NXF3

nuclear RNA export factor 3

Basic information

Region (hg38): X:103075810-103093143

Links

ENSG00000147206 ∙ NCBI:56000 ∙ OMIM:300316 ∙ HGNC:8073 ∙ Uniprot:Q9H4D5 ∙ 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 NXF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXF3 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			23	6		29
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	23	6	0

Variants in NXF3

This is a list of pathogenic ClinVar variants found in the NXF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-103077628-C-G		not specified	Uncertain significance (Mar 08, 2024)
X-103077650-G-T		not specified	Uncertain significance (Oct 26, 2021)
X-103077655-A-T		not specified	Uncertain significance (Dec 28, 2024)
X-103077715-G-A		not specified	Likely benign (May 30, 2024)
X-103077736-C-T		not specified	Uncertain significance (Sep 15, 2021)
X-103078561-T-G		not specified	Uncertain significance (Feb 26, 2025)
X-103078603-C-T		not specified	Uncertain significance (Oct 18, 2021)
X-103079263-C-T		not specified	Uncertain significance (Dec 19, 2023)
X-103079366-T-C		not specified	Likely benign (Sep 29, 2023)
X-103079373-T-C		not specified	Uncertain significance (Sep 29, 2023)
X-103079417-G-C			Likely benign (Apr 01, 2023)
X-103079468-C-T		not specified	Uncertain significance (Jan 23, 2025)
X-103079623-A-G		not specified	Uncertain significance (Aug 27, 2024)
X-103079794-T-G		not specified	Uncertain significance (Apr 25, 2023)
X-103079815-C-T		not specified	Uncertain significance (Feb 05, 2025)
X-103080017-G-T		not specified	Uncertain significance (May 21, 2024)
X-103080596-A-G		not specified	Uncertain significance (Feb 09, 2025)
X-103082318-C-T		not specified	Likely benign (Jan 16, 2025)
X-103082319-C-A		Male infertility	Likely pathogenic (May 07, 2024)
X-103082334-T-C		not specified	Uncertain significance (Oct 06, 2023)
X-103082846-T-C		not specified	Uncertain significance (Apr 05, 2023)
X-103083256-G-T		not specified	Uncertain significance (Jul 05, 2023)
X-103083620-C-T		not specified	Likely benign (Apr 20, 2023)
X-103083632-T-C		not specified	Uncertain significance (Nov 24, 2024)
X-103083660-C-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXF3	protein_coding	protein_coding	ENST00000395065	19	17420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00852	0.991	125725	6	14	125745	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.775	175	206	0.848	0.0000154	3557
Missense in Polyphen		28	40.096	0.69833		802
Synonymous	0.396	72	76.4	0.942	0.00000605	928
Loss of Function	3.04	8	24.1	0.332	0.00000167	417

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00108	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.0000367	0.0000264
Middle Eastern	0.00108	0.000816
South Asian	0.0000528	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a tissue-specific nuclear mRNA export factor.
• 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) (Consensus)

Recessive Scores

• pRec: 0.0854

Intolerance Scores

• loftool: 0.572
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.566
• hipred: N
• hipred_score: 0.347
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxf3
• 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); reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: mRNA export from nucleus;poly(A)+ mRNA export from nucleus
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear RNA export factor complex
• Molecular function: RNA binding;mRNA binding;protein binding