INPP1

inositol polyphosphate-1-phosphatase, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 2:190343569-190371665

Links

ENSG00000151689 ∙ NCBI:3628 ∙ OMIM:147263 ∙ HGNC:6071 ∙ Uniprot:P49441 ∙ 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 INPP1 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INPP1 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	1
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in INPP1

This is a list of pathogenic ClinVar variants found in the INPP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-190360158-C-T		not specified	Uncertain significance (Apr 25, 2022)
2-190360171-AC-A		Cleft palate;Retinopathy	Uncertain significance (-)
2-190360201-C-T			Benign (Mar 30, 2018)
2-190360253-A-T		not specified	Uncertain significance (Jan 16, 2024)
2-190366729-G-T		not specified	Uncertain significance (Nov 19, 2022)
2-190366854-A-G		not specified	Likely benign (May 27, 2022)
2-190369216-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-190369222-C-T		not specified	Uncertain significance (Sep 23, 2023)
2-190370864-G-C		not specified	Uncertain significance (Feb 23, 2023)
2-190370891-T-C		not specified	Uncertain significance (Mar 28, 2023)
2-190370965-G-T		not specified	Uncertain significance (Dec 14, 2023)
2-190371047-A-C		not specified	Uncertain significance (Jan 10, 2023)
2-190371082-A-C		not specified	Uncertain significance (May 27, 2022)
2-190371142-A-C		not specified	Uncertain significance (Dec 07, 2021)
2-190371213-C-G		not specified	Uncertain significance (Dec 01, 2022)
2-190371252-G-T		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INPP1	protein_coding	protein_coding	ENST00000392329	5	28196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.90e-7	0.508	125547	1	199	125747	0.000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	168	217	0.774	0.0000108	2600
Missense in Polyphen		60	87.279	0.68745		1120
Synonymous	0.728	73	81.3	0.897	0.00000408	795
Loss of Function	0.808	11	14.3	0.769	6.97e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000692	0.000690
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000416	0.000416
European (Non-Finnish)	0.00123	0.00123
Middle Eastern	0.000109	0.000109
South Asian	0.000819	0.000817
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;Inositol phosphate metabolism;D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation;Metabolism;Inositol phosphate metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.170
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inpp1
• Phenotype: hematopoietic system phenotype; immune system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: phosphate-containing compound metabolic process;signal transduction;inositol phosphate metabolic process;phosphatidylinositol phosphorylation;inositol phosphate dephosphorylation
• Cellular component: cytosol
• Molecular function: inositol-1,4-bisphosphate 1-phosphatase activity;protein binding;metal ion binding;inositol-1,3,4-trisphosphate 1-phosphatase activity