BBX

BBX high mobility group box domain containing

Basic information

Region (hg38): 3:107522936-107811339

Links

ENSG00000114439 ∙ NCBI:56987 ∙ ∙ HGNC:14422 ∙ Uniprot:Q8WY36 ∙ 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 BBX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BBX 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			45	1	3	49
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	45	3	3

Variants in BBX

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

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

Position	Type	Phenotype	Significance	ClinVar
3-107710480-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-107710485-G-A		not specified	Uncertain significance (Aug 04, 2024)
3-107716613-C-A		not specified	Uncertain significance (May 28, 2024)
3-107716624-C-T			Likely benign (Dec 08, 2017)
3-107716626-A-G		not specified	Uncertain significance (Apr 26, 2023)
3-107716668-C-T		not specified	Uncertain significance (Oct 05, 2021)
3-107716727-C-T		not specified	Uncertain significance (Mar 28, 2024)
3-107716731-C-G		not specified	Uncertain significance (Oct 17, 2024)
3-107716740-G-A		not specified	Uncertain significance (Nov 07, 2022)
3-107716755-G-C		not specified	Uncertain significance (Aug 14, 2024)
3-107716756-G-C		not specified	Uncertain significance (Aug 14, 2024)
3-107716791-A-G		not specified	Uncertain significance (Dec 05, 2022)
3-107728772-A-T		not specified	Uncertain significance (Feb 06, 2023)
3-107728774-G-A		not specified	Uncertain significance (May 21, 2024)
3-107728787-C-G		not specified	Uncertain significance (Aug 04, 2024)
3-107728804-T-C		not specified	Uncertain significance (Sep 11, 2024)
3-107728940-A-G		not specified	Uncertain significance (Aug 20, 2024)
3-107744682-A-C		not specified	Uncertain significance (Dec 07, 2023)
3-107747965-A-T		not specified	Uncertain significance (May 21, 2024)
3-107747993-C-T			Benign (Jun 06, 2017)
3-107748019-G-C		not specified	Uncertain significance (Jul 06, 2021)
3-107748038-A-C		not specified	Uncertain significance (Dec 07, 2024)
3-107755643-C-T		not specified	Uncertain significance (Jun 02, 2023)
3-107772691-G-A		not specified	Uncertain significance (Jun 27, 2022)
3-107772742-A-C		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BBX	protein_coding	protein_coding	ENST00000325805	15	288389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.518	0.482	125703	0	31	125734	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	436	505	0.863	0.0000261	6229
Missense in Polyphen		194	238.1	0.8148		2879
Synonymous	0.486	173	181	0.954	0.00000996	1732
Loss of Function	4.90	10	45.8	0.218	0.00000265	585

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that is necessary for cell cycle progression from G1 to S phase. {ECO:0000269|PubMed:11680820}.

Recessive Scores

• pRec: 0.0903

Intolerance Scores

• loftool: 0.0750
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.1

Haploinsufficiency Scores

• pHI: 0.486
• hipred: N
• hipred_score: 0.414
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bbx
• Phenotype: craniofacial phenotype; hematopoietic system phenotype; 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; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;bone development
• Cellular component: nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding