BIRC3

baculoviral IAP repeat containing 3, the group of Ring finger proteins|Baculoviral IAP repeat containing|Caspase recruitment domain containing

Basic information

Region (hg38): 11:102317449-102339403

Previous symbols: [ "API2" ]

Links

ENSG00000023445 ∙ NCBI:330 ∙ OMIM:601721 ∙ HGNC:591 ∙ Uniprot:Q13489 ∙ 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 BIRC3 gene.

• Inborn genetic diseases (21 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BIRC3 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	2	3
missense			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	2

Variants in BIRC3

This is a list of pathogenic ClinVar variants found in the BIRC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-102324519-G-C		not specified	Uncertain significance (May 09, 2022)
11-102324530-C-A		not specified	Uncertain significance (Feb 28, 2023)
11-102324558-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-102324562-A-G		not specified	Uncertain significance (Mar 07, 2024)
11-102324657-C-G		not specified	Uncertain significance (Nov 19, 2022)
11-102324687-G-A		not specified	Uncertain significance (Dec 28, 2022)
11-102324725-G-C		not specified	Uncertain significance (Jun 18, 2021)
11-102324770-A-G			Benign (May 16, 2018)
11-102324882-C-T		not specified	Uncertain significance (Mar 07, 2024)
11-102324912-C-T		not specified	Uncertain significance (May 13, 2022)
11-102324968-T-C			Likely benign (Jun 01, 2023)
11-102324986-A-T		not specified	Uncertain significance (Jun 10, 2022)
11-102325089-T-G		not specified	Uncertain significance (Sep 14, 2023)
11-102325102-G-A		not specified	Uncertain significance (Feb 21, 2024)
11-102325144-T-G		not specified	Uncertain significance (Dec 18, 2023)
11-102325221-C-G		not specified	Uncertain significance (Dec 16, 2021)
11-102325225-T-C		not specified	Uncertain significance (Jan 18, 2023)
11-102325314-G-A		not specified	Uncertain significance (Jan 31, 2022)
11-102325466-G-T		not specified	Uncertain significance (Feb 28, 2024)
11-102328092-C-T		not specified	Uncertain significance (Jan 10, 2022)
11-102328101-C-G		not specified	Uncertain significance (Jul 26, 2022)
11-102331119-G-A			Likely benign (Dec 01, 2023)
11-102331149-G-A		not specified	Likely benign (Dec 03, 2021)
11-102331226-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-102331231-A-C		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BIRC3	protein_coding	protein_coding	ENST00000263464	8	21920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0656	0.934	125731	0	12	125743	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	254	311	0.817	0.0000158	3963
Missense in Polyphen		57	105.06	0.54254		1353
Synonymous	0.460	109	115	0.945	0.00000634	1131
Loss of Function	3.37	7	25.3	0.277	0.00000116	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000360	0.0000352
Middle Eastern	0.000164	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Multi-functional protein which regulates not only caspases and apoptosis, but also modulates inflammatory signaling and immunity, mitogenic kinase signaling and cell proliferation, as well as cell invasion and metastasis. Acts as an E3 ubiquitin- protein ligase regulating NF-kappa-B signaling and regulates both canonical and non-canonical NF-kappa-B signaling by acting in opposite directions: acts as a positive regulator of the canonical pathway and suppresses constitutive activation of non-canonical NF-kappa-B signaling. The target proteins for its E3 ubiquitin- protein ligase activity include: RIPK1, RIPK2, RIPK3, RIPK4, CASP3, CASP7, CASP8, IKBKE, TRAF1, and BCL10. Acts as an important regulator of innate immune signaling via regulation of Toll-like receptors (TLRs), Nodlike receptors (NLRs) and RIG-I like receptors (RLRs), collectively referred to as pattern recognition receptors (PRRs). Protects cells from spontaneous formation of the ripoptosome, a large multi-protein complex that has the capability to kill cancer cells in a caspase-dependent and caspase- independent manner. Suppresses ripoptosome formation by ubiquitinating RIPK1 and CASP8. {ECO:0000269|PubMed:21931591, ECO:0000269|PubMed:23453969}.
• Disease: DISEASE: Note=A chromosomal aberration involving BIRC3 is recurrent in low-grade mucosa-associated lymphoid tissue (MALT lymphoma). Translocation t(11;18)(q21;q21) with MALT1. This translocation is found in approximately 50% of cytogenetically abnormal low-grade MALT lymphoma.
• Pathway: Focal adhesion - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Apoptosis - multiple species - Homo sapiens (human);Ubiquitin mediated proteolysis - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Apoptosis Modulation and Signaling;TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway;TNF alpha Signaling Pathway;Apoptosis;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Focal Adhesion;Photodynamic therapy-induced NF-kB survival signaling;Apoptotic Signaling Pathway;Hepatitis C and Hepatocellular Carcinoma;Signal Transduction;tnfr1 signaling pathway;caspase cascade in apoptosis;role of mitochondria in apoptotic signaling;hiv-1 nef: negative effector of fas and tnf;keratinocyte differentiation;TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway;TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;TICAM1, RIP1-mediated IKK complex recruitment ;Toll Like Receptor 3 (TLR3) Cascade;Toll-Like Receptors Cascades;NOD1/2 Signaling Pathway;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Regulated Necrosis;Programmed Cell Death;RIPK1-mediated regulated necrosis;ceramide signaling pathway;TNFR1-induced NFkappaB signaling pathway;TNF signaling;sodd/tnfr1 signaling pathway;Ub-specific processing proteases;Deubiquitination;Death Receptor Signalling;Regulation of TNFR1 signaling;C-MYB transcription factor network;TNFalpha;IKK complex recruitment mediated by RIP1;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Caspase Cascade in Apoptosis;HIV-1 Nef: Negative effector of Fas and TNF-alpha;CD40/CD40L signaling;TNF receptor signaling pathway ;p75(NTR)-mediated signaling;FAS (CD95) signaling pathway;Ceramide signaling pathway (Consensus)

Recessive Scores

• pRec: 0.286

Intolerance Scores

• loftool: 0.509
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.361
• hipred: Y
• hipred_score: 0.579
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Birc3
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; normal 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); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: apoptotic process;cell surface receptor signaling pathway;I-kappaB kinase/NF-kappaB signaling;spermatogenesis;regulation of tumor necrosis factor-mediated signaling pathway;protein ubiquitination;protein deubiquitination;positive regulation of protein ubiquitination;tumor necrosis factor-mediated signaling pathway;regulation of toll-like receptor signaling pathway;NIK/NF-kappaB signaling;regulation of RIG-I signaling pathway;regulation of apoptotic process;negative regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;regulation of innate immune response;regulation of inflammatory response;protein heterooligomerization;regulation of necroptotic process;negative regulation of necroptotic process;regulation of nucleotide-binding oligomerization domain containing signaling pathway;inhibition of cysteine-type endopeptidase activity involved in apoptotic process;regulation of cysteine-type endopeptidase activity
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;protein-containing complex;membrane raft
• Molecular function: ubiquitin-protein transferase activity;protein binding;transferase activity;cysteine-type endopeptidase inhibitor activity involved in apoptotic process;metal ion binding;ubiquitin protein ligase activity