BABAM1
BRISC and BRCA1 A complex member 1, the group of BRISC complex|BRCA1 A complex
Basic information
Region (hg38): 19:17267376-17281249
Previous symbols: [ "C19orf62" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 14 | 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) | ||
| 19-17275810-G-A | not specified | Uncertain significance (May 13, 2024) | ||
| 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) | ||
| 19-17278918-C-T | not specified | Uncertain significance (May 15, 2024) |
GnomAD
Source:
| 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:
- 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
- loftool
- 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
- Phenotype
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