BBOX1

gamma-butyrobetaine hydroxylase 1

Basic information

Region (hg38): 11:27040724-27127809

Previous symbols: [ "BBOX" ]

Links

ENSG00000129151 ∙ NCBI:8424 ∙ OMIM:603312 ∙ HGNC:964 ∙ Uniprot:O75936 ∙ 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 BBOX1 gene.

• Inborn genetic diseases (18 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BBOX1 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					3	3
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	3

Variants in BBOX1

This is a list of pathogenic ClinVar variants found in the BBOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-27055438-G-C		not specified	Uncertain significance (Sep 15, 2021)
11-27055507-A-C		not specified	Uncertain significance (Nov 08, 2022)
11-27055546-C-T		not specified	Uncertain significance (Nov 15, 2021)
11-27055581-C-T		not specified	Uncertain significance (Aug 12, 2021)
11-27055639-A-T		not specified	Uncertain significance (Aug 10, 2023)
11-27057213-T-A		not specified	Uncertain significance (Dec 26, 2023)
11-27057222-G-A		not specified	Uncertain significance (Oct 07, 2022)
11-27057228-T-A		not specified	Uncertain significance (Aug 17, 2021)
11-27057247-A-T		not specified	Uncertain significance (Jun 24, 2022)
11-27093179-T-C		not specified	Uncertain significance (May 31, 2023)
11-27093183-G-T		not specified	Uncertain significance (Jul 26, 2023)
11-27093196-G-C		not specified	Uncertain significance (Dec 05, 2022)
11-27093232-T-C			Benign (Nov 15, 2018)
11-27093338-A-C		not specified	Uncertain significance (May 03, 2023)
11-27115453-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-27115534-C-G		not specified	Uncertain significance (Jul 19, 2022)
11-27115539-C-T			Benign (May 21, 2018)
11-27115544-A-G		not specified	Uncertain significance (Jan 17, 2024)
11-27119752-C-T		not specified	Uncertain significance (Sep 26, 2023)
11-27119779-T-C		not specified	Uncertain significance (Oct 05, 2023)
11-27125658-G-C		not specified	Uncertain significance (Dec 18, 2023)
11-27125747-T-C			Benign (Nov 15, 2018)
11-27125776-T-G		not specified	Uncertain significance (May 03, 2023)
11-27125777-C-A		BBOX1-related disorder	Likely benign (Feb 25, 2023)
11-27125798-G-C		not specified	Uncertain significance (Jul 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BBOX1	protein_coding	protein_coding	ENST00000263182	7	87085

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.09e-12	0.0341	125619	0	128	125747	0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.594	180	204	0.883	0.0000101	2559
Missense in Polyphen		77	78.646	0.97907		933
Synonymous	0.376	66	70.0	0.943	0.00000354	690
Loss of Function	0.0109	18	18.1	0.997	8.46e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000604	0.000602
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000548	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000727	0.000712
Middle Eastern	0.000548	0.000489
South Asian	0.000779	0.000719
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the formation of L-carnitine from gamma- butyrobetaine.
• Pathway: Lysine degradation - Homo sapiens (human);Carnitine Synthesis;Branched-chain amino acid catabolism;Metabolism of amino acids and derivatives;Metabolism;Lysine degradation;Carnitine synthesis;L-carnitine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.363
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.303
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bbox1
• Phenotype: 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); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; craniofacial phenotype

Gene ontology

• Biological process: carnitine biosynthetic process;oxidation-reduction process
• Cellular component: mitochondrion;cytosol;extracellular exosome
• Molecular function: iron ion binding;protein binding;zinc ion binding;gamma-butyrobetaine dioxygenase activity;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;identical protein binding