FBXL13

protein-coding

F-box and leucine rich repeat protein 13, the group of Cilia and flagella associated|Dynein regulatory complex|F-box and leucine rich repeat proteins

Gene summary

Members of the F-box protein family, such as FBXL13, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001394494.2

Inheritance

—

ClinVar variants

U:94B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr7:102,811,189-103,074,839

External References & Databases

Ensembl (ENSG00000161040)

Transcript & Mutation Effects

hg38 • Region Span ~263.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FBXL13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 153

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394494.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			90 clinvar	7 clinvar		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	94	7	0	101

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394494.2	RefSeq	NP_001381423.1	21	MANE Select
ENST00000440067.4	Ensembl	ENSP00000390126.2	21	MANE Select
NM_001111038.2	RefSeq	NP_001104508.1	17	Standard
NM_001287150.2	RefSeq	NP_001274079.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
Immune System
Adaptive Immune System
Antigen processing: Ubiquitination & Proteasome degradation

Biological Process

protein polyubiquitination
ubiquitin-dependent protein catabolic process
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
post-translational protein modification

Molecular Function

ubiquitin-protein transferase activity

Cellular Component

cytosol
cytoskeleton
SCF ubiquitin ligase complex
motile cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000313221
Coding exons: 18
Length: 261979
Individuals with no LoFs: 125630
Homozygous LoFs: 0
Heterozygous LoFs: 118
Defined: 125748
p: 0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.548	348	378	0.921	0.0000192	4830
Missense (PolyPhen)		70	77.863	0.89902		1113
Synonymous	1.38	113	133	0.848	0.00000648	1338
Loss of Function	1.84	24	35.9	0.668	0.00000187	476

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.0012	0.0011	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0013	0.0013	notable
Finnish	0.00018	0.000092	rare
European (Non-Finnish)	0.00031	0.00031	rare
South Asian	0.00024	0.00023	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the nexin-dynein regulatory complex (N- DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. Substrate- recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. {ECO:0000250, ECO:0000250|UniProtKB:A8JHD7}.;

Recessive Scores

pRec: 0.0885

Intolerance Scores

LoFtool: 0.995
RVIS EVS: 0.49
RVIS percentile EVS: 79.61

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0944

Gene Damage Prediction

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