PAX1

paired box 1, the group of Paired boxes

Basic information

Region (hg38): 20:21705659-21718481

Links

ENSG00000125813 ∙ NCBI:5075 ∙ OMIM:167411 ∙ HGNC:8615 ∙ Uniprot:P15863 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• otofaciocervical syndrome 2 (Limited), mode of inheritance: AD
• otofaciocervical syndrome 2 (Definitive), mode of inheritance: AR
• otofaciocervical syndrome 2 (Strong), mode of inheritance: AR
• otofaciocervical syndrome 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Otofaciocervical syndrome 2, with T-cell deficiency	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; The condition has been described as including thymic anomalies and T-cell immunodeficiency associated with severe infections, and awareness may allow preventative measures and early and aggressive management of infections	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic	23851939; 28657137; 29681087; 32111619

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PAX1 gene.

• not_provided (357 variants)
• Inborn_genetic_diseases (87 variants)
• Otofaciocervical_syndrome_2 (21 variants)
• PAX1-related_disorder (10 variants)
• not_specified (6 variants)
• Craniofacial_microsomia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001257096.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			9	127	4	140
missense	2	2	190	14	2	210
nonsense	3	4	1			8
start loss						0
frameshift	7	8	1			16
splice donor/acceptor (+/-2bp)		2				2
Total	12	16	201	141	6

Highest pathogenic variant AF is 0.0003927273

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAX1	protein_coding	protein_coding	ENST00000398485	5	10324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125571	0	4	125575	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.758	305	270	1.13	0.0000129	3303
Missense in Polyphen		83	95.948	0.86505		1136
Synonymous	-2.44	154	120	1.28	0.00000593	1203
Loss of Function	2.77	2	12.6	0.158	5.51e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000181	0.0000176
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column (By similarity). {ECO:0000250}.
• Disease: DISEASE: Otofaciocervical syndrome 2 (OTFCS2) [MIM:615560]: A disorder characterized by facial dysmorphism, cup-shaped low-set ears, preauricular fistulas, hearing loss, branchial defects, skeletal anomalies including vertebral defects, low-set clavicles, winged scapulae, sloping shoulders, and mild intellectual disability. {ECO:0000269|PubMed:23851939}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.302

Intolerance Scores

• loftool: 0.182
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.896

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: pax1b
• Affected structure: fin bud
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: skeletal system development;somitogenesis;transcription by RNA polymerase II;cell population proliferation;CD4-positive, alpha-beta T cell differentiation;CD8-positive, alpha-beta T cell differentiation;positive regulation of transcription by RNA polymerase II;thymus development;parathyroid gland development;bone morphogenesis;sclerotome development
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific