INPP5J

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

Basic information

Region (hg38): 22:31122731-31134697

Previous symbols: [ "PIB5PA" ]

Links

ENSG00000185133 ∙ NCBI:27124 ∙ OMIM:606481 ∙ HGNC:8956 ∙ Uniprot:Q15735 ∙ 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 INPP5J gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INPP5J 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			55	1	2	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	56	1	2

Variants in INPP5J

This is a list of pathogenic ClinVar variants found in the INPP5J region.

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

Position	Type	Phenotype	Significance	ClinVar
22-31123063-G-A		not specified	Uncertain significance (Apr 27, 2022)
22-31123096-G-A		not specified	Uncertain significance (Apr 06, 2023)
22-31123097-C-T		not specified	Uncertain significance (Mar 11, 2025)
22-31123111-C-A		not specified	Uncertain significance (Feb 08, 2025)
22-31124846-T-G		not specified	Uncertain significance (Apr 08, 2024)
22-31125722-G-A			Likely benign (Nov 01, 2024)
22-31126386-G-T		not specified	Uncertain significance (Aug 16, 2022)
22-31126400-G-C		not specified	Likely benign (Jan 21, 2025)
22-31126412-G-C		not specified	Uncertain significance (Jan 22, 2025)
22-31126434-C-T		not specified	Uncertain significance (Oct 06, 2023)
22-31126449-G-A		not specified	Uncertain significance (Jan 23, 2024)
22-31126479-A-T		not specified	Uncertain significance (Sep 02, 2024)
22-31126482-G-A		not specified	Uncertain significance (Sep 02, 2024)
22-31126486-T-C		not specified	Uncertain significance (Jan 23, 2023)
22-31126620-G-A		not specified	Uncertain significance (May 02, 2024)
22-31126666-C-T		not specified	Uncertain significance (Dec 06, 2021)
22-31126963-G-A		not specified	Uncertain significance (Jan 26, 2023)
22-31126996-G-A		not specified	Uncertain significance (Feb 02, 2022)
22-31127012-C-G		not specified	Uncertain significance (Nov 22, 2021)
22-31127012-C-T		not specified	Uncertain significance (Jan 26, 2023)
22-31127029-G-A		not specified	Uncertain significance (Feb 24, 2025)
22-31127030-G-A		not specified	Uncertain significance (Jan 08, 2024)
22-31127372-G-A		not specified	Uncertain significance (Nov 15, 2024)
22-31127376-G-A		not specified	Uncertain significance (Aug 21, 2023)
22-31127381-C-T		not specified	Uncertain significance (Dec 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INPP5J	protein_coding	protein_coding	ENST00000404390	13	11966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-16	0.0500	124639	1	78	124718	0.000317

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.898	339	389	0.872	0.0000248	4108
Missense in Polyphen		139	170.29	0.81627		1746
Synonymous	1.79	125	153	0.816	0.00000993	1256
Loss of Function	0.773	27	31.7	0.852	0.00000183	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000698	0.000677
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000653	0.0000556
Finnish	0.0000950	0.0000928
European (Non-Finnish)	0.000183	0.000177
Middle Eastern	0.0000653	0.0000556
South Asian	0.00127	0.00121
Other	0.000363	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inositol 5-phosphatase, which converts inositol 1,4,5- trisphosphate to inositol 1,4-bisphosphate. Also converts phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 4- phosphate and inositol 1,3,4,5-tetrakisphosphate to inositol 1,3,4-trisphosphate in vitro. May be involved in modulation of the function of inositol and phosphatidylinositol polyphosphate- binding proteins that are present at membranes ruffles (By similarity). {ECO:0000250}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;D-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;Metabolism of lipids;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);3-phosphoinositide degradation;D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation;Metabolism;superpathway of inositol phosphate compounds;Synthesis of IP3 and IP4 in the cytosol;Inositol phosphate metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.363
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.444
• hipred: N
• hipred_score: 0.230
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.678

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inpp5j
• Phenotype: neoplasm; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;negative regulation of peptidyl-serine phosphorylation;inositol phosphate metabolic process;inositol phosphate dephosphorylation;phosphatidylinositol dephosphorylation
• Cellular component: ruffle;cytoplasm;cytosol;plasma membrane
• Molecular function: phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity;protein binding;SH3 domain binding;phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity;inositol-1,4,5-trisphosphate 5-phosphatase activity;inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity