PAX7

Chr 1ARSomatic

paired box 7

Also known as: CMYO19, CMYP19, HUP1, MYOSCO, PAX7B, RMS2

NCBI Gene: 5081ENSG00000009709UniProt: P23759OMIM: 167410

PAX7 encodes a transcription factor that regulates muscle stem cell proliferation and plays a critical role in myogenesis and muscle regeneration. Mutations cause autosomal recessive congenital myopathy 19, while somatic mutations are associated with alveolar rhabdomyosarcoma. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.558), reflecting its important role in muscle development and maintenance.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismAR/SomaticLOEUF 0.562 OMIM phenotypes
Clinical Summary— PAX7
🧬
Gene-Disease Validity (ClinGen)
congenital myopathy with myasthenic-like onset · ARModerate

Moderate evidence — consider for supplementary testing

⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.
📋
ClinVar Variants
21 unique Pathogenic / Likely Pathogenic· 88 VUS of 144 total submissions
💊
Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — PAX7
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.56LOEUF
pLI 0.145
Z-score 2.96
OE 0.27 (0.14–0.56)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.80Z-score
OE missense 0.88 (0.80–0.96)
292 obs / 333.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.27 (0.14–0.56)
0≤0.351.4
Missense OE0.88 (0.80–0.96)
0≤0.61.4
Synonymous OE1.16
0≤1.21.6
LoF obs/exp: 5 / 18.8Missense obs/exp: 292 / 333.3Syn Z: -1.50
DN
0.79top 25%
GOF
0.4875th %ile
LOF
0.54top 25%

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

144 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic19
Likely Pathogenic2
VUS88
Likely Benign22
Benign8
19
Pathogenic
2
Likely Pathogenic
88
VUS
22
Likely Benign
8
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
1
15
0
19
Likely Pathogenic
1
0
1
0
2
VUS
1
77
10
0
88
Likely Benign
0
2
1
19
22
Benign
0
0
1
7
8
Total5802826139

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

View in ClinVar →

Protein Context — Lollipop Plot

PAX7 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Biallelic PAX7 variants cause a novel Satellite Cell-opathy with progressive muscle involvement resembling facioscapulohumeral muscular dystrophy.
Ganassi M et al.·Cell Death Dis
2026
Expression Characteristics of PAX7 and Its Prognostic Correlation in Breast Cancer.
Silafu B et al.·Breast J
2026Open Access
Intracellular autofluorescence enables the isolation of viable, functional human muscle reserve cells with distinct Pax7 levels and stem cell states.
Bouche A et al.·Stem Cell Res Ther
2025Open AccessFunctional
Hemizygous mutation of Jmjd3 in muscle stem cells increases H3K27 methylation on Pax7 leading to impaired myogenesis.
Tidball JG et al.·Am J Physiol Cell Physiol
2025
Dual transcriptional activities of PAX3 and PAX7 spatially encode spinal cell fates through distinct gene networks.
Rondon R et al.·PLoS Biol
2025Open Access
Top 5 resultsSearch Europe PMC ↗

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