ABRAXAS1

abraxas 1, BRCA1 A complex subunit, the group of BRCA1 A complex

Basic information

Region (hg38): 4:83459516-83523348

Previous symbols: [ "CCDC98", "FAM175A" ]

Links

ENSG00000163322 ∙ NCBI:84142 ∙ OMIM:611143 ∙ HGNC:25829 ∙ Uniprot:Q6UWZ7 ∙ 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 ABRAXAS1 gene.

• Hereditary cancer-predisposing syndrome (419 variants)
• not provided (393 variants)
• not specified (73 variants)
• Inborn genetic diseases (10 variants)
• Hereditary breast ovarian cancer syndrome (7 variants)
• Malignant tumor of breast (1 variants)
• Hereditary breast cancer, ABRAXAS1-related (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABRAXAS1 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			1	144	1	146
missense			347	11	1	359
nonsense			11			11
start loss			5			5
frameshift			9			9
inframe indel			6			6
splice donor/acceptor (+/-2bp)			5			5
splice region			8	6	2	16
non coding			17	36	28	81
Total	0	0	401	191	30

Variants in ABRAXAS1

This is a list of pathogenic ClinVar variants found in the ABRAXAS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-83459755-G-A		not specified	Likely benign (Sep 26, 2022)
4-83461030-T-C		not specified	Uncertain significance (Nov 04, 2022)
4-83461144-G-A		not specified	Uncertain significance (Sep 16, 2021)
4-83461184-G-C		not specified	Uncertain significance (Dec 21, 2022)
4-83461185-A-T		not specified	Uncertain significance (Aug 08, 2022)
4-83462219-TC-T			Benign (Jun 18, 2021)
4-83462476-G-A		not specified	Uncertain significance (Aug 26, 2023)
4-83462479-G-A		not specified	Uncertain significance (Jul 27, 2022)
4-83462482-G-A		not specified	Uncertain significance (Jun 23, 2022)
4-83462482-G-T		not specified	Uncertain significance (Feb 11, 2022)
4-83462485-C-G		not specified	Likely benign (Oct 22, 2023)
4-83462485-C-T		not specified	Conflicting classifications of pathogenicity (Oct 23, 2023)
4-83462486-G-A		Inborn genetic diseases	Uncertain significance (Jul 30, 2023)
4-83462488-G-A		not specified	Uncertain significance (Feb 13, 2022)
4-83462492-A-T		not specified	Uncertain significance (May 19, 2022)
4-83462493-T-C		not specified	Likely benign (Jun 30, 2022)
4-83462497-C-G		not specified	Uncertain significance (Mar 24, 2022)
4-83462498-C-T		not specified	Uncertain significance (May 01, 2022)
4-83462501-A-C		not specified	Uncertain significance (Apr 19, 2022)
4-83462504-C-T		not specified	Uncertain significance (Feb 13, 2024)
4-83462505-C-G		not specified	Uncertain significance (Jun 27, 2023)
4-83462505-C-T		not specified	Likely benign (Jul 13, 2022)
4-83462508-C-A		not specified	Uncertain significance (Oct 24, 2022)
4-83462510-T-C		not specified	Uncertain significance (Feb 22, 2024)
4-83462511-CT-C		not specified	Uncertain significance (Nov 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABRAXAS1	protein_coding	protein_coding	ENST00000321945	9	62410

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.07e-7	0.862	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0384	211	213	0.993	0.0000104	2715
Missense in Polyphen		54	69.833	0.77327		936
Synonymous	-0.428	78	73.3	1.06	0.00000336	730
Loss of Function	1.54	13	20.5	0.634	0.00000112	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000213
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000232	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.000205	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in DNA damage response and double-strand break (DSB) repair. Component of the BRCA1-A complex, acting as a central scaffold protein that assembles the various components of the complex and mediates the recruitment of BRCA1. The BRCA1-A complex specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesion sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at DSBs. This complex also possesses deubiquitinase activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. {ECO:0000269|PubMed:17525340, ECO:0000269|PubMed:17643121, ECO:0000269|PubMed:17643122, ECO:0000269|PubMed:18077395, ECO:0000269|PubMed:19261748, ECO:0000269|PubMed:22357538, ECO:0000269|PubMed:26778126}.
• Disease: DISEASE: Breast cancer (BC) [MIM:114480]: A common malignancy originating from breast epithelial tissue. Breast neoplasms can be distinguished by their histologic pattern. Invasive ductal carcinoma is by far the most common type. Breast cancer is etiologically and genetically heterogeneous. Important genetic factors have been indicated by familial occurrence and bilateral involvement. Mutations at more than one locus can be involved in different families or even in the same case. {ECO:0000269|PubMed:22357538, ECO:0000269|PubMed:25105795}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• 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;ATM pathway (Consensus)

Intolerance Scores

• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.01

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.632
• ghis: 0.411

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Abraxas1

Gene ontology

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