BABAM1

BRISC and BRCA1 A complex member 1, the group of BRISC complex|BRCA1 A complex

Basic information

Region (hg38): 19:17267375-17281249

Previous symbols: [ "C19orf62" ]

Links

ENSG00000105393 ∙ NCBI:29086 ∙ OMIM:612766 ∙ HGNC:25008 ∙ Uniprot:Q9NWV8 ∙ 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 BABAM1 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BABAM1 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	0	1

Variants in BABAM1

This is a list of pathogenic ClinVar variants found in the BABAM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17268749-C-T			Benign (Feb 23, 2021)
19-17268975-A-G		not specified	Uncertain significance (Sep 26, 2022)
19-17269000-C-T		not specified	Uncertain significance (Oct 06, 2023)
19-17269060-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-17274114-G-T		not specified	Uncertain significance (Nov 09, 2023)
19-17275816-T-G		not specified	Uncertain significance (Jun 01, 2023)
19-17276528-C-A		not specified	Uncertain significance (Oct 16, 2023)
19-17276539-T-C		not specified	Uncertain significance (Jun 26, 2023)
19-17276560-G-C		not specified	Uncertain significance (May 08, 2023)
19-17276599-A-T		not specified	Uncertain significance (Jan 02, 2024)
19-17276859-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-17276889-G-A		not specified	Uncertain significance (Aug 08, 2022)
19-17278845-G-A		not specified	Uncertain significance (Jan 25, 2024)
19-17278845-G-C		not specified	Uncertain significance (Feb 14, 2023)
19-17278891-A-G		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BABAM1	protein_coding	protein_coding	ENST00000359435	8	13900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0373	124629	0	7	124636	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	153	199	0.767	0.0000118	2142
Missense in Polyphen		46	73.577	0.6252		697
Synonymous	-0.0254	79	78.7	1.00	0.00000505	619
Loss of Function	3.31	1	14.7	0.0683	6.20e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000118	0.0000994
East Asian	0.0000569	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000472	0.0000442
Middle Eastern	0.0000569	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

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. In the BRCA1-A complex, it is required for the complex integrity and its localization at DSBs. Component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys- 63'-linked ubiquitin in various substrates (PubMed:24075985, PubMed:26195665). In these 2 complexes, it is probably required to maintain the stability of BABAM2 and help the 'Lys-63'-linked deubiquitinase activity mediated by BRCC3/BRCC36 component. The BRISC complex is required for normal mitotic spindle assembly and microtubule attachment to kinetochores via its role in deubiquitinating NUMA1 (PubMed:26195665). 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). {ECO:0000269|PubMed:19261746, ECO:0000269|PubMed:19261748, ECO:0000269|PubMed:19261749}.
• 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: 0.109

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.107
• hipred: Y
• hipred_score: 0.697
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Babam1

Gene ontology

• Biological process: double-strand break repair;double-strand break repair via nonhomologous end joining;chromatin organization;cell cycle;response to ionizing radiation;protein deubiquitination;positive regulation of DNA repair;cell division;protein K63-linked deubiquitination;signal transduction involved in G2 DNA damage checkpoint
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;nuclear body;BRCA1-A complex;BRISC complex
• Molecular function: protein binding