NXF5

nuclear RNA export factor 5

Basic information

Region (hg38): X:101832537-101843278

Links

ENSG00000126952 ∙ NCBI:55998 ∙ OMIM:300319 ∙ HGNC:8075 ∙ Uniprot:Q9H1B4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Familial heart block and focal segmental glomerulosclerosis	XL	Cardiovascular	In Familial heart block and focal segmental glomerulosclerosis, awareness of the risk of cardiac complications, including progressive heart block, may allow surveillance (eg, with electrocardiogram) and treatment (eg, with pacemaker placement); Renal transplant has been described	Cardiovascular; Neurologic; Renal	11566096; 23686279; 23871722
For Mental retardation, syndromic, X-linked, the evidence of variants as being related to disease causation has been questioned due to subsequent population-based studies

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NXF5 gene.

• not provided (37 variants)
• Inborn genetic diseases (13 variants)
• Focal segmental glomerulosclerosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXF5 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			21	10	18	49
Total	0	0	22	10	18

Variants in NXF5

This is a list of pathogenic ClinVar variants found in the NXF5 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-101836760-GAAGGTCC-G			Likely benign (Jul 01, 2023)
X-101837488-C-T			Uncertain significance (Apr 23, 2023)
X-101837511-C-A		not specified	Uncertain significance (Jan 28, 2025)
X-101837514-G-A		NXF5-related disorder	Benign (Jan 13, 2025)
X-101837518-G-A			Likely benign (Oct 05, 2024)
X-101837536-G-A			Benign (Jan 24, 2025)
X-101837552-T-C		not specified	Conflicting classifications of pathogenicity (Oct 29, 2024)
X-101837564-G-A		not specified	Uncertain significance (Oct 25, 2023)
X-101837576-T-C			Uncertain significance (Jun 03, 2024)
X-101837593-T-C			Likely benign (Jun 28, 2023)
X-101837596-A-T			Uncertain significance (Jul 26, 2023)
X-101837610-C-T		NXF5-related disorder	Uncertain significance (Sep 06, 2022)
X-101837611-G-A			Likely benign (Mar 22, 2024)
X-101837615-C-T			Benign (Dec 02, 2024)
X-101837616-G-A			Benign (Nov 30, 2024)
X-101837623-T-G		not specified	Uncertain significance (Mar 31, 2024)
X-101837627-G-A		not specified	Uncertain significance (Jul 17, 2024)
X-101837636-A-G			Uncertain significance (Jan 23, 2025)
X-101837644-C-T			Likely benign (Dec 02, 2024)
X-101837777-C-A			Uncertain significance (Sep 03, 2024)
X-101837792-G-C			Likely benign (Oct 17, 2024)
X-101837797-T-C		not specified	Uncertain significance (Nov 17, 2023)
X-101838149-T-TG			Benign (Jul 09, 2018)
X-101838403-C-T		NXF5-related disorder	Benign (Jul 09, 2018)
X-101838414-G-A		NXF5-related disorder	Likely benign (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXF5	protein_coding	protein_coding	ENST00000537026	14	25465

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-14	0.00620	125711	9	26	125746	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.374	141	129	1.09	0.0000100	2418
Missense in Polyphen		19	24.419	0.77807		579
Synonymous	-1.16	61	50.5	1.21	0.00000395	645
Loss of Function	-0.630	19	16.3	1.17	0.00000132	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000845	0.000830
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000977	0.0000703
Middle Eastern	0.0000722	0.0000544
South Asian	0.000105	0.0000653
Other	0.000445	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be involved in the export of mRNA from the nucleus to the cytoplasm. Could also have a role in polarized cytoplasmic transport and localization of mRNA in neurons.
• Disease: DISEASE: Note=A chromosomal aberration involving NXF5 has been observed in one patient with a syndromic form of mental retardation and short stature. Pericentric inversion inv(X)(p21.1;q22) that interrupts NXF5. {ECO:0000269|PubMed:11566096}.
• 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)

Intolerance Scores

• loftool: 0.720
• rvis_EVS: 1.93
• rvis_percentile_EVS: 97.46

Haploinsufficiency Scores

• pHI: 0.198
• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxf2
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system 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)

Gene ontology

• Biological process: mRNA export from nucleus;multicellular organism development;poly(A)+ mRNA export from nucleus;RNA transport
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;protein binding