PHAX

phosphorylated adaptor for RNA export

Basic information

Region (hg38): 5:126600925-126627252

Previous symbols: [ "RNUXA" ]

Links

ENSG00000164902

∙ NCBI:51808 ∙ OMIM:604924 ∙ HGNC:10241 ∙ Uniprot:Q9H814 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (44 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. These statistics are base on transcript: NM_000032177.4. 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				1 clinvar		1
missense			44 clinvar			44
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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