XPO4

exportin 4, the group of Exportins

Basic information

Region (hg38): 13:20777329-20903048

Links

ENSG00000132953 ∙ NCBI:64328 ∙ OMIM:611449 ∙ HGNC:17796 ∙ Uniprot:Q9C0E2 ∙ 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 XPO4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XPO4 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	2
missense			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	1

Variants in XPO4

This is a list of pathogenic ClinVar variants found in the XPO4 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-20783742-C-G		not specified	Uncertain significance (Jun 26, 2023)
13-20783807-G-A		not specified	Uncertain significance (Dec 06, 2021)
13-20783808-T-C		not specified	Uncertain significance (Sep 17, 2021)
13-20783845-A-T		not specified	Uncertain significance (Sep 21, 2021)
13-20786991-A-G		not specified	Uncertain significance (Apr 09, 2024)
13-20788609-G-C		not specified	Uncertain significance (Jan 26, 2022)
13-20790537-T-A		not specified	Uncertain significance (Dec 14, 2021)
13-20796145-C-A		not specified	Uncertain significance (Nov 03, 2022)
13-20796187-G-A		not specified	Uncertain significance (Nov 21, 2023)
13-20796211-C-G		not specified	Uncertain significance (Jun 24, 2022)
13-20796830-C-A		not specified	Uncertain significance (Sep 14, 2022)
13-20796837-G-T		not specified	Uncertain significance (Nov 19, 2022)
13-20796843-T-C		not specified	Uncertain significance (Feb 14, 2023)
13-20796850-C-A		not specified	Uncertain significance (Nov 03, 2023)
13-20799320-A-T		not specified	Uncertain significance (Apr 20, 2024)
13-20800213-T-C		not specified	Uncertain significance (Mar 06, 2023)
13-20800229-C-T		not specified	Uncertain significance (Jun 21, 2021)
13-20800244-T-C		not specified	Uncertain significance (Mar 20, 2023)
13-20800267-A-G		not specified	Uncertain significance (Mar 07, 2023)
13-20800959-C-T		not specified	Uncertain significance (Nov 21, 2022)
13-20807466-G-C		not specified	Uncertain significance (Jun 16, 2024)
13-20807598-G-A		not specified	Uncertain significance (Dec 22, 2023)
13-20808490-T-C		not specified	Uncertain significance (May 14, 2024)
13-20808516-G-A		not specified	Uncertain significance (Oct 10, 2023)
13-20809106-T-A		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XPO4	protein_coding	protein_coding	ENST00000255305	23	125719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.83e-8	124770	0	7	124777	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.02	313	587	0.533	0.0000292	7548
Missense in Polyphen		46	106.65	0.43133		1389
Synonymous	1.20	190	212	0.895	0.0000106	2163
Loss of Function	6.96	4	64.2	0.0623	0.00000355	750

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.0000556	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the nuclear export of proteins (cargos) with broad substrate specificity. In the nucleus binds cooperatively to its cargo and to the GTPase Ran in its active GTP-bound form. Docking of this trimeric complex to the nuclear pore complex (NPC) is mediated through binding to nucleoporins. Upon transit of a nuclear export complex into the cytoplasm, disassembling of the complex and hydrolysis of Ran-GTP to Ran-GDP (induced by RANBP1 and RANGAP1, respectively) cause release of the cargo from the export receptor. XPO4 then return to the nuclear compartment and mediate another round of transport. 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. {ECO:0000269|PubMed:10944119, ECO:0000269|PubMed:16449645}.
• Pathway: eIF5A regulation in response to inhibition of the nuclear export system;TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.0261
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.97

Haploinsufficiency Scores

• pHI: 0.228
• hipred: Y
• hipred_score: 0.673
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.728

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Xpo4

Gene ontology

• Biological process: protein export from nucleus;positive regulation of protein export from nucleus
• Cellular component: nuclear pore;nucleoplasm;cytoplasm;cytosol
• Molecular function: nuclear export signal receptor activity;protein binding