BBC3

BCL2 binding component 3, the group of MicroRNA protein coding host genes|BCL2 homology region 3 (BH3) only

Basic information

Region (hg38): 19:47220822-47232766

Links

ENSG00000105327 ∙ NCBI:27113 ∙ OMIM:605854 ∙ HGNC:17868 ∙ Uniprot:Q96PG8, Q9BXH1 ∙ 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 BBC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BBC3 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			14	6		20
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	7	0

Variants in BBC3

This is a list of pathogenic ClinVar variants found in the BBC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47221708-G-A		not specified	Uncertain significance (Feb 14, 2023)
19-47221738-G-C		not specified	Uncertain significance (Oct 16, 2023)
19-47221745-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-47221779-G-A			Benign/Likely benign (Jan 01, 2023)
19-47221887-G-A		not specified	Likely benign (Jan 03, 2024)
19-47221899-C-T		not specified	Likely benign (Sep 14, 2023)
19-47226572-C-G		not specified	Uncertain significance (Dec 02, 2022)
19-47226580-G-T		not specified	Likely benign (Apr 27, 2024)
19-47226619-A-G		not specified	Likely benign (Feb 28, 2024)
19-47226626-G-A		not specified	Uncertain significance (Aug 01, 2024)
19-47226627-G-A		not specified	Uncertain significance (Dec 07, 2024)
19-47226686-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-47226720-G-C		not specified	Uncertain significance (Apr 25, 2022)
19-47228171-G-A		not specified	Uncertain significance (Mar 02, 2023)
19-47228185-T-G		not specified	Uncertain significance (May 18, 2023)
19-47228208-G-A		not specified	Likely benign (Jun 02, 2023)
19-47228277-G-A		not specified	Likely benign (Oct 12, 2024)
19-47228284-C-T		not specified	Uncertain significance (Sep 04, 2024)
19-47228306-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-47228309-C-A		not specified	Uncertain significance (Mar 26, 2024)
19-47228311-C-A		not specified	Uncertain significance (May 26, 2022)
19-47228354-C-A		not specified	Uncertain significance (Apr 05, 2023)
19-47228355-G-C		not specified	Likely benign (Aug 10, 2024)
19-47228358-A-T		not specified	Likely benign (Feb 06, 2024)
19-47228366-C-G		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BBC3	protein_coding	protein_coding	ENST00000449228	4	11943

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00398	0.665	124132	0	38	124170	0.000153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.155	80	84.0	0.953	0.00000459	1559
Missense in Polyphen		18	15.666	1.149		153
Synonymous	0.548	33	37.3	0.886	0.00000220	657
Loss of Function	0.593	4	5.50	0.727	3.31e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000245	0.000243
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000163
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 3: Does not affect cell growth. {ECO:0000269|PubMed:11463392}.
• Pathway: p53 signaling pathway - Homo sapiens (human);Apoptosis - multiple species - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Apoptosis - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;Colorectal cancer - Homo sapiens (human);miRNA Regulation of DNA Damage Response;TP53 Network;Apoptosis Modulation and Signaling;Integrated Cancer Pathway;Intrinsic Pathway for Apoptosis;Apoptosis;Photodynamic therapy-induced unfolded protein response;Apoptotic Signaling Pathway;TP53 Regulates Transcription of Cell Death Genes;miRNA regulation of p53 pathway in prostate cancer;Chromosomal and microsatellite instability in colorectal cancer;DNA Damage Response;DNA Damage Response (only ATM dependent);Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;Activation of PUMA and translocation to mitochondria;Activation of BH3-only proteins;Intrinsic Pathway for Apoptosis;Apoptosis;Programmed Cell Death;p73 transcription factor network;TP53 Regulates Transcription of Genes Involved in Cytochrome C Release;Validated transcriptional targets of TAp63 isoforms;Transcriptional Regulation by TP53;Direct p53 effectors;BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members (Consensus)

Haploinsufficiency Scores

• pHI: 0.760
• hipred: Y
• hipred_score: 0.502
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bbc3
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); 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); immune system phenotype

Gene ontology

• Biological process: release of cytochrome c from mitochondria;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of apoptotic process;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;positive regulation of release of cytochrome c from mitochondria;execution phase of apoptosis;positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway;positive regulation of cysteine-type endopeptidase activity
• Cellular component: mitochondrion;lysosome
• Molecular function: protein binding;ATPase binding