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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			69	5	3	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					37	37
Total	0	0	69	6	42

Variants in INPP5B

This is a list of pathogenic ClinVar variants found in the INPP5B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-37862263-CAG-C			Benign (May 12, 2021)
1-37862310-G-T			Benign (May 04, 2021)
1-37862358-T-G		not specified	Uncertain significance (Nov 03, 2023)
1-37862359-T-C		not specified	Uncertain significance (Nov 03, 2023)
1-37862389-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-37862482-G-T			Benign (May 12, 2021)
1-37862482-GAC-G			Benign (May 12, 2021)
1-37864327-C-G			Benign (May 04, 2021)
1-37864362-C-T		not specified	Likely benign (Dec 28, 2022)
1-37864384-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-37864405-T-G		not specified	Uncertain significance (Nov 02, 2023)
1-37865793-C-T		not specified	Uncertain significance (Jul 13, 2022)
1-37865814-T-C		not specified	Uncertain significance (Dec 28, 2024)
1-37865823-T-C		not specified	Uncertain significance (Jun 11, 2021)
1-37865886-C-A		not specified	Uncertain significance (Dec 16, 2023)
1-37866127-C-G			Benign (May 12, 2021)
1-37866385-T-TTC			Benign (May 13, 2021)
1-37866385-T-TTCTC			Benign (May 12, 2021)
1-37866385-T-TTCTCTCTC			Benign (May 12, 2021)
1-37866402-TCTCTCACA-T			Benign (May 12, 2021)
1-37866402-TCTCTCACACA-T			Benign (May 14, 2021)
1-37866468-C-T		not specified	Uncertain significance (Nov 09, 2023)
1-37866470-A-G		not specified	Uncertain significance (Oct 09, 2024)
1-37866526-T-A		not specified	Uncertain significance (Dec 20, 2023)
1-37866664-A-AC			Benign (May 12, 2021)

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-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);Inositol phosphate metabolism;3-phosphoinositide degradation;D-<i>myo</i>-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