INPP4B

inositol polyphosphate-4-phosphatase type II B, the group of C2 domain containing|Phosphoinositide phosphatases

Basic information

Region (hg38): 4:142023159-142847432

Links

ENSG00000109452 ∙ NCBI:8821 ∙ OMIM:607494 ∙ HGNC:6075 ∙ Uniprot:O15327 ∙ 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 INPP4B gene.

• Inborn genetic diseases (29 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INPP4B 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						0
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in INPP4B

This is a list of pathogenic ClinVar variants found in the INPP4B region.

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

Position	Type	Phenotype	Significance	ClinVar
4-142028804-G-T		not specified	Uncertain significance (Jun 06, 2023)
4-142028816-G-T		not specified	Uncertain significance (May 27, 2022)
4-142028851-C-A		not specified	Uncertain significance (Aug 22, 2023)
4-142028870-C-T		not specified	Uncertain significance (Sep 01, 2021)
4-142082064-T-G		not specified	Uncertain significance (Jul 14, 2021)
4-142082137-T-C		not specified	Uncertain significance (May 17, 2023)
4-142086235-T-C		not specified	Uncertain significance (Sep 29, 2022)
4-142086239-C-T		not specified	Uncertain significance (Sep 26, 2022)
4-142086248-G-A		not specified	Uncertain significance (Jan 29, 2024)
4-142122189-C-T		not specified	Uncertain significance (Feb 14, 2024)
4-142122201-C-T		not specified	Uncertain significance (Sep 13, 2023)
4-142122213-C-T		not specified	Uncertain significance (Jul 26, 2022)
4-142122229-C-T		not specified	Uncertain significance (Dec 22, 2023)
4-142122243-C-T		not specified	Uncertain significance (Jun 24, 2022)
4-142123360-G-A		not specified	Uncertain significance (Dec 27, 2023)
4-142124619-G-A		not specified	Uncertain significance (Feb 14, 2023)
4-142124760-T-A		not specified	Uncertain significance (Sep 14, 2022)
4-142145852-A-T		not specified	Likely benign (Oct 05, 2023)
4-142145984-C-T		not specified	Uncertain significance (Dec 17, 2023)
4-142145991-C-G		not specified	Uncertain significance (Dec 28, 2023)
4-142160380-G-A		not specified	Uncertain significance (Nov 10, 2022)
4-142160405-C-G		not specified	Likely benign (Jun 07, 2023)
4-142160426-C-T		not specified	Uncertain significance (Feb 10, 2022)
4-142160441-C-T		not specified	Uncertain significance (Mar 20, 2023)
4-142160532-A-T		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INPP4B	protein_coding	protein_coding	ENST00000513000	23	824273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.552	0.448	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	410	480	0.855	0.0000233	6080
Missense in Polyphen		126	178.51	0.70584		2347
Synonymous	-0.139	181	179	1.01	0.00000930	1698
Loss of Function	5.37	12	55.0	0.218	0.00000308	647

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000273	0.000272
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000546	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of the 4-position phosphate of phosphatidylinositol 3,4-bisphosphate, inositol 1,3,4- trisphosphate and inositol 1,4-bisphosphate.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;Phosphatidylinositol Phosphate Metabolism;Joubert syndrome;VEGFA-VEGFR2 Signaling Pathway;Metabolism of lipids;Inositol phosphate metabolism;3-phosphoinositide degradation;Metabolism;Inositol phosphate metabolism;Synthesis of PIPs at the early endosome membrane;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.575
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.6

Haploinsufficiency Scores

• pHI: 0.0492
• hipred: N
• hipred_score: 0.492
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inpp4b
• Phenotype: cellular phenotype; hematopoietic system phenotype; immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;signal transduction;dephosphorylation;phosphatidylinositol-3-phosphate biosynthetic process;inositol phosphate metabolic process
• Cellular component: cytoplasm;cytosol
• Molecular function: protein binding;phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity;inositol-1,3,4-trisphosphate 4-phosphatase activity;phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity;inositol-3,4-bisphosphate 4-phosphatase activity