PAX7

paired box 7, the group of Paired boxes|PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 1:18630846-18748866

Links

ENSG00000009709 ∙ NCBI:5081 ∙ OMIM:167410 ∙ HGNC:8621 ∙ Uniprot:P23759 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopathy, congenital, progressive, with scoliosis (Moderate), mode of inheritance: AR
• myopathy, congenital, progressive, with scoliosis (Strong), mode of inheritance: AR
• congenital myopathy with myasthenic-like onset (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital myopathy 19	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal	31092906

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PAX7 gene.

• Myopathy, congenital, progressive, with scoliosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAX7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				18	5	23
missense			33	1		34
nonsense		1				1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			1	2		3
non coding					1	1
Total	1	1	34	19	6

Variants in PAX7

This is a list of pathogenic ClinVar variants found in the PAX7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-18631624-G-T			Likely benign (Mar 01, 2023)
1-18634302-G-A		Myopathy, congenital, progressive, with scoliosis	Pathogenic (Apr 28, 2020)
1-18634310-C-T			Likely benign (Jun 01, 2022)
1-18634312-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-18634327-G-A		not specified	Uncertain significance (Dec 10, 2024)
1-18634329-G-T		not specified	Uncertain significance (Oct 04, 2022)
1-18634363-G-A		not specified	Uncertain significance (Nov 14, 2024)
1-18634383-C-T		Myopathy, congenital, progressive, with scoliosis	Pathogenic (Jul 16, 2024)
1-18634406-C-A		PAX7-related disorder	Likely benign (Feb 15, 2023)
1-18634418-C-G		not specified	Uncertain significance (Feb 16, 2023)
1-18634437-C-T		Myopathy, congenital, progressive, with scoliosis • Alveolar rhabdomyosarcoma;Myopathy, congenital, progressive, with scoliosis	Likely pathogenic (Jun 20, 2019)
1-18634446-C-T		not specified	Uncertain significance (Aug 22, 2023)
1-18634447-G-A		not specified	Uncertain significance (Nov 15, 2024)
1-18634493-G-A		PAX7-related disorder	Likely benign (Jul 25, 2022)
1-18634504-T-C		not specified	Uncertain significance (Jul 14, 2022)
1-18634508-G-A		PAX7-related disorder	Likely benign (May 31, 2022)
1-18634524-G-A			Uncertain significance (Jun 28, 2023)
1-18635124-C-T		Alveolar rhabdomyosarcoma • PAX7-related disorder • See cases	Uncertain significance (Dec 13, 2021)
1-18635125-G-A		PAX7-related disorder	Likely benign (Apr 01, 2022)
1-18635125-G-T		PAX7-related disorder	Likely benign (Aug 15, 2019)
1-18635126-G-A		not specified	Uncertain significance (Sep 22, 2023)
1-18635129-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-18635131-A-G			Likely benign (Aug 01, 2023)
1-18635187-T-C		Myopathy, congenital, progressive, with scoliosis	Uncertain significance (Nov 08, 2020)
1-18635197-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAX7	protein_coding	protein_coding	ENST00000375375	8	117861

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.145	0.855	125735	0	7	125742	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.804	292	333	0.876	0.0000194	3368
Missense in Polyphen		111	126.57	0.87698		1245
Synonymous	-1.50	167	144	1.16	0.00000919	1067
Loss of Function	2.96	5	18.8	0.265	8.95e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor playing a role in myogenesis through regulation of muscle precursor cells proliferation. {ECO:0000250|UniProtKB:P47239}.
• Disease: DISEASE: Rhabdomyosarcoma 2 (RMS2) [MIM:268220]: A form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchymal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. {ECO:0000269|PubMed:8187070}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration involving PAX7 is found in rhabdomyosarcoma. Translocation t(1;13)(p36;q14) with FOXO1. The resulting protein is a transcriptional activator. {ECO:0000269|PubMed:8187070}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);miRs in Muscle Cell Differentiation;Cell Differentiation - Index expanded;Neural Crest Differentiation (Consensus)

Recessive Scores

• pRec: 0.350

Intolerance Scores

• loftool: 0.00758
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.78

Haploinsufficiency Scores

• pHI: 0.899
• hipred: Y
• hipred_score: 0.789
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pax7
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; skeleton phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; neoplasm; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: pax7a
• Affected structure: xanthophore
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: chromatin remodeling;transcription by RNA polymerase II;anatomical structure morphogenesis;regulation of cell fate commitment;skeletal muscle satellite cell commitment;spinal cord association neuron differentiation;dorsal/ventral neural tube patterning;positive regulation of histone methylation;negative regulation of apoptotic process;regulation of protein binding;skeletal muscle tissue regeneration;positive regulation of transcription by RNA polymerase II;neuron fate commitment;embryonic skeletal system development;cartilage development;muscle tissue morphogenesis;positive regulation of myoblast proliferation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;RNA polymerase II general transcription initiation factor activity;sequence-specific DNA binding