FBXW12

F-box and WD repeat domain containing 12, the group of F-box and WD repeat domain containing|WD repeat domain containing

Basic information

Region (hg38): 3:48372219-48401259

Previous symbols: [ "FBXO35" ]

Links

ENSG00000164049 ∙ NCBI:285231 ∙ OMIM:609075 ∙ HGNC:20729 ∙ Uniprot:Q6X9E4 ∙ 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 FBXW12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXW12 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			23	4		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	5	0

Variants in FBXW12

This is a list of pathogenic ClinVar variants found in the FBXW12 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48372800-G-C		not specified	Uncertain significance (Nov 22, 2024)
3-48372822-C-A		not specified	Uncertain significance (Jun 02, 2023)
3-48372828-G-A		not specified	Likely benign (Oct 13, 2023)
3-48373610-C-A		not specified	Uncertain significance (Apr 09, 2024)
3-48373618-C-A		not specified	Uncertain significance (Jul 09, 2021)
3-48373670-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-48375377-C-G		not specified	Uncertain significance (Nov 25, 2024)
3-48375410-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-48375413-A-C		not specified	Uncertain significance (May 26, 2022)
3-48375446-G-C		not specified	Uncertain significance (Oct 13, 2023)
3-48375461-G-C		not specified	Uncertain significance (Apr 07, 2022)
3-48378318-G-C		not specified	Uncertain significance (May 21, 2024)
3-48378382-G-T		not specified	Uncertain significance (Jan 06, 2023)
3-48378397-C-G		not specified	Uncertain significance (Mar 12, 2024)
3-48378467-A-G			Likely benign (Feb 01, 2023)
3-48378488-A-C		not specified	Likely benign (Apr 20, 2024)
3-48379401-T-C		not specified	Uncertain significance (Mar 21, 2023)
3-48379521-T-C		not specified	Uncertain significance (Jun 13, 2024)
3-48379538-T-A		not specified	Uncertain significance (Sep 24, 2024)
3-48379538-T-C		not specified	Likely benign (Jun 28, 2022)
3-48379544-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-48379548-C-T		not specified	Likely benign (May 07, 2024)
3-48380767-A-G			Likely benign (Feb 01, 2023)
3-48380772-A-C		not specified	Uncertain significance (Aug 14, 2023)
3-48380773-A-C		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXW12	protein_coding	protein_coding	ENST00000296438	10	28958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.08e-10	0.675	125641	0	103	125744	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.402	234	252	0.929	0.0000126	3063
Missense in Polyphen		51	60.934	0.83697		778
Synonymous	1.33	80	96.6	0.828	0.00000521	870
Loss of Function	1.40	18	25.6	0.702	0.00000136	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00342	0.00343
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000980	0.000980
Other	0.000489	0.000489

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: 0.0621

Intolerance Scores

• loftool: 0.992
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.18

Haploinsufficiency Scores

• pHI: 0.0422
• hipred: N
• hipred_score: 0.123
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0467

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxw28

Gene ontology

• Biological process: protein polyubiquitination;post-translational protein modification
• Cellular component: cytosol
• Molecular function: ubiquitin-protein transferase activity