INPP1

Chr 2

inositol polyphosphate-1-phosphatase

NCBI Gene: 3628ENSG00000151689UniProt: P49441

This gene encodes the enzyme inositol polyphosphate-1-phosphatase, one of the enzymes involved in phosphatidylinositol signaling pathways. This enzyme removes the phosphate group at position 1 of the inositol ring from the polyphosphates inositol 1,4-bisphosphate and inositol 1,3,4-trisphophosphate. [provided by RefSeq, Jul 2008]

86
ClinVar variants
28
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— INPP1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
28 Pathogenic / Likely Pathogenic· 52 VUS of 86 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.27LOEUF
pLI 0.000
Z-score 0.81
OE 0.77 (0.48–1.27)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.18Z-score
OE missense 0.77 (0.68–0.88)
168 obs / 217.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.77 (0.48–1.27)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.77 (0.68–0.88)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.90
0≤1.21.6
LoF obs/exp: 11 / 14.3Missense obs/exp: 168 / 217.1Syn Z: 0.73

ClinVar Variant Classifications

86 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic27
Likely Pathogenic1
VUS52
Likely Benign5
Benign1
27
Pathogenic
1
Likely Pathogenic
52
VUS
5
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
27
0
27
Likely Pathogenic
0
0
1
0
1
VUS
1
50
1
0
52
Likely Benign
0
5
0
0
5
Benign
0
0
0
1
1
Total15529186

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

INPP1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
INPP1 up-regulation by miR-27a contributes to the growth, migration and invasion of human cervical cancer.
Li P et al.·J Cell Mol Med
2019
Exploring Genetic Variability at PI, GSK3, HPA, and Glutamatergic Pathways in Lithium Response: Association With IMPA2, INPP1, and GSK3B Genes.
Mitjans M et al.·J Clin Psychopharmacol
2015
Inositol phosphate recycling regulates glycolytic and lipid metabolism that drives cancer aggressiveness.
Benjamin DI et al.·ACS Chem Biol
2014
Construction and validation of a novel NAD(+) metabolism-related risk model for prognostic prediction in osteosarcoma.
Yu R et al.·J Orthop Res
2024Functional
The pharmacogenetics of lithium response depends upon clinical co-morbidity.
Bremer T et al.·Mol Diagn Ther
2007
A simultaneous LightCycler detection assay for five genetic polymorphisms influencing drug sensitivity.
Hiratsuka M et al.·Clin Biochem
2002
Manic-depressive illness: an association study with the inositol polyphosphate 1-phosphatase and serotonin transporter genes.
Piccardi MP et al.·Psychiatr Genet
2002
Lithium long-term treatment in mood disorders: clinical and genetic predictors.
Serretti A·Pharmacogenomics
2002Review
Integrated analysis of the genetic basis of suicidal behavior: what has been shown by structural genetic studies so far.
Bozorgmehr A et al.·Psychiatr Genet
2018
[Development of simplified and rapid detection assay for genetic polymorphisms influencing drug response and its clinical applications].
Hiratsuka M·Yakugaku Zasshi
2002Review
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools