BABAM2

BRISC and BRCA1 A complex member 2, the group of MicroRNA protein coding host genes|BRISC complex|BRCA1 A complex

Basic information

Region (hg38): 2:27889940-28338901

Previous symbols: [ "BRE" ]

Links

ENSG00000158019 ∙ NCBI:9577 ∙ OMIM:610497 ∙ HGNC:1106 ∙ Uniprot:Q9NXR7 ∙ 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 BABAM2 gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BABAM2 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						0
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	7	1	0

Variants in BABAM2

This is a list of pathogenic ClinVar variants found in the BABAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27894669-C-T		not specified	Uncertain significance (Oct 25, 2022)
2-27929851-G-C		not specified	Uncertain significance (Jul 20, 2022)
2-27929881-A-G		not specified	Uncertain significance (Nov 14, 2023)
2-28025250-A-G		not specified	Uncertain significance (Jul 11, 2023)
2-28025323-G-A		not specified	Uncertain significance (Dec 06, 2021)
2-28025340-A-T		not specified	Uncertain significance (Dec 14, 2023)
2-28025394-A-G		not specified	Uncertain significance (Dec 21, 2022)
2-28025410-A-G		not specified	Uncertain significance (Mar 29, 2022)
2-28045744-G-A		not specified	Uncertain significance (Jan 26, 2022)
2-28129326-A-G		Malignant tumor of prostate	Uncertain significance (-)
2-28129359-A-G		not specified	Uncertain significance (Apr 07, 2023)
2-28129371-G-A		not specified	Uncertain significance (Sep 26, 2022)
2-28237202-T-G		not specified	Uncertain significance (Mar 02, 2023)
2-28244787-G-A		not specified	Uncertain significance (May 03, 2023)
2-28298391-G-A		not specified	Uncertain significance (Jan 09, 2024)
2-28298446-C-T		not specified	Uncertain significance (May 17, 2023)
2-28310080-A-C			Likely benign (Feb 01, 2023)
2-28327306-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-28327369-G-A		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BABAM2	protein_coding	protein_coding	ENST00000344773	11	448961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.167	0.833	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	158	223	0.707	0.0000115	2695
Missense in Polyphen		26	59.12	0.43978		713
Synonymous	-0.524	89	82.9	1.07	0.00000425	802
Loss of Function	3.69	7	28.1	0.249	0.00000159	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000452	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000106	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). The BRCA1-A complex also possesses deubiquitinase activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX (PubMed:17525341, PubMed:19261746, PubMed:19261749, PubMed:19261748). In the BRCA1-A complex, it acts as an adapter that bridges the interaction between BABAM1/NBA1 and the rest of the complex, thereby being required for the complex integrity and modulating the E3 ubiquitin ligase activity of the BRCA1-BARD1 heterodimer (PubMed:21282113, PubMed:19261748). Component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates (PubMed:19214193, PubMed:24075985, PubMed:25283148, PubMed:26195665). Within the BRISC complex, acts as an adapter that bridges the interaction between BABAM1/NBA1 and the rest of the complex, thereby being required for the complex integrity (PubMed:21282113). The BRISC complex is required for normal mitotic spindle assembly and microtubule attachment to kinetochores via its role in deubiquitinating NUMA1 (PubMed:26195665). The BRISC complex plays a role in interferon signaling via its role in the deubiquitination of the interferon receptor IFNAR1; deubiquitination increases IFNAR1 activity by enhancing its stability and cell surface expression (PubMed:24075985). Down- regulates the response to bacterial lipopolysaccharide (LPS) via its role in IFNAR1 deubiquitination (PubMed:24075985). May play a role in homeostasis or cellular differentiation in cells of neural, epithelial and germline origins. May also act as a death receptor-associated anti-apoptotic protein, which inhibits the mitochondrial apoptotic pathway. May regulate TNF-alpha signaling through its interactions with TNFRSF1A; however these effects may be indirect (PubMed:15465831). {ECO:0000269|PubMed:14636569, ECO:0000269|PubMed:19261748, ECO:0000269|PubMed:19261749, ECO:0000269|PubMed:24075985, ECO:0000269|PubMed:26195665, ECO:0000305|PubMed:15465831}.
• Pathway: Homologous recombination - Homo sapiens (human);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;Nonhomologous End-Joining (NHEJ);DNA Double-Strand Break Repair;Homology Directed Repair;Post-translational protein modification;Metabolism of proteins;G2/M DNA damage checkpoint;G2/M Checkpoints;Cell Cycle Checkpoints;Metalloprotease DUBs;Deubiquitination;Cell Cycle;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response;Processing of DNA double-strand break ends (Consensus)

Recessive Scores

• pRec: 0.236

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.708
• ghis: 0.417

Essentials

• essential_gene_gene_trap: K

Mouse Genome Informatics

• Gene name: Babam2
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: double-strand break repair;double-strand break repair via nonhomologous end joining;chromatin organization;apoptotic process;cellular response to DNA damage stimulus;cell cycle;signal transduction;response to ionizing radiation;protein deubiquitination;negative regulation of apoptotic process;positive regulation of DNA repair;cell division;protein K63-linked deubiquitination;signal transduction involved in G2 DNA damage checkpoint
• Cellular component: nuclear ubiquitin ligase complex;nucleus;nucleoplasm;cytoplasm;cytosol;BRCA1-A complex;BRISC complex
• Molecular function: peroxisome targeting sequence binding;tumor necrosis factor receptor binding;protein binding;polyubiquitin modification-dependent protein binding