INPP1

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

Basic information

Region (hg38): 2:190343570-190371665

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.

• not_specified (52 variants)
• not_provided (2 variants)
• Cleft_palate (1 variants)
• Retinal_disorder (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. These statistics are base on transcript: NM_001128928.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			47	5		52
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	5	1

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