FBXL19

F-box and leucine rich repeat protein 19, the group of Zinc fingers CXXC-type|F-box and leucine rich repeat proteins|PHD finger proteins

Basic information

Region (hg38): 16:30923055-30948783

Links

ENSG00000099364 ∙ NCBI:54620 ∙ OMIM:609085 ∙ HGNC:25300 ∙ Uniprot:Q6PCT2 ∙ 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 FBXL19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXL19 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	4
missense			27		1	28
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	30	2	3

Variants in FBXL19

This is a list of pathogenic ClinVar variants found in the FBXL19 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30925767-A-AGCCGGGG		Neurodevelopmental delay	Uncertain significance (Jan 03, 2023)
16-30925782-G-A		not specified	Uncertain significance (Jun 06, 2023)
16-30925782-G-T		not specified	Uncertain significance (Sep 06, 2022)
16-30925783-C-T		not specified	Uncertain significance (Sep 06, 2022)
16-30925790-G-A			Likely benign (Jan 01, 2023)
16-30925907-G-A			Benign (Jul 11, 2018)
16-30925932-G-A			Uncertain significance (Feb 21, 2024)
16-30927321-A-G		not specified	Uncertain significance (Jun 06, 2022)
16-30927371-G-A		not specified	Uncertain significance (May 11, 2022)
16-30927641-G-A			Likely benign (Jan 01, 2023)
16-30927751-G-A		not specified	Uncertain significance (Aug 10, 2021)
16-30927862-A-C		not specified	Uncertain significance (Aug 04, 2023)
16-30927867-C-T			Benign (Dec 11, 2018)
16-30927883-C-T		not specified	Uncertain significance (Apr 25, 2022)
16-30927887-C-T		not specified	Uncertain significance (Aug 15, 2023)
16-30927943-C-G		not specified	Uncertain significance (Aug 23, 2021)
16-30928503-G-A		not specified	Uncertain significance (Jun 21, 2023)
16-30928546-C-T		not specified	Uncertain significance (May 04, 2023)
16-30930083-C-T		not specified	Uncertain significance (Dec 08, 2023)
16-30930110-C-T		not specified	Uncertain significance (Dec 28, 2022)
16-30930265-G-A		not specified	Uncertain significance (Oct 21, 2021)
16-30930331-C-T		not specified	Uncertain significance (Oct 22, 2021)
16-30930334-C-T		not specified	Uncertain significance (Jul 14, 2023)
16-30930407-C-T		not specified	Uncertain significance (Nov 29, 2021)
16-30930419-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXL19	protein_coding	protein_coding	ENST00000380310	11	25729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000271	122681	0	1	122682	0.00000408

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.87	189	409	0.462	0.0000282	4269
Missense in Polyphen		59	141.56	0.41679		1422
Synonymous	0.0281	179	179	0.997	0.0000124	1532
Loss of Function	5.05	0	29.7	0.00	0.00000195	311

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)	0.00000902	0.00000902
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: 0.113

Intolerance Scores

• loftool: 0.460
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.374
• hipred: Y
• hipred_score: 0.785
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxl19
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: protein polyubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification
• Cellular component: cytosol;SCF ubiquitin ligase complex
• Molecular function: DNA binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding