PHAX

phosphorylated adaptor for RNA export

Basic information

Region (hg38): 5:126600924-126627252

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.

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.

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				1		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in PHAX

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

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

Position	Type	Phenotype	Significance	ClinVar
5-126600985-T-G		not specified	Uncertain significance (Feb 27, 2024)
5-126600987-G-A		not specified	Uncertain significance (Jun 11, 2021)
5-126600994-G-A		not specified	Uncertain significance (Aug 01, 2022)
5-126601017-G-T		not specified	Uncertain significance (Jan 04, 2022)
5-126603611-C-G		not specified	Uncertain significance (Mar 07, 2024)
5-126603613-C-T		not specified	Uncertain significance (Jun 02, 2023)
5-126603658-G-A		not specified	Uncertain significance (Sep 14, 2021)
5-126603724-G-A		not specified	Uncertain significance (Feb 27, 2023)
5-126603852-C-T		Aganglionic megacolon	Uncertain significance (May 16, 2019)
5-126603855-G-A		not specified	Uncertain significance (Jun 06, 2022)
5-126603890-G-C		not specified	Uncertain significance (Oct 25, 2023)
5-126603920-C-T			Likely benign (May 16, 2018)
5-126604003-A-C		not specified	Uncertain significance (Feb 05, 2024)
5-126608443-G-A		not specified	Uncertain significance (Jun 03, 2022)
5-126608449-G-A		not specified	Uncertain significance (Nov 14, 2023)
5-126608474-T-G		not specified	Uncertain significance (Nov 15, 2021)
5-126624696-A-G		not specified	Uncertain significance (Jan 17, 2024)

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

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