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    BRAT1 BRCA1 associated ATM activator 1 [ Homo sapiens (human) ]

    Gene ID: 221927, updated on 14-Nov-2024

    Summary

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    Official Symbol
    BRAT1provided by HGNC
    Official Full Name
    BRCA1 associated ATM activator 1provided by HGNC
    Primary source
    HGNC:HGNC:21701
    See related
    Ensembl:ENSG00000106009 MIM:614506; AllianceGenome:HGNC:21701
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BAAT1; RMFSL; NEDCAS; C7orf27
    Summary
    The protein encoded by this ubiquitously expressed gene interacts with the tumor suppressing BRCA1 (breast cancer 1) protein and and the ATM (ataxia telangiectasia mutated) protein. ATM is thought to be a master controller of cell cycle checkpoint signalling pathways that are required for cellular responses to DNA damage such as double-strand breaks that are induced by ionizing radiation and complexes with BRCA1 in the multi-protein complex BASC (BRAC1-associated genome surveillance complex). The protein encoded by this gene is thought to play a role in the DNA damage pathway regulated by BRCA1 and ATM. [provided by RefSeq, Mar 2012]
    Expression
    Ubiquitous expression in testis (RPKM 8.5), spleen (RPKM 7.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BRAT1 in Genome Data Viewer
    Location:
    7p22.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (2537810..2555524, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (2651326..2669118, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (2577444..2595158, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986759 Neighboring gene nonconserved acetylation island sequence 106 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2562611-2563123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2568003-2568977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2568978-2569951 Neighboring gene LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2570927-2571899 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:2573085-2574005 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:2574006-2574925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2575635-2576136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2576137-2576636 Neighboring gene microRNA 4648 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:2586847-2587013 Neighboring gene uncharacterized LOC124901849 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2595065-2595742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2606477-2607079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2607080-2607681 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:2611286-2612485 Neighboring gene IQ motif containing E Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2624592-2625163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2649707-2650280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2650281-2650854 Neighboring gene uncharacterized LOC107986760 Neighboring gene Sharpr-MPRA regulatory region 835 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2662913-2663422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2671045-2671776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2672509-2673241 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2673974-2674706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2676733-2677406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2677407-2678078 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2680771-2681442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2681443-2682114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25541 Neighboring gene Sharpr-MPRA regulatory region 8408 Neighboring gene tweety family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2692145-2692912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2699787-2700287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25543

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Compound heterozygous loss-of-function variants in BRAT1 cause lethal neonatal rigidity and multifocal seizure syndrome. Li S, et al. Mol Genet Genomic Med, 2023 Jan. PMID 36367347, Free PMC Article
    2. Clinical variability at the mild end of BRAT1-related spectrum: Evidence from two families with genotype-phenotype discordance. Nuovo S, et al. Hum Mutat, 2022 Jan. PMID 34747546
    3. Novel variant in BRAT1 with the lethal neonatal rigidity and multifocal seizure syndrome. Li W, et al. Pediatr Res, 2022 Feb. PMID 33790413
    4. Compound heterozygous BRAT1 mutations cause familial Ohtahara syndrome with hypertonia and microcephaly. Saitsu H, et al. J Hum Genet, 2014 Dec. PMID 25319849
    5. A novel pathogenic variant of BRAT1 gene causes rigidity and multifocal seizure syndrome, lethal neonatal. Pourahmadiyan A, et al. Int J Neurosci, 2021 Sep. PMID 32345087

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Neuronal differentiation requires BRAT1 complex to remove REST from chromatin.
      Title: Neuronal differentiation requires BRAT1 complex to remove REST from chromatin.
    2. BRAT1-related disorders: phenotypic spectrum and phenotype-genotype correlations from 97 patients.
      Title: BRAT1-related disorders: phenotypic spectrum and phenotype-genotype correlations from 97 patients.
    3. Clinical and Neurophysiologic Phenotypes in Neonates With BRAT1 Encephalopathy.
      Title: Clinical and Neurophysiologic Phenotypes in Neonates With BRAT1 Encephalopathy.
    4. Compound heterozygous loss-of-function variants in BRAT1 cause lethal neonatal rigidity and multifocal seizure syndrome.
      Title: Compound heterozygous loss-of-function variants in BRAT1 cause lethal neonatal rigidity and multifocal seizure syndrome.
    5. BRAT1 links Integrator and defective RNA processing with neurodegeneration.
      Title: BRAT1 links Integrator and defective RNA processing with neurodegeneration.
    6. Clinical variability at the mild end of BRAT1-related spectrum: Evidence from two families with genotype-phenotype discordance.
      Title: Clinical variability at the mild end of BRAT1-related spectrum: Evidence from two families with genotype-phenotype discordance.
    7. A novel pathogenic variant of BRAT1 gene causes rigidity and multifocal seizure syndrome, lethal neonatal.
      Title: A novel pathogenic variant of BRAT1 gene causes rigidity and multifocal seizure syndrome, lethal neonatal.
    8. Novel variant in BRAT1 with the lethal neonatal rigidity and multifocal seizure syndrome.
      Title: Novel variant in BRAT1 with the lethal neonatal rigidity and multifocal seizure syndrome.
    9. BRAT1 encephalopathy: a recessive cause of epilepsy of infancy with migrating focal seizures.
      Title: BRAT1 encephalopathy: a recessive cause of epilepsy of infancy with migrating focal seizures.
    10. A first reported case of Chinese origin was identified with a BRAT1 mutation linked to lethal neonatal rigidity and multifocal seizure syndrome.
      Title: BRAT1 Mutation: The First Reported Case of Chinese Origin and Review of the Literature.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Neonatal-onset encephalopathy with rigidity and seizures
    MedGen: C3281029 OMIM: 614498 GeneReviews: Not available
    		not available
    Neurodevelopmental disorder with cerebellar atrophy and with or without seizures
    MedGen: C4748032 OMIM: 618056 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC22916

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glucose metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrion localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to ionizing radiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    BRCA1-associated ATM activator 1
    Names
    BRCA1-associated protein required for ATM activation protein 1
    HEAT repeat-containing protein C7orf27

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_032167.1 RefSeqGene

      Range
      5235..22949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350626.2 → NP_001337555.1  BRCA1-associated ATM activator 1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC092488
      Conserved Domains (1) summary
      sd00044
      Location:449 → 490
      HEAT; HEAT repeat [structural motif]

    2. NM_001350627.2 → NP_001337556.1  BRCA1-associated ATM activator 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon and uses an alternate in-frame splice junction in the 3' coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus and lacks an internal segment compared to isoform 1.
      Source sequence(s)
      AC092488
      Conserved Domains (1) summary
      sd00044
      Location:274 → 315
      HEAT; HEAT repeat [structural motif]

    3. NM_152743.4 → NP_689956.2  BRCA1-associated ATM activator 1 isoform 2

      See identical proteins and their annotated locations for NP_689956.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 3' end of the coding sequence compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC092488, AI963076, BC015632, BP363179
      Consensus CDS
      CCDS5334.1
      UniProtKB/Swiss-Prot
      A4D200, C9JY24, Q6PJG6, Q8IW85, Q8IZ43, Q8WVR8, Q96IV9, Q9H7J8, Q9UFA3
      Related
      ENSP00000339637.4, ENST00000340611.9
      Conserved Domains (1) summary
      sd00044
      Location:449 → 490
      HEAT; HEAT repeat [structural motif]

    RNA

    1. NR_146879.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' end and contains an alternate exon in the 3' end compared to variant 1.
      Source sequence(s)
      AC092488

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      2537810..2555524 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420033.1 → XP_047275989.1  BRCA1-associated ATM activator 1 isoform X11

    2. XM_017011834.2 → XP_016867323.1  BRCA1-associated ATM activator 1 isoform X5

    3. XM_047420028.1 → XP_047275984.1  BRCA1-associated ATM activator 1 isoform X3

    4. XM_047420032.1 → XP_047275988.1  BRCA1-associated ATM activator 1 isoform X9

    5. XM_011515179.3 → XP_011513481.1  BRCA1-associated ATM activator 1 isoform X2

      Conserved Domains (1) summary
      sd00044
      Location:449 → 475
      HEAT; HEAT repeat [structural motif]

    6. XM_017011836.3 → XP_016867325.1  BRCA1-associated ATM activator 1 isoform X10

    7. XM_011515186.3 → XP_011513488.1  BRCA1-associated ATM activator 1 isoform X8

    8. XM_011515181.3 → XP_011513483.1  BRCA1-associated ATM activator 1 isoform X4

      Conserved Domains (1) summary
      sd00044
      Location:450 → 476
      HEAT; HEAT repeat [structural motif]

    9. XM_011515177.3 → XP_011513479.1  BRCA1-associated ATM activator 1 isoform X1

      See identical proteins and their annotated locations for XP_011513479.1

      Conserved Domains (1) summary
      sd00044
      Location:450 → 476
      HEAT; HEAT repeat [structural motif]

    10. XM_011515178.2 → XP_011513480.1  BRCA1-associated ATM activator 1 isoform X1

      See identical proteins and their annotated locations for XP_011513480.1

      Conserved Domains (1) summary
      sd00044
      Location:450 → 476
      HEAT; HEAT repeat [structural motif]

    11. XM_047420031.1 → XP_047275987.1  BRCA1-associated ATM activator 1 isoform X7

    12. XM_047420030.1 → XP_047275986.1  BRCA1-associated ATM activator 1 isoform X6

    13. XM_011515184.4 → XP_011513486.1  BRCA1-associated ATM activator 1 isoform X6

      See identical proteins and their annotated locations for XP_011513486.1

      Conserved Domains (1) summary
      sd00044
      Location:275 → 301
      HEAT; HEAT repeat [structural motif]

    14. XM_024446682.2 → XP_024302450.1  BRCA1-associated ATM activator 1 isoform X15

      Conserved Domains (2) summary
      sd00044
      Location:52 → 88
      HEAT; HEAT repeat [structural motif]
      pfam02985
      Location:53 → 82
      HEAT; HEAT repeat

    15. XM_047420036.1 → XP_047275992.1  BRCA1-associated ATM activator 1 isoform X14

    16. XM_047420034.1 → XP_047275990.1  BRCA1-associated ATM activator 1 isoform X12

    17. XM_047420035.1 → XP_047275991.1  BRCA1-associated ATM activator 1 isoform X13

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      2651326..2669118 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357549.1 → XP_054213524.1  BRCA1-associated ATM activator 1 isoform X11

    2. XM_054357542.1 → XP_054213517.1  BRCA1-associated ATM activator 1 isoform X5

    3. XM_054357540.1 → XP_054213515.1  BRCA1-associated ATM activator 1 isoform X3

    4. XM_054357547.1 → XP_054213522.1  BRCA1-associated ATM activator 1 isoform X9

    5. XM_054357539.1 → XP_054213514.1  BRCA1-associated ATM activator 1 isoform X2

    6. XM_054357548.1 → XP_054213523.1  BRCA1-associated ATM activator 1 isoform X10

    7. XM_054357546.1 → XP_054213521.1  BRCA1-associated ATM activator 1 isoform X8

    8. XM_054357541.1 → XP_054213516.1  BRCA1-associated ATM activator 1 isoform X4

    9. XM_054357537.1 → XP_054213512.1  BRCA1-associated ATM activator 1 isoform X1

    10. XM_054357538.1 → XP_054213513.1  BRCA1-associated ATM activator 1 isoform X1

    11. XM_054357545.1 → XP_054213520.1  BRCA1-associated ATM activator 1 isoform X7

    12. XM_054357544.1 → XP_054213519.1  BRCA1-associated ATM activator 1 isoform X6

    13. XM_054357543.1 → XP_054213518.1  BRCA1-associated ATM activator 1 isoform X6

    14. XM_054357553.1 → XP_054213528.1  BRCA1-associated ATM activator 1 isoform X15

    15. XM_054357552.1 → XP_054213527.1  BRCA1-associated ATM activator 1 isoform X14

    16. XM_054357550.1 → XP_054213525.1  BRCA1-associated ATM activator 1 isoform X12

    17. XM_054357551.1 → XP_054213526.1  BRCA1-associated ATM activator 1 isoform X13

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PJG6.2 GenPept UniProtKB/Swiss-Prot:Q6PJG6

    Gene LinkOut

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