FBXL12

F-box and leucine rich repeat protein 12, the group of F-box and leucine rich repeat proteins

Basic information

Region (hg38): 19:9810267-9827816

Links

ENSG00000127452 ∙ NCBI:54850 ∙ OMIM:609079 ∙ HGNC:13611 ∙ Uniprot:Q9NXK8 ∙ 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 FBXL12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXL12 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in FBXL12

This is a list of pathogenic ClinVar variants found in the FBXL12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9810937-C-T		not specified	Uncertain significance (Oct 25, 2023)
19-9810967-A-C		not specified	Uncertain significance (Dec 21, 2022)
19-9810981-G-A		not specified	Uncertain significance (May 31, 2023)
19-9810988-G-T		not specified	Uncertain significance (Mar 07, 2024)
19-9810999-C-A		not specified	Uncertain significance (Jun 29, 2023)
19-9811036-T-C		not specified	Uncertain significance (Dec 09, 2023)
19-9811087-C-T		not specified	Likely benign (Apr 06, 2024)
19-9811186-G-A		not specified	Uncertain significance (Nov 24, 2024)
19-9811191-T-A		not specified	Uncertain significance (Dec 14, 2023)
19-9811194-C-A		not specified	Uncertain significance (Mar 20, 2024)
19-9811194-C-T		not specified	Uncertain significance (Feb 06, 2024)
19-9811308-G-A		not specified	Uncertain significance (Mar 02, 2023)
19-9811326-C-T		not specified	Uncertain significance (Sep 14, 2022)
19-9811350-C-T		not specified	Uncertain significance (Dec 13, 2022)
19-9811359-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-9811362-A-G		not specified	Uncertain significance (Jul 26, 2022)
19-9811378-C-T		not specified	Uncertain significance (Jan 07, 2022)
19-9811384-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-9811408-C-T		not specified	Uncertain significance (Mar 11, 2024)
19-9811441-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-9811462-C-A		not specified	Uncertain significance (Aug 12, 2024)
19-9811486-G-C		not specified	Uncertain significance (Sep 19, 2022)
19-9811528-C-G		not specified	Uncertain significance (Nov 25, 2024)
19-9811533-C-A		not specified	Uncertain significance (Sep 30, 2024)
19-9811561-G-A		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXL12	protein_coding	protein_coding	ENST00000247977	3	17550

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0439	0.932	125692	0	9	125701	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.919	169	206	0.820	0.0000125	2055
Missense in Polyphen		33	44.937	0.73437		492
Synonymous	1.24	75	89.9	0.834	0.00000507	725
Loss of Function	1.96	4	11.0	0.363	7.01e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000496	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000211	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. Mediates the polyubiquitination and proteasomal degradation of CAMK1 leading to disruption of cyclin D1/CDK4 complex assembly which results in G1 cell cycle arrest in lung epithelia. {ECO:0000269|PubMed:23707388}.
• 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: 0.112

Intolerance Scores

• loftool: 0.646
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.719
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.844

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxl12
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); 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); growth/size/body region phenotype

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;protein polyubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;post-translational protein modification;regulation of cell cycle
• Cellular component: nucleus;cytosol;SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding;ubiquitin protein ligase activity