FBXO28

F-box protein 28, the group of F-boxes other

Basic information

Region (hg38): 1:224114110-224162047

Links

ENSG00000143756 ∙ NCBI:23219 ∙ OMIM:609100 ∙ HGNC:29046 ∙ Uniprot:Q9NVF7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy 100 (Moderate), mode of inheritance: AD
• developmental and epileptic encephalopathy 100 (Strong), mode of inheritance: AD
• developmental and epileptic encephalopathy 100 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 100	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	30160831; 33280099

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FBXO28 gene.

• Developmental and epileptic encephalopathy 100 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO28 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				2		2
missense			21	2		23
nonsense						0
start loss						0
frameshift	1	1				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding				1		1
Total	1	1	21	5	0

Variants in FBXO28

This is a list of pathogenic ClinVar variants found in the FBXO28 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-224114129-G-C		FBXO28-related disorder	Likely benign (Sep 10, 2019)
1-224114142-GC-AA		Developmental and epileptic encephalopathy 100	Uncertain significance (-)
1-224114143-C-G			Uncertain significance (Feb 01, 2023)
1-224114149-A-T		FBXO28-related disorder	Uncertain significance (Apr 04, 2023)
1-224114151-C-A			Likely benign (Mar 01, 2024)
1-224114173-G-C		Inborn genetic diseases	Uncertain significance (May 30, 2022)
1-224114191-G-A		FBXO28-related disorder	Uncertain significance (Nov 15, 2022)
1-224114215-C-G		Inborn genetic diseases	Uncertain significance (May 15, 2023)
1-224114226-C-T		FBXO28-related developmental and epileptic encephalopathy	Uncertain significance (Jan 27, 2021)
1-224114320-T-G		Developmental and epileptic encephalopathy 100	Pathogenic (Mar 09, 2022)
1-224114351-C-A		Inborn genetic diseases	Uncertain significance (Apr 22, 2024)
1-224114380-T-C		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
1-224114387-G-C		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
1-224134094-A-G		Inborn genetic diseases	Uncertain significance (Aug 15, 2023)
1-224134216-A-T		FBXO28-related disorder	Uncertain significance (Feb 12, 2024)
1-224153161-G-A			Uncertain significance (May 01, 2023)
1-224153178-A-G		FBXO28-related disorder	Uncertain significance (Nov 15, 2023)
1-224153179-A-G		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
1-224153194-C-T		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
1-224153268-A-G			Uncertain significance (Aug 01, 2022)
1-224153328-T-C		FBXO28-associated epileptic encephalopathy	Uncertain significance (Apr 23, 2021)
1-224153329-C-G		Inborn genetic diseases	Uncertain significance (Oct 20, 2021)
1-224153334-C-T		FBXO28-related disorder	Likely benign (Feb 15, 2022)
1-224157365-T-C		Inborn genetic diseases	Likely benign (Jul 31, 2023)
1-224157471-C-A		Inborn genetic diseases	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO28	protein_coding	protein_coding	ENST00000366862	5	47961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0132	125595	0	1	125596	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	112	203	0.552	0.0000108	2361
Missense in Polyphen		16	31.186	0.51304		457
Synonymous	-0.430	78	73.3	1.06	0.00000361	737
Loss of Function	3.65	1	17.5	0.0571	0.00000104	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. {ECO:0000250}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.0770
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.563
• hipred: Y
• hipred_score: 0.673
• ghis: 0.680

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo28

Gene ontology

• Cellular component: kinetochore;condensed chromosome kinetochore
• Molecular function: protein binding