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    BICRA BRD4 interacting chromatin remodeling complex associated protein [ Homo sapiens (human) ]

    Gene ID: 29998, updated on 10-Dec-2024

    Summary

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    Official Symbol
    BICRAprovided by HGNC
    Official Full Name
    BRD4 interacting chromatin remodeling complex associated proteinprovided by HGNC
    Primary source
    HGNC:HGNC:4332
    See related
    Ensembl:ENSG00000063169 MIM:605690; AllianceGenome:HGNC:4332
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CSS12; GLTSCR1; SMARCK1
    Summary
    Enables transcription regulator activator activity. Involved in positive regulation of DNA-templated transcription. Located in nucleus. Part of SWI/SNF complex. Implicated in Coffin-Siris syndrome 12. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 1.9), prostate (RPKM 1.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BICRA in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47608196..47703277)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (50439021..50534101)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48111453..48206534)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14868 Neighboring gene RNA, 7SL, cytoplasmic 322, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48115860-48116691 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48118354-48119183 Neighboring gene BICRA antisense RNA 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48123829-48124389 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48130149-48130723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48135834-48136477 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48148954-48149534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48153858-48154564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48164109-48164610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48164611-48165110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48196325-48196884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48196885-48197442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48201812-48202354 Neighboring gene Sharpr-MPRA regulatory region 9389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48228755-48229521 Neighboring gene uncharacterized LOC124904733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48238171-48238671 Neighboring gene EH domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48249496-48249996 Neighboring gene small nucleolar RNA, C/D box 23 Neighboring gene NOP53 ribosome biogenesis factor

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of a novel BICRA variant leading to the newly described Coffin-Siris syndrome 12. Asadauskaitė G, et al. Brain Dev, 2023 Mar. PMID 36437209
    2. Association of chromosome 19q13.2-3 haplotypes with basal cell carcinoma: tentative delineation of an involved region using data for single nucleotide polymorphisms in two cohorts. Rockenbauer E, et al. Carcinogenesis, 2002 Jul. PMID 12117772
    3. Genome-wide association study identifies an acute myeloid leukemia susceptibility locus near BICRA. Walker CJ, et al. Leukemia, 2019 Mar. PMID 30291333, Free PMC Article
    4. Polymorphisms in GLTSCR1 and ERCC2 are associated with the development of oligodendrogliomas. Yang P, et al. Cancer, 2005 Jun 1. PMID 15834925
    5. GLTSCR1 coordinates alternative splicing and transcription elongation of ZO1 to regulate colorectal cancer progression. Han F, et al. J Mol Cell Biol, 2022 Jun 11. PMID 35218185, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of a novel BICRA variant leading to the newly described Coffin-Siris syndrome 12.
      Title: Identification of a novel BICRA variant leading to the newly described Coffin-Siris syndrome 12.
    2. GLTSCR1 coordinates alternative splicing and transcription elongation of ZO1 to regulate colorectal cancer progression.
      Title: GLTSCR1 coordinates alternative splicing and transcription elongation of ZO1 to regulate colorectal cancer progression.
    3. BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms.
      Title: BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms.
    4. Identifies an acute myeloid leukemia susceptibility locus near BICRA.
      Title: Genome-wide association study identifies an acute myeloid leukemia susceptibility locus near BICRA.
    5. No significant association of GLTSCR1 rs1035938 and lung cancer was found in five genetic models in Chinese population. Haplotypes consisting of PPP1R13L, CD3EAP and GLTSCR1 SNPs on Chr19q13.3 may associate with lung cancer risk in the Chinese population.
      Title: GLTSCR1, ATM, PPP1R13L and CD3EAP Genetic Variants and Lung Cancer Risk in a Chinese Population.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: DNA repair gene polymorphisms and risk of adult meningioma, glioma, and acoustic neuroma.
    8. Polymorphisms in GLTSCR1 are associated with the development of oligodendrogliomas.
      Title: Polymorphisms in GLTSCR1 and ERCC2 are associated with the development of oligodendrogliomas.
    Submit: New GeneRIF Correction

    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
    Coffin-Siris syndrome 12
    MedGen: C5444111 OMIM: 619325 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription regulator activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cell population proliferation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of GBAF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of SWI/SNF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    BRD4-interacting chromatin-remodeling complex-associated protein
    Names
    BRD4 interacting chromatin remodelling complex associated protein
    glioma tumor suppressor candidate region gene 1 protein

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001394372.1 → NP_001381301.1  BRD4-interacting chromatin-remodeling complex-associated protein

      Status: VALIDATED

      Source sequence(s)
      AC008985, AC010331, AC010519
      Consensus CDS
      CCDS46134.1
      UniProtKB/Swiss-Prot
      A8MW01, Q9NZM4
      UniProtKB/TrEMBL
      A0A087WWH3
      Related
      ENSP00000469738.2, ENST00000594866.3
      Conserved Domains (2) summary
      PHA03247
      Location:314 → 792
      PHA03247; large tegument protein UL36; Provisional
      pfam15249
      Location:1091 → 1192
      GLTSCR1; Conserved region of unknown function on GLTSCR protein

    2. NM_015711.3 → NP_056526.3  BRD4-interacting chromatin-remodeling complex-associated protein

      See identical proteins and their annotated locations for NP_056526.3

      Status: VALIDATED

      Source sequence(s)
      AA961479, AA994408, AF182077, BC032065, BX362862
      Consensus CDS
      CCDS46134.1
      UniProtKB/Swiss-Prot
      A8MW01, Q9NZM4
      UniProtKB/TrEMBL
      A0A087WWH3
      Related
      ENSP00000379946.2, ENST00000396720.7
      Conserved Domains (2) summary
      PHA03247
      Location:314 → 792
      PHA03247; large tegument protein UL36; Provisional
      pfam15249
      Location:1091 → 1192
      GLTSCR1; Conserved region of unknown function on GLTSCR protein

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      47608196..47703277
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      50439021..50534101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZM4.2 GenPept UniProtKB/Swiss-Prot:Q9NZM4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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