	0.861	0.0000270	6050
Missense in Polyphen		150	200.32	0.74878		2508
Synonymous	1.22	175	197	0.890	0.0000110	1683
Loss of Function	2.54	33	52.9	0.623	0.00000291	575

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00212	0.00212
Ashkenazi Jewish	0.000304	0.000298
East Asian	0.000446	0.000389
Finnish	0.00390	0.00390
European (Non-Finnish)	0.00303	0.00302
Middle Eastern	0.000446	0.000389
South Asian	0.00200	0.00196
Other	0.000827	0.000825

dbNSFP

Source: dbNSFP

Function: FUNCTION: Hydrolyzes phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signaling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signaling events. {ECO:0000269|PubMed:7721860}.;
Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Signal Transduction;D-myo-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism;1D-myo-inositol hexakisphosphate biosynthesis II (mammalian);Inositol phosphate metabolism;3-phosphoinositide degradation;D-myo-inositol (1,4,5)-trisphosphate degradation;Metabolism;superpathway of inositol phosphate compounds;Rho GTPase cycle;Signaling by Rho GTPases;Synthesis of IP3 and IP4 in the cytosol;Inositol phosphate metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

pRec: 0.127

Intolerance Scores

loftool: 0.290
rvis_EVS: -0.91
rvis_percentile_EVS: 10.07

Haploinsufficiency Scores

pHI: 0.155
hipred: N
hipred_score: 0.415
ghis: 0.569

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.271

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Inpp5b
Phenotype: renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name: inpp5b
Affected structure: post-vent region
Phenotype tag: abnormal
Phenotype quality: kinked

Gene ontology

Biological process: signal transduction;positive regulation of GTPase activity;inositol phosphate metabolic process;inositol phosphate dephosphorylation;phosphatidylinositol dephosphorylation;regulation of small GTPase mediated signal transduction
Cellular component: endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cytosol;plasma membrane;membrane;phagocytic vesicle membrane;early endosome membrane
Molecular function: phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity;GTPase activator activity;protein binding;metal ion binding;inositol-1,4,5-trisphosphate 5-phosphatase activity;inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity