FBXO31

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

Basic information

Region (hg38): 16:87326987-87392142

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
intellectual disability, autosomal recessive (Limited), mode of inheritance: AR
cerebral palsy (Limited), mode of inheritance: AD

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_specified (70 variants)
not_provided (26 variants)
FBXO31-related_disorder (10 variants)
Intellectual_disability,_autosomal_recessive_45 (7 variants)
Ectopic_thyroid (1 variants)
Spastic_cerebral_palsy (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. These statistics are base on transcript: NM_000024735.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar		3 clinvar	20 clinvar	3 clinvar	27
missense		1 clinvar	65 clinvar	3 clinvar		69
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	2	2	68	23	3

Loading clinvar variants...

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