WIPI1

Chr 17

WD repeat domain, phosphoinositide interacting 1

Also known as: ATG18, ATG18A, WIPI49

NCBI Gene: 55062UniProt: Q5MNZ9

This gene encodes a WD40 repeat protein. Members of the WD40 repeat family are key components of many essential biologic functions. They regulate the assembly of multiprotein complexes by presenting a beta-propeller platform for simultaneous and reversible protein-protein interactions. Members of the WIPI subfamily of WD40 repeat proteins have a 7-bladed propeller structure and contain a conserved motif for interaction with phospholipids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

0
Active trials
77
ClinVar variants
11
Pathogenic / LP
1.3
Missense Z
0.65
LOEUF
6
Pubs (2 yr)
Clinical Summary— WIPI1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
11 Pathogenic / Likely Pathogenic· 61 VUS of 77 total submissions
Some data sources returned errors (1)

ensembl: TimeoutError: The operation was aborted due to timeout

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.
0.65LOEUF
pLI 0.002
Z-score 2.86
OE 0.37 (0.22–0.65)
Tolerant

Typical tolerance to LoF variation

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.
1.32Z-score
OE missense 0.77 (0.68–0.86)
196 obs / 255.3 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.0.37 (0.22–0.65)
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 (0.68–0.86)
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.0.84
0≤1.21.6
LoF obs/exp: 9 / 24.2Missense obs/exp: 196 / 255.3Syn Z: 1.28

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic10
Likely Pathogenic1
VUS61
Likely Benign2
Benign3
10
Pathogenic
1
Likely Pathogenic
61
VUS
2
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
10
0
10
Likely Pathogenic
0
0
1
0
1
VUS
0
58
3
0
61
Likely Benign
0
1
0
1
2
Benign
0
1
1
1
3
Total06015277

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

View in ClinVar →

Protein Context — Lollipop Plot

WIPI1 · 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
Identification of signature gene set as highly accurate determination of metabolic dysfunction-associated steatotic liver disease progression.
Oh S et al.·Clin Mol Hepatol
2024
Nitazoxanide alleviates experimental pulmonary fibrosis by inhibiting the development of cellular senescence.
Wang X et al.·Life Sci
2025
KLHL21, a novel gene that contributes to the progression of hepatocellular carcinoma.
Shi L et al.·BMC Cancer
2016Meta-analysis
Expression Patterns and Corepressor Function of Retinoic Acid-induced 2 in Prostate Cancer.
Besler K et al.·Clin Chem
2022
Autophagy-related prognostic signature for survival prediction of triple negative breast cancer.
Yang Q et al.·PeerJ
2022
Loci for insulin processing and secretion provide insight into type 2 diabetes risk.
Broadaway KA et al.·Am J Hum Genet
2023
Enhanced autophagic-lysosomal activity and increased BAG3-mediated selective macroautophagy as adaptive response of neuronal cells to chronic oxidative stress.
Chakraborty D et al.·Redox Biol
2019
Prognostic Signature of Osteosarcoma Based on 14 Autophagy-Related Genes.
Qi W et al.·Pathol Oncol Res
2021
Identification of a Ferroptosis-Related Prognostic Signature in Sepsis via Bioinformatics Analyses and Experiment Validation.
Zhu S et al.·Biomed Res Int
2022
Application of ex-vivo spheroid model system for the analysis of senescence and senolytic phenotypes in uterine leiomyoma.
Xie J et al.·Lab Invest
2018Functional
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Development and validation of the prediction model based on autophagy-associated genes in bronchopulmonary dysplasia
Liu Q et al.·Ann Med
2024Functional
WIPI1 promotes fission of endosomal transport carriers and formation of autophagosomes through distinct mechanisms
De Leo MG et al.·Autophagy
2021Functional
WIPI1 promotes osteosarcoma cell proliferation by inhibiting CDKN1A.
Ran T et al.·Gene
2021
Identification and validation of autophagy-related genes in Kawasaki disease
Zhu H et al.·Hereditas
2023
Identification and validation of molecular subtypes' characteristics in bladder urothelial carcinoma based on autophagy-dependent ferroptosis
Liu S et al.·Heliyon
2023
Identification of autophagy-related genes and immune cell infiltration characteristics in sepsis via bioinformatic analysis
Di C et al.·J Thorac Dis
2023
Top 6 full-text resultsSearch PubTator3 ↗

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

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients