BABAM1

protein-coding

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

Gene summary

Enables identical protein binding activity. Involved in several processes, including DNA repair-dependent chromatin remodeling; mitotic G2 DNA damage checkpoint signaling; and positive regulation of DNA repair. Located in cytoplasm and nuclear body. Part of BRCA1-A complex and BRISC complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C19orf62

MANE transcript

NM_014173.4

Inheritance

—

ClinVar variants

U:48B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr19:17,267,376-17,281,249

External References & Databases

Ensembl (ENSG00000105393)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BABAM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014173.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	1 clinvar		5
missense			36 clinvar			36
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	48	1	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 149 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014173.4	RefSeq	NP_054892.2	8	MANE Select
ENST00000598188.6	Ensembl	ENSP00000471605.1	8	MANE Select
NM_001033549.3	RefSeq	NP_001028721.1	8	Standard
NM_001288756.2	RefSeq	NP_001275685.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

double-strand break repair
double-strand break repair via nonhomologous end joining
chromatin organization
cell cycle
response to ionizing radiation

Molecular Function

protein binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
cytosol
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359435
Coding exons: 8
Length: 13900
Individuals with no LoFs: 124629
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 124636
p: 0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.17	153	199	0.767	0.0000118	2142
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00012	0.000099	rare
East Asian	0.000057	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000047	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

RVIS EVS: -0.32
RVIS percentile EVS: 31.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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