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GeneBe

PHAX

phosphorylated adaptor for RNA export

Basic information

Region (hg38): 5:126600924-126627252

Previous symbols: [ "RNUXA" ]

Links

ENSG00000164902NCBI:51808OMIM:604924HGNC:10241Uniprot:Q9H814AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (9 variants)
  • not provided (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.

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
clinvar
1
missense
9
clinvar
9
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 9 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)3211963
5-126600987-G-A not specified Uncertain significance (Jun 11, 2021)2232275
5-126600994-G-A not specified Uncertain significance (Aug 01, 2022)2399820
5-126601017-G-T not specified Uncertain significance (Jan 04, 2022)2381605
5-126603611-C-G not specified Uncertain significance (Mar 07, 2024)3211962
5-126603613-C-T not specified Uncertain significance (Jun 02, 2023)2545020
5-126603658-G-A not specified Uncertain significance (Sep 14, 2021)2349837
5-126603724-G-A not specified Uncertain significance (Feb 27, 2023)2489824
5-126603852-C-T Aganglionic megacolon Uncertain significance (May 16, 2019)691477
5-126603855-G-A not specified Uncertain significance (Jun 06, 2022)2382766
5-126603890-G-C not specified Uncertain significance (Oct 25, 2023)3211965
5-126603920-C-T Likely benign (May 16, 2018)723334
5-126604003-A-C not specified Uncertain significance (Feb 05, 2024)3211966
5-126608443-G-A not specified Uncertain significance (Jun 03, 2022)2216702
5-126608449-G-A not specified Uncertain significance (Nov 14, 2023)3211967
5-126608474-T-G not specified Uncertain significance (Nov 15, 2021)2261462
5-126624696-A-G not specified Uncertain significance (Jan 17, 2024)3211961

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PHAXprotein_codingprotein_codingENST00000297540 526985
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000003040.9361257130351257480.000139
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4751892080.9070.00001012623
Missense in Polyphen2951.0180.56843659
Synonymous-1.308974.71.190.00000375715
Loss of Function1.771220.70.5800.00000146208

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002790.000278
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0001920.000185
European (Non-Finnish)0.0001450.000141
Middle Eastern0.0001090.000109
South Asian0.0002030.000196
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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