FBXL16

F-box and leucine rich repeat protein 16, the group of F-box and leucine rich repeat proteins

Basic information

Region (hg38): 16:692498-705801

Previous symbols: [ "C16orf22" ]

Links

ENSG00000127585 ∙ NCBI:146330 ∙ OMIM:609082 ∙ HGNC:14150 ∙ Uniprot:Q8N461 ∙ 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 FBXL16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXL16 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				1		1
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in FBXL16

This is a list of pathogenic ClinVar variants found in the FBXL16 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-694283-T-C		not specified	Uncertain significance (Jan 20, 2025)
16-694380-C-T			Likely benign (Jan 01, 2023)
16-695434-C-G		not specified	Uncertain significance (Apr 05, 2023)
16-695458-C-A		not specified	Uncertain significance (Dec 10, 2024)
16-695497-A-C		not specified	Uncertain significance (Jan 29, 2024)
16-695610-A-C		not specified	Uncertain significance (Oct 05, 2023)
16-695832-G-A		not specified	Uncertain significance (Dec 27, 2023)
16-696802-G-A		not specified	Uncertain significance (Nov 09, 2024)
16-696946-C-T		not specified	Uncertain significance (Feb 18, 2025)
16-696963-T-G		not specified	Uncertain significance (Jan 10, 2025)
16-697027-C-G		not specified	Uncertain significance (Jan 08, 2025)
16-697032-C-T		not specified	Uncertain significance (Oct 17, 2023)
16-697033-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-697087-A-G		not specified	Uncertain significance (Oct 07, 2024)
16-697125-G-A		not specified	Uncertain significance (Jan 09, 2025)
16-697137-G-A		not specified	Likely benign (Dec 07, 2021)
16-697165-C-G		not specified	Uncertain significance (Mar 11, 2025)
16-697209-C-T		not specified	Uncertain significance (Nov 25, 2024)
16-697273-G-A		not specified	Uncertain significance (Nov 11, 2024)
16-697333-C-T		not specified	Uncertain significance (Oct 06, 2021)
16-697384-C-T		not specified	Uncertain significance (Apr 19, 2023)
16-697387-C-T		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXL16	protein_coding	protein_coding	ENST00000397621	5	13330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.970	0.0302	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.14	128	274	0.466	0.0000152	3010
Missense in Polyphen		17	88.315	0.19249		1038
Synonymous	-0.365	138	133	1.04	0.00000832	1034
Loss of Function	3.38	1	15.2	0.0656	7.11e-7	169

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.0307
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.516
• hipred: Y
• hipred_score: 0.789
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxl16
• Phenotype: skeleton phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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: protein polyubiquitination;ubiquitin-dependent protein catabolic process;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;post-translational protein modification
• Cellular component: cytosol;SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity