PHAX
phosphorylated adaptor for RNA export
Basic information
Region (hg38): 5:126600924-126627252
Previous symbols: [ "RNUXA" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (7 variants)
- not provided (1 variants)
- Aganglionic megacolon (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHAX gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 7 | 7 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in PHAX
This is a list of pathogenic ClinVar variants found in the PHAX region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-126600987-G-A | Inborn genetic diseases | Uncertain significance (Jun 11, 2021) | ||
| 5-126600994-G-A | Inborn genetic diseases | Uncertain significance (Aug 01, 2022) | ||
| 5-126601017-G-T | Inborn genetic diseases | Uncertain significance (Jan 04, 2022) | ||
| 5-126603613-C-T | Inborn genetic diseases | Uncertain significance (Jun 02, 2023) | ||
| 5-126603658-G-A | Inborn genetic diseases | Uncertain significance (Sep 14, 2021) | ||
| 5-126603724-G-A | Inborn genetic diseases | Uncertain significance (Feb 27, 2023) | ||
| 5-126603852-C-T | Aganglionic megacolon | Uncertain significance (May 16, 2019) | ||
| 5-126603855-G-A | Inborn genetic diseases | Uncertain significance (Jun 06, 2022) | ||
| 5-126603920-C-T | Likely benign (May 16, 2018) | |||
| 5-126608443-G-A | Inborn genetic diseases | Uncertain significance (Jun 03, 2022) | ||
| 5-126608474-T-G | Inborn genetic diseases | Uncertain significance (Nov 15, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PHAX | protein_coding | protein_coding | ENST00000297540 | 5 | 26985 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000304 | 0.936 | 125713 | 0 | 35 | 125748 | 0.000139 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.475 | 189 | 208 | 0.907 | 0.0000101 | 2623 |
| Missense in Polyphen | 29 | 51.018 | 0.56843 | 659 | ||
| Synonymous | -1.30 | 89 | 74.7 | 1.19 | 0.00000375 | 715 |
| Loss of Function | 1.77 | 12 | 20.7 | 0.580 | 0.00000146 | 208 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000279 | 0.000278 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000192 | 0.000185 |
| European (Non-Finnish) | 0.000145 | 0.000141 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000203 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: A phosphoprotein adapter involved in the XPO1-mediated U snRNA export from the nucleus. Bridge components required for U snRNA export, the cap binding complex (CBC)-bound snRNA on the one hand and the GTPase Ran in its active GTP-bound form together with the export receptor XPO1 on the other. Its phosphorylation in the nucleus is required for U snRNA export complex assembly and export, while its dephosphorylation in the cytoplasm causes export complex disassembly. It is recycled back to the nucleus via the importin alpha/beta heterodimeric import receptor. The directionality of nuclear export is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Its compartmentalized phosphorylation cycle may also contribute to the directionality of export. Binds strongly to m7G-capped U1 and U5 small nuclear RNAs (snRNAs) in a sequence-unspecific manner and phosphorylation- independent manner (By similarity). Plays also a role in the biogenesis of U3 small nucleolar RNA (snoRNA). Involved in the U3 snoRNA transport from nucleoplasm to Cajal bodies. Binds strongly to m7G-capped U3, U8 and U13 precursor snoRNAs and weakly to trimethylated (TMG)-capped U3, U8 and U13 snoRNAs. Binds also to telomerase RNA. {ECO:0000250, ECO:0000269|PubMed:15574332, ECO:0000269|PubMed:15574333}.;
- Pathway
- RNA transport - Homo sapiens (human);Gene expression (Transcription);snRNP Assembly;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Metabolism of RNA;Metabolism of non-coding RNA
(Consensus)
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- loftool
- 0.871
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.71
Haploinsufficiency Scores
- pHI
- 0.178
- hipred
- N
- hipred_score
- 0.331
- ghis
- 0.627
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.714
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Phax
- Phenotype
Gene ontology
- Biological process
- snRNA export from nucleus;protein transport;snRNA transcription by RNA polymerase II;nuclear export
- Cellular component
- nucleus;nucleoplasm;centrosome;cytosol;Cajal body;neuronal cell body
- Molecular function
- RNA binding;protein binding;toxic substance binding