NXF1

nuclear RNA export factor 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 11:62792122-62806302

Links

ENSG00000162231 ∙ NCBI:10482 ∙ OMIM:602647 ∙ HGNC:8071 ∙ Uniprot:Q9UBU9 ∙ 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 NXF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXF1 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	16	2	0

Variants in NXF1

This is a list of pathogenic ClinVar variants found in the NXF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62792705-G-T			Likely benign (Jul 21, 2018)
11-62794271-C-G		not specified	Uncertain significance (Nov 06, 2023)
11-62796071-G-C		not specified	Uncertain significance (Apr 04, 2024)
11-62796097-T-A		not specified	Uncertain significance (Jun 05, 2023)
11-62796115-T-C		not specified	Uncertain significance (Jan 18, 2022)
11-62796154-G-A		not specified	Uncertain significance (Dec 16, 2021)
11-62797367-G-A		not specified	Uncertain significance (Nov 22, 2023)
11-62800398-C-T		not specified	Uncertain significance (May 11, 2022)
11-62801595-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-62801631-G-C			Likely benign (May 18, 2018)
11-62801756-G-C		not specified	Uncertain significance (Apr 20, 2024)
11-62801780-T-C		not specified	Likely benign (Dec 07, 2021)
11-62801956-G-A		not specified	Uncertain significance (Jan 02, 2024)
11-62802013-C-T		not specified	Uncertain significance (Oct 13, 2023)
11-62802181-A-G		not specified	Uncertain significance (Nov 08, 2022)
11-62803465-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-62803517-G-A		not specified	Uncertain significance (Jul 11, 2023)
11-62803877-C-A		not specified	Uncertain significance (Feb 28, 2023)
11-62803877-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-62803882-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-62803897-T-G		not specified	Uncertain significance (Jan 30, 2024)
11-62805332-T-C		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXF1	protein_coding	protein_coding	ENST00000532297	21	14180

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0237	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	231	376	0.614	0.0000233	4065
Missense in Polyphen		12	68.504	0.17517		855
Synonymous	0.656	132	142	0.930	0.00000837	1181
Loss of Function	5.03	7	42.4	0.165	0.00000250	447

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the nuclear export of mRNA species bearing retroviral constitutive transport elements (CTE) and in the export of mRNA from the nucleus to the cytoplasm (TAP/NFX1 pathway) (PubMed:10924507). The NXF1-NXT1 heterodimer is involved in the export of HSP70 mRNA in conjunction with ALYREF/THOC4 and THOC5 components of the TREX complex (PubMed:18364396, PubMed:19165146, PubMed:9660949). ALYREF/THOC4-bound mRNA is thought to be transferred to the NXF1-NXT1 heterodimer for export (PubMed:18364396, PubMed:19165146, PubMed:9660949). Also involved in nuclear export of m6A-containing mRNAs: interaction between SRSF3 and YTHDC1 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export (PubMed:28984244). {ECO:0000269|PubMed:10924507, ECO:0000269|PubMed:18364396, ECO:0000269|PubMed:19165146, ECO:0000269|PubMed:28984244, ECO:0000269|PubMed:9660949}.
• Pathway: Influenza A - Homo sapiens (human);Ribosome biogenesis in eukaryotes - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);mRNA Processing;Metabolism of RNA;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;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: 0.160

Intolerance Scores

• loftool: 0.250
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.587
• hipred: Y
• hipred_score: 0.746
• ghis: 0.532

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxf1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; 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); pigmentation phenotype

Zebrafish Information Network

• Gene name: nxf1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: RNA export from nucleus;mRNA export from nucleus;viral process;poly(A)+ mRNA export from nucleus
• Cellular component: transcription export complex;nucleus;nuclear pore;nucleoplasm;cytoplasm;cytosol;nuclear speck;nuclear inclusion body
• Molecular function: RNA binding;mRNA binding;protein binding