GeneBe

ABRAXAS1

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

Basic information

Region (hg38): 4:83459517-83523348

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.

  • not_specified (699 variants)
  • not_provided (435 variants)
  • Hereditary_cancer-predisposing_syndrome (15 variants)
  • ABRAXAS1-related_disorder (7 variants)
  • Hereditary_breast_ovarian_cancer_syndrome (6 variants)
  • Hereditary_breast_cancer,_ABRAXAS1-related (1 variants)
  • Malignant_tumor_of_breast (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. These statistics are base on transcript: NM_000139076.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
198
clinvar
2
clinvar
 201
missense
1
clinvar
510
clinvar
46
clinvar
 557
nonsense
1
clinvar
11
clinvar
 12
start loss
5
 5
frameshift
1
clinvar
14
clinvar
1
clinvar
 16
splice donor/acceptor (+/-2bp)
6
clinvar
 6
Total 0 3 547 245 2

Highest pathogenic variant AF is 0.0000724873

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ABRAXAS1protein_codingprotein_codingENST00000321945 962410
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
5.07e-70.8621256960521257480.000207
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.03842112130.9930.00001042715
Missense in Polyphen5469.8330.77327936
Synonymous-0.4287873.31.060.00000336730
Loss of Function1.541320.50.6340.00000112257

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002160.000213
Ashkenazi Jewish0.0001030.0000992
East Asian0.0001090.000109
Finnish0.0005080.000508
European (Non-Finnish)0.0002320.000229
Middle Eastern0.0001090.000109
South Asian0.0002050.000196
Other0.0003260.000326

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

loftool
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_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Abraxas1
Phenotype

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