FBXL9P

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

Basic information

Region (hg38): 16:67207605-67226998

Previous symbols: [ "FBXL9", "LRRC29" ]

Links

ENSG00000125122 ∙ NCBI:26231 ∙ ∙ HGNC:13605 ∙ ∙ ∙ 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 FBXL9P gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXL9P 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)						0
splice region						0
non coding			20	4		24
Total	0	0	20	4	0

Variants in FBXL9P

This is a list of pathogenic ClinVar variants found in the FBXL9P region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67207613-T-C		not specified	Uncertain significance (Jun 07, 2023)
16-67207637-C-T		not specified	Uncertain significance (Feb 20, 2025)
16-67207670-G-T		not specified	Uncertain significance (Mar 29, 2022)
16-67207684-C-T		not specified	Likely benign (Dec 21, 2022)
16-67207685-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-67207685-G-C		not specified	Uncertain significance (May 09, 2022)
16-67207735-C-T		not specified	Uncertain significance (Jun 22, 2021)
16-67207750-G-A		not specified	Uncertain significance (Oct 17, 2023)
16-67207750-G-C		not specified	Uncertain significance (Mar 28, 2023)
16-67207900-A-C		not specified	Uncertain significance (Sep 15, 2021)
16-67207927-G-A		not specified	Uncertain significance (Dec 08, 2023)
16-67207942-G-A		not specified	Uncertain significance (Aug 08, 2022)
16-67207963-C-T		not specified	Uncertain significance (Nov 07, 2022)
16-67207981-G-A		not specified	Likely benign (Dec 25, 2024)
16-67208357-C-G		not specified	Uncertain significance (Apr 26, 2023)
16-67208377-G-T		not specified	Uncertain significance (Sep 06, 2024)
16-67208379-G-A		not specified	Likely benign (Dec 22, 2023)
16-67208392-G-A		not specified	Uncertain significance (Aug 04, 2024)
16-67208395-C-T		not specified	Uncertain significance (Jan 31, 2024)
16-67208413-C-T		not specified	Uncertain significance (Aug 17, 2021)
16-67208414-G-T		not specified	Likely benign (Dec 18, 2023)
16-67210080-A-G		not specified	Uncertain significance (Mar 29, 2023)
16-67210094-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-67210101-C-T		not specified	Likely benign (Mar 19, 2024)
16-67210133-C-T		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXL9P	protein_coding	protein_coding	ENST00000409037	4	19910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000223	0.761	125699	0	22	125721	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.361	114	125	0.909	0.00000729	1394
Missense in Polyphen		14	24.48	0.57189		347
Synonymous	1.16	46	57.2	0.805	0.00000337	491
Loss of Function	1.04	7	10.7	0.656	6.68e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000690	0.000644
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000713	0.0000703
Middle Eastern	0.000113	0.000109
South Asian	0.0000383	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.771
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.146
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc29

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
• Cellular component: SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding