INPP5F

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

Basic information

Region (hg38): 10:119726042-119829147

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.

not_specified (119 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. These statistics are base on transcript: NM_000014937.4. 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				1 clinvar		1
missense			117 clinvar	1 clinvar		118
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	117	2	0

Loading clinvar variants...

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