MAGI1

Chr 3

membrane associated guanylate kinase, WW and PDZ domain containing 1

Also known as: AIP-3, AIP3, BAIAP1, BAP-1, BAP1, MAGI-1, MAGI-1b, Magi1d

NCBI Gene: 9223ENSG00000151276UniProt: Q96QZ7

The protein encoded by this gene is a member of the membrane-associated guanylate kinase homologue (MAGUK) family. MAGUK proteins participate in the assembly of multiprotein complexes on the inner surface of the plasma membrane at regions of cell-cell contact. The product of this gene may play a role as scaffolding protein at cell-cell junctions. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

181
ClinVar variants
10
Pathogenic / LP
0.56
pLI score
0
Active trials
Clinical Summary— MAGI1
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.56) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
10 Pathogenic / Likely Pathogenic· 156 VUS of 181 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
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.
0.33LOEUF
pLI 0.560
Z-score 6.16
OE 0.22 (0.15–0.33)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

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.
1.36Z-score
OE missense 0.87 (0.82–0.93)
785 obs / 900.1 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.0.22 (0.15–0.33)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.87 (0.82–0.93)
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.1.02
0≤1.21.6
LoF obs/exp: 16 / 72.7Missense obs/exp: 785 / 900.1Syn Z: -0.32

ClinVar Variant Classifications

181 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic10
VUS156
Likely Benign12
Benign3
10
Pathogenic
156
VUS
12
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
0
0
0
VUS
0
138
18
0
156
Likely Benign
0
5
4
3
12
Benign
0
1
1
1
3
Total0144334181

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

View in ClinVar →

Protein Context — Lollipop Plot

MAGI1 · 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
MAGI1, a Scaffold Protein with Tumor Suppressive and Vascular Functions.
Wörthmüller J et al.·Cells
2021Review
MAGI1 Prevents Senescence and Promotes the DNA Damage Response in ER(+) Breast Cancer.
Wörthmüller J et al.·Cells
2023
Genetic Variation and Gene Expression Levels of Tight Junction Genes Indicates Relationships Between PTEN as well as MAGI1 and Microscopic Colitis.
Norén E et al.·Dig Dis Sci
2018
Long noncoding RNA MAGI1-IT1 promoted invasion and metastasis of epithelial ovarian cancer via the miR-200a/ZEB axis.
Gao H et al.·Cell Cycle
2019
Quantitative proteomic analysis unveils a critical role of VARS1 in hepatocellular carcinoma aggressiveness through the modulation of MAGI1 expression.
Hermán-Sánchez N et al.·Mol Cancer
2025
Skin barrier damage after exposure to paraphenylenediamine.
Meisser SS et al.·J Allergy Clin Immunol
2020
Downregulation of MAGI1 associates with poor prognosis of hepatocellular carcinoma.
Zhang G et al.·J Invest Surg
2012
Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder.
Genetics of Personality Consortium et al.·JAMA Psychiatry
2015Meta-analysis
Whole genome sequence analysis of pulmonary function and COPD in 44,287 multi-ancestry participants.
Kim W et al.·Genome Biol
2026
Sex-Specific Genetic Determinants of Asthma-COPD Phenotype and COPD in Middle-Aged and Older Canadian Adults: An Analysis of CLSA Data.
Odimba U et al.·COPD
2023
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