MNX1

Chr 7

motor neuron and pancreas homeobox 1

Also known as: HB9, HLXB9, HOXHB9, SCRA1

NCBI Gene: 3110ENSG00000130675UniProt: P50219

This gene encodes a nuclear protein, which contains a homeobox domain and is a transcription factor. Mutations in this gene result in Currarino syndrome, an autosomic dominant congenital malformation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

Primary Disease Associations & Inheritance

UniProtCurrarino syndrome
0
ClinVar variants
0
Pathogenic / LP
0.79
pLI score
0
Active trials
Clinical Summary— MNX1
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.79) — some intolerance to loss-of-function variants.
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
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.
0.50LOEUF
pLI 0.788
Z-score 2.55
OE 0.11 (0.04–0.50)
Moderately constrained

More LoF-intolerant than ~75% 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.
0.73Z-score
OE missense 0.84 (0.73–0.97)
133 obs / 158.9 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.0.11 (0.04–0.50)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.84 (0.73–0.97)
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.0.93
0≤1.21.6
LoF obs/exp: 1 / 9.5Missense obs/exp: 133 / 158.9Syn Z: 0.49

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

MNX1 · protein map & ClinVar variants

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

Gene2Phenotype Curations

MNX1-related Currarino syndrome

definitive
ADLoss Of FunctionAbsent Gene Product
Dev. DisordersSkeletal
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

📖
GeneReview available — MNX1
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Currarino syndrome: a comprehensive genetic review of a rare congenital disorder.
Dworschak GC et al.·Orphanet J Rare Dis
2021Review
LncRNA MNX1-AS1: A novel oncogenic propellant in cancers.
Li T et al.·Biomed Pharmacother
2022Review
Loss of MNX1 Sensitizes Tumors to Cytotoxic T Cells by Degradation of PD-L1 mRNA.
Li Z et al.·Adv Sci (Weinh)
2025
MNX1-AS1 Promotes Phase Separation of IGF2BP1 to Drive c-Myc-Mediated Cell-Cycle Progression and Proliferation in Lung Cancer.
Zhu Q et al.·Cancer Res
2022
Clinical significance of long noncoding RNA MNX1-AS1 in human cancers: a meta-analysis of cohort studies and bioinformatics analysis based on TCGA datasets.
Chen K et al.·Bioengineered
2021Meta-analysis
Abnormally Activated MNX1 Promotes Tumor Growth and Osimertinib Resistance and Predicts Survival in EGFR-Mutant Lung Adenocarcinoma.
Gu W et al.·Drug Des Devel Ther
2025
Novel MNX1 mutations and genotype-phenotype analysis of patients with Currarino syndrome.
Han L et al.·Orphanet J Rare Dis
2020Cohort
MNX1 mutations causing neonatal diabetes: Review of the literature and report of a case with extra-pancreatic congenital defects presenting in severe diabetic ketoacidosis.
Aly HH et al.·J Diabetes Investig
2023Review
Pan-Cancer Analysis Identifies MNX1 and Associated Antisense Transcripts as Biomarkers for Cancer.
Ragusa D et al.·Cells
2022
Prognostic potential of MNX1-AS1 in chemotherapy of colorectal carcinoma.
Zhong G et al.·Cell Mol Biol (Noisy-le-grand)
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