XPOT

exportin for tRNA, the group of Exportins

Basic information

Region (hg38): 12:64404392-64451125

Links

ENSG00000184575 ∙ NCBI:11260 ∙ OMIM:603180 ∙ HGNC:12826 ∙ Uniprot:O43592 ∙ 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 XPOT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XPOT 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						0
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in XPOT

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

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

Position	Type	Phenotype	Significance	ClinVar
12-64414968-C-G		not specified	Uncertain significance (Oct 12, 2021)
12-64414979-A-G		not specified	Uncertain significance (May 29, 2024)
12-64419070-T-G		not specified	Uncertain significance (Dec 28, 2022)
12-64419071-C-T		not specified	Uncertain significance (Jul 19, 2023)
12-64420236-C-T		not specified	Uncertain significance (Aug 14, 2023)
12-64420360-A-C		not specified	Uncertain significance (Dec 21, 2022)
12-64420363-A-G		not specified	Uncertain significance (Apr 15, 2024)
12-64420514-T-C		not specified	Uncertain significance (Nov 21, 2023)
12-64421245-T-G		not specified	Uncertain significance (Mar 17, 2023)
12-64421311-G-A		not specified	Uncertain significance (Jun 22, 2023)
12-64421457-C-T		not specified	Uncertain significance (Apr 18, 2023)
12-64424689-G-A		not specified	Uncertain significance (Jul 09, 2021)
12-64424699-G-A		not specified	Uncertain significance (May 01, 2024)
12-64424704-G-A		not specified	Uncertain significance (Apr 15, 2024)
12-64425046-A-G		not specified	Uncertain significance (Jun 29, 2022)
12-64425157-G-A		not specified	Uncertain significance (Oct 06, 2022)
12-64425395-G-A		not specified	Uncertain significance (Sep 25, 2023)
12-64425843-G-A		not specified	Uncertain significance (Apr 03, 2023)
12-64428061-A-T		not specified	Uncertain significance (Jul 26, 2022)
12-64430049-G-C		not specified	Uncertain significance (Sep 25, 2023)
12-64430121-G-A		not specified	Uncertain significance (Nov 10, 2022)
12-64430185-T-C		not specified	Uncertain significance (May 08, 2024)
12-64430205-T-G		not specified	Uncertain significance (Dec 12, 2023)
12-64430230-A-G		not specified	Uncertain significance (Jun 13, 2024)
12-64430256-G-A		not specified	Uncertain significance (Jul 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XPOT	protein_coding	protein_coding	ENST00000332707	24	46778

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00289	125726	0	17	125743	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	369	497	0.742	0.0000249	6335
Missense in Polyphen		62	118.77	0.52202		1523
Synonymous	1.13	162	181	0.893	0.00000948	1786
Loss of Function	5.88	9	56.9	0.158	0.00000282	669

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000151	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.000120	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000809	0.0000791
Middle Eastern	0.000120	0.000109
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the nuclear export of aminoacylated tRNAs. In the nucleus binds to tRNA 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 tRNA from the export receptor. XPOT 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:12138183, ECO:0000269|PubMed:9512417, ECO:0000269|PubMed:9660920}.
• Pathway: RNA transport - Homo sapiens (human);tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.383

Intolerance Scores

• loftool: 0.517
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.2

Haploinsufficiency Scores

• pHI: 0.580
• hipred: Y
• hipred_score: 0.708
• ghis: 0.627

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xpot
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Gene ontology

• Biological process: tRNA export from nucleus;tRNA re-export from nucleus
• Cellular component: nuclear pore;nucleoplasm;cytoplasm;cytosol;nuclear matrix
• Molecular function: tRNA binding;Ran GTPase binding