ABRAXAS2

abraxas 2, BRISC complex subunit, the group of BRISC complex

Basic information

Region (hg38): 10:124801819-124836667

Previous symbols: [ "KIAA0157", "FAM175B" ]

Links

ENSG00000165660 ∙ NCBI:23172 ∙ OMIM:611144 ∙ HGNC:28975 ∙ Uniprot:Q15018 ∙ 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 ABRAXAS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABRAXAS2 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in ABRAXAS2

This is a list of pathogenic ClinVar variants found in the ABRAXAS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-124801890-A-C		not specified	Uncertain significance (May 23, 2023)
10-124806899-C-G		not specified	Uncertain significance (Jan 29, 2025)
10-124819397-G-A		not specified	Uncertain significance (Jan 29, 2024)
10-124826622-C-T		not specified	Uncertain significance (Mar 28, 2023)
10-124826629-C-T		not specified	Uncertain significance (Mar 01, 2025)
10-124826640-A-T		not specified	Uncertain significance (Nov 06, 2023)
10-124826647-A-T		not specified	Uncertain significance (Aug 01, 2024)
10-124826676-A-T		not specified	Uncertain significance (Jan 10, 2023)
10-124826688-G-A		not specified	Uncertain significance (Jul 19, 2022)
10-124826691-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-124826718-A-G		not specified	Uncertain significance (Apr 23, 2024)
10-124828778-G-T		not specified	Uncertain significance (Dec 27, 2023)
10-124828779-C-A		not specified	Uncertain significance (Jun 29, 2022)
10-124829436-G-A		not specified	Uncertain significance (Dec 04, 2023)
10-124829460-C-G		not specified	Uncertain significance (Jan 23, 2025)
10-124829470-A-C		not specified	Uncertain significance (Jun 06, 2023)
10-124831352-G-A		not specified	Uncertain significance (Mar 21, 2023)
10-124831405-A-T		not specified	Uncertain significance (Jul 12, 2023)
10-124834523-G-C		not specified	Uncertain significance (Jan 08, 2024)
10-124834561-A-G		not specified	Uncertain significance (Oct 11, 2024)
10-124834574-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-124834636-C-T		not specified	Uncertain significance (Jan 18, 2023)
10-124834681-T-G		not specified	Uncertain significance (Mar 22, 2023)
10-124834699-G-A		not specified	Uncertain significance (Oct 20, 2021)
10-124834727-A-C		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABRAXAS2	protein_coding	protein_coding	ENST00000298492	9	34886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0202	0.979	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	189	237	0.796	0.0000127	2764
Missense in Polyphen		31	56.317	0.55046		685
Synonymous	0.561	81	87.7	0.924	0.00000520	759
Loss of Function	2.97	7	22.0	0.318	0.00000116	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000936	0.0000904
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000164	0.000163
South Asian	0.0000654	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates (PubMed:19214193, PubMed:20032457, PubMed:20656690, PubMed:24075985). May act as a central scaffold protein that assembles the various components of the BRISC complex and retains them in the cytoplasm (PubMed:20656690). Plays a role in regulating the onset of apoptosis via its role in modulating 'Lys- 63'-linked ubiquitination of target proteins (By similarity). 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 activities by enhancing its stability and cell surface expression (PubMed:24075985, PubMed:26344097). Down-regulates the response to bacterial lipopolysaccharide (LPS) via its role in IFNAR1 deubiquitination (PubMed:24075985). Required for normal induction of p53/TP53 in response to DNA damage (PubMed:25283148). Independent of the BRISC complex, promotes interaction between USP7 and p53/TP53, and thereby promotes deubiquitination of p53/TP53, preventing its degradation and resulting in increased p53/TP53-mediated transcription regulation and p53/TP53-dependent apoptosis in response to DNA damage (PubMed:25283148). {ECO:0000250|UniProtKB:Q3TCJ1, ECO:0000269|PubMed:19214193, ECO:0000269|PubMed:20032457, ECO:0000269|PubMed:20656690, ECO:0000269|PubMed:24075985, ECO:0000269|PubMed:25283148}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Metalloprotease DUBs;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.655
• hipred: Y
• hipred_score: 0.670
• ghis: 0.669

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Abraxas2
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: mitotic cell cycle;response to ischemia;chromosome segregation;attachment of spindle microtubules to kinetochore;protein deubiquitination;cell division;protein K63-linked deubiquitination;mitotic spindle assembly
• Cellular component: cytoplasm;centrosome;cytosol;midbody;spindle pole centrosome;microtubule minus-end;BRISC complex
• Molecular function: protein binding;microtubule binding;polyubiquitin modification-dependent protein binding