INPP5F

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

Basic information

Region (hg38): 10:119726041-119829147

Links

ENSG00000198825 ∙ NCBI:22876 ∙ OMIM:609389 ∙ HGNC:17054 ∙ Uniprot:Q9Y2H2 ∙ 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 INPP5F gene.

• Inborn genetic diseases (46 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INPP5F 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			45	1	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	1	1

Variants in INPP5F

This is a list of pathogenic ClinVar variants found in the INPP5F region.

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

Position	Type	Phenotype	Significance	ClinVar
10-119726276-A-G		not specified	Uncertain significance (Apr 26, 2023)
10-119726349-G-T		not specified	Uncertain significance (Jun 05, 2023)
10-119791566-C-T		not specified	Uncertain significance (Jun 26, 2023)
10-119791601-T-C		not specified	Uncertain significance (Feb 15, 2023)
10-119791605-C-T		not specified	Uncertain significance (Mar 06, 2023)
10-119791623-T-A		not specified	Uncertain significance (Oct 06, 2022)
10-119792016-G-A		not specified	Uncertain significance (Dec 20, 2022)
10-119796842-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-119797501-T-G		not specified	Uncertain significance (Jun 16, 2023)
10-119798561-C-T		not specified	Uncertain significance (Aug 08, 2022)
10-119804197-G-T		not specified	Uncertain significance (Feb 06, 2023)
10-119805392-T-C		not specified	Uncertain significance (Oct 18, 2021)
10-119805416-T-C		not specified	Uncertain significance (Aug 11, 2022)
10-119806439-G-A		not specified	Uncertain significance (Nov 15, 2021)
10-119806458-C-T		not specified	Uncertain significance (Apr 07, 2022)
10-119810182-A-G		not specified	Uncertain significance (Oct 18, 2021)
10-119810199-T-C		not specified	Uncertain significance (Feb 27, 2024)
10-119811826-C-A		not specified	Uncertain significance (Dec 06, 2022)
10-119811871-A-C		not specified	Uncertain significance (Jan 20, 2023)
10-119820877-G-A		not specified	Uncertain significance (Mar 30, 2022)
10-119820901-G-T		not specified	Uncertain significance (Dec 15, 2023)
10-119823187-G-C		not specified	Uncertain significance (Dec 18, 2023)
10-119823854-A-G		not specified	Uncertain significance (Mar 24, 2023)
10-119823862-A-G		not specified	Uncertain significance (Oct 22, 2021)
10-119823880-A-G		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INPP5F	protein_coding	protein_coding	ENST00000361976	20	103044

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.36e-7	1.00	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	503	596	0.844	0.0000304	7470
Missense in Polyphen		154	232.71	0.66176		3046
Synonymous	-0.154	218	215	1.01	0.0000115	2097
Loss of Function	4.60	23	62.2	0.370	0.00000371	700

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00100	0.000994
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000439	0.000435
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000433	0.000431
Middle Eastern	0.000439	0.000435
South Asian	0.000329	0.000327
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inositol 4-phosphatase which mainly acts on phosphatidylinositol 4-phosphate. May be functionally linked to OCRL, which converts phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol, for a sequential dephosphorylation of phosphatidylinositol 4,5-bisphosphate at the 5 and 4 position of inositol, thus playing an important role in the endocytic recycling (PubMed:25869669). Regulator of TF:TFRC and integrins recycling pathway, is also involved in cell migration mechanisms (PubMed:25869669). Modulates AKT/GSK3B pathway by decreasing AKT and GSK3B phosphorylation (PubMed:17322895). Negatively regulates STAT3 signaling pathway through inhibition of STAT3 phosphorylation and translocation to the nucleus (PubMed:25476455). Functionally important modulator of cardiac myocyte size and of the cardiac response to stress (By similarity). May play a role as negative regulator of axon regeneration after central nervous system injuries (By similarity). {ECO:0000250|UniProtKB:Q8CDA1, ECO:0000269|PubMed:17322895, ECO:0000269|PubMed:25476455, ECO:0000269|PubMed:25869669}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;Metabolism of lipids;3-phosphoinositide degradation;D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation;Metabolism;Synthesis of PIPs at the early endosome membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.952
• rvis_EVS: -0.79
• rvis_percentile_EVS: 12.57

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.414
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inpp5f
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: positive regulation of receptor recycling;phosphatidylinositol biosynthetic process;adult locomotory behavior;cardiac muscle hypertrophy in response to stress;phosphatidylinositol catabolic process;negative regulation of peptidyl-serine phosphorylation;negative regulation of tyrosine phosphorylation of STAT protein;phosphatidylinositol dephosphorylation;phosphatidylinositol-mediated signaling;negative regulation of axon regeneration;regulation of protein kinase B signaling;clathrin-dependent endocytosis;regulation of cell motility;regulation of endocytic recycling
• Cellular component: early endosome;clathrin-coated pit;axon;dendrite;early endosome membrane;neuronal cell body;clathrin-coated endocytic vesicle;recycling endosome
• Molecular function: protein binding;inositol monophosphate 1-phosphatase activity;phosphatidylinositol phosphate 5-phosphatase activity;phosphatidylinositol phosphate 4-phosphatase activity;protein homodimerization activity;phosphatidylinositol-4-phosphate phosphatase activity;inositol monophosphate 3-phosphatase activity;inositol monophosphate 4-phosphatase activity