FBXO31

F-box protein 31, the group of F-boxes other

Basic information

Region (hg38): 16:87326986-87392142

Links

ENSG00000103264 ∙ NCBI:79791 ∙ OMIM:609102 ∙ HGNC:16510 ∙ Uniprot:Q5XUX0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual disability, autosomal recessive 45 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 45	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	24623383

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FBXO31 gene.

• not provided (24 variants)
• Inborn genetic diseases (19 variants)
• not specified (9 variants)
• Intellectual disability, autosomal recessive 45 (5 variants)
• FBXO31-related condition (3 variants)
• Spastic cerebral palsy (1 variants)
• Ectopic thyroid (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO31 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	17	3	21
missense		1	26	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			4			4
non coding			1		2	3
Total	0	1	28	18	5

Variants in FBXO31

This is a list of pathogenic ClinVar variants found in the FBXO31 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-87331342-C-T		not specified	Likely benign (Jan 07, 2019)
16-87331363-G-A			Likely benign (Dec 31, 2019)
16-87331372-G-A			Likely benign (Apr 01, 2023)
16-87331404-C-G		not specified	Uncertain significance (Jan 07, 2022)
16-87331453-G-A			Likely benign (Nov 01, 2022)
16-87333876-G-A		FBXO31-related disorder	Benign (Dec 31, 2019)
16-87333935-C-A		not specified	Uncertain significance (Jan 19, 2024)
16-87333935-C-T		Intellectual disability, autosomal recessive 45	Uncertain significance (Dec 24, 2019)
16-87333944-C-T		not specified	Uncertain significance (Dec 16, 2023)
16-87333945-G-A			Benign (Jan 02, 2018)
16-87333985-G-T		not specified	Uncertain significance (Jan 26, 2022)
16-87334031-C-T		not specified	Uncertain significance (May 03, 2023)
16-87334101-C-T			Likely benign (May 01, 2022)
16-87334102-C-T			Benign/Likely benign (Dec 31, 2019)
16-87334108-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-87334119-C-T			Likely benign (Jul 01, 2023)
16-87334130-C-T		not specified	Uncertain significance (Oct 06, 2021)
16-87334150-C-T		FBXO31-related disorder	Uncertain significance (Apr 28, 2023)
16-87334218-G-A		not specified	Benign (Dec 31, 2019)
16-87334235-G-A		not specified	Uncertain significance (Mar 22, 2023)
16-87334283-C-T		Spastic cerebral palsy • Ectopic thyroid • Intellectual disability, autosomal recessive 45	Pathogenic/Likely pathogenic (Jun 01, 2023)
16-87334284-G-A		not specified	Uncertain significance (Mar 14, 2016)
16-87335294-C-T		not specified	Uncertain significance (Aug 01, 2016)
16-87335295-G-A		FBXO31-related disorder	Likely benign (Aug 26, 2019)
16-87335300-T-C		Intellectual disability, autosomal recessive 45	Uncertain significance (Dec 24, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO31	protein_coding	protein_coding	ENST00000311635	9	65156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.444	0.556	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	214	342	0.626	0.0000229	3483
Missense in Polyphen		45	142.71	0.31532		1479
Synonymous	-0.443	159	152	1.05	0.0000111	1091
Loss of Function	3.48	5	23.0	0.217	0.00000125	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000536	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of some SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in G1 arrest following DNA damage. Specifically recognizes phosphorylated cyclin-D1 (CCND1), promoting its ubiquitination and degradation by the proteasome, resulting in G1 arrest. May act as a tumor suppressor. {ECO:0000269|PubMed:16357137, ECO:0000269|PubMed:19412162}.
• Disease: DISEASE: Mental retardation, autosomal recessive 45 (MRT45) [MIM:615979]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT45 manifestations include mild to moderate intellectual disability and dysmorphic features, including coarse facies, broad nasal bridge, fleshy nares, and thick, prominent lips. {ECO:0000269|PubMed:24623383}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• 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)

Intolerance Scores

• loftool: 0.0902
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.77

Haploinsufficiency Scores

• pHI: 0.108
• hipred: Y
• hipred_score: 0.783
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo31
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein polyubiquitination;cellular response to DNA damage stimulus;anaphase-promoting complex-dependent catabolic process;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;mitotic G1 DNA damage checkpoint;post-translational protein modification;positive regulation of dendrite morphogenesis;positive regulation of neuron migration
• Cellular component: centrosome;cytosol;SCF ubiquitin ligase complex;neuronal cell body
• Molecular function: ubiquitin-protein transferase activity;protein binding;cyclin binding