NXT1

nuclear transport factor 2 like export factor 1

Basic information

Region (hg38): 20:23350791-23354771

Links

ENSG00000132661 ∙ NCBI:29107 ∙ OMIM:605811 ∙ HGNC:15913 ∙ Uniprot:Q9UKK6 ∙ 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 NXT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXT1 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in NXT1

This is a list of pathogenic ClinVar variants found in the NXT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23354159-A-G		not specified	Uncertain significance (Jul 13, 2021)
20-23354190-A-G		not specified	Uncertain significance (Aug 17, 2022)
20-23354254-A-T		not specified	Uncertain significance (Mar 03, 2025)
20-23354260-C-A		not specified	Uncertain significance (Apr 17, 2023)
20-23354287-T-G		not specified	Uncertain significance (Jan 03, 2022)
20-23354355-A-G		not specified	Uncertain significance (Mar 20, 2024)
20-23354390-G-A		not specified	Uncertain significance (Sep 27, 2021)
20-23354411-A-G		not specified	Uncertain significance (Sep 08, 2024)
20-23354448-A-G		not specified	Uncertain significance (Feb 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXT1	protein_coding	protein_coding	ENST00000254998	1	4042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.646	0.330	125703	0	1	125704	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	34	84.4	0.403	0.00000514	927
Missense in Polyphen		6	25.635	0.23405		295
Synonymous	0.921	25	31.6	0.791	0.00000180	270
Loss of Function	1.69	0	3.34	0.00	1.44e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulator of protein export for NES-containing proteins (PubMed:10567585). Also plays a role in the nuclear export of U1 snRNA, tRNA, and mRNA (PubMed:10848583). The NXF1-NXT1 heterodimer is involved in the export of HSP70 mRNA in conjunction with ALYREF/THOC4 and THOC5 (PubMed:19165146, PubMed:11259602). {ECO:0000269|PubMed:10567585, ECO:0000269|PubMed:10848583, ECO:0000269|PubMed:11259602, ECO:0000269|PubMed:19165146}.
• Pathway: Influenza A - Homo sapiens (human);Ribosome biogenesis in eukaryotes - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Metabolism of RNA;Transport of Mature mRNA derived from an Intron-Containing Transcript;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.422
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxt1

Gene ontology

• Biological process: mRNA export from nucleus;protein import into nucleus;nucleocytoplasmic transport
• Cellular component: nuclear pore;nucleoplasm;cytoplasm;cytosol;nuclear speck;nuclear pore central transport channel
• Molecular function: protein binding;Ran GTPase binding;protein transporter activity