PHOX2A
paired like homeobox 2A, the group of PRD class homeoboxes and pseudogenes
Basic information
Region (hg38): 11:72239077-72245664
Previous symbols: [ "ARIX", "FEOM2" ]
Links
Phenotypes
GenCC
Source:
- fibrosis of extraocular muscles, congenital, 2 (Strong), mode of inheritance: AR
- congenital fibrosis of extraocular muscles (Supportive), mode of inheritance: AD
- fibrosis of extraocular muscles, congenital, 2 (Strong), mode of inheritance: AR
- fibrosis of extraocular muscles, congenital, 2 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Fibrosis of extraocular muscles, congenital, 2 | 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 | Musculoskeletal | 11600883 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (25 variants)
- not_provided (5 variants)
- PHOX2A-related_disorder (5 variants)
- Fibrosis_of_extraocular_muscles,_congenital,_2 (3 variants)
- not_specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHOX2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005169.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 30 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 2 | 0 | 30 | 4 | 0 |
Highest pathogenic variant AF is 0.0000018273084
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PHOX2A | protein_coding | protein_coding | ENST00000298231 | 3 | 6588 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.490 | 0.491 | 125589 | 0 | 2 | 125591 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.60 | 63 | 110 | 0.571 | 0.00000585 | 1761 |
| Missense in Polyphen | 11 | 21.643 | 0.50825 | 217 | ||
| Synonymous | 2.29 | 29 | 49.5 | 0.586 | 0.00000267 | 625 |
| Loss of Function | 1.88 | 1 | 5.96 | 0.168 | 2.55e-7 | 94 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in regulating the specificity of expression of the catecholamine biosynthetic genes. Acts as a transcription activator/factor. Could maintain the noradrenergic phenotype.;
- Disease
- DISEASE: Fibrosis of extraocular muscles, congenital, 2 (CFEOM2) [MIM:602078]: A congenital ocular motility disorder marked by restrictive ophthalmoplegia affecting extraocular muscles innervated by the oculomotor and/or trochlear nerves. It is clinically characterized by anchoring of the eyes in downward gaze, ptosis, and backward tilt of the head. Congenital fibrosis of extraocular muscles type 2 may result from the defective development of the oculomotor (nIII), trochlear (nIV) and abducens (nVI) cranial nerve nuclei. {ECO:0000269|PubMed:11600883}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways
(Consensus)
Recessive Scores
- pRec
- 0.156
Haploinsufficiency Scores
- pHI
- 0.339
- hipred
- Y
- hipred_score
- 0.634
- ghis
- 0.471
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Phox2a
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- phox2a
- Affected structure
- pharyngeal arch
- Phenotype tag
- abnormal
- Phenotype quality
- has fewer parts of type
Gene ontology
- Biological process
- noradrenergic neuron differentiation;nervous system development;somatic motor neuron differentiation;oculomotor nerve formation;trochlear nerve formation;locus ceruleus development;midbrain development;regulation of respiratory gaseous exchange;positive regulation of transcription by RNA polymerase II;autonomic nervous system development;enteric nervous system development;sympathetic nervous system development;dopaminergic neuron differentiation
- Cellular component
- nuclear chromatin;nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity