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

Gene ID: 29998, updated on 5-Mar-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 transcription, DNA-templated. Located in nucleus. Part of SWI/SNF complex. Implicated in Coffin-Siris syndrome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 1.9), prostate (RPKM 1.7) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47608196..47703277)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (50439021..50534101)
105.20220307 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: 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. 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. 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
  3. 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
  4. 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
  5. Polymorphisms in GLTSCR1 and ERCC2 are associated with the development of oligodendrogliomas. Yang P, et al. Cancer, 2005 Jun 1. PMID 15834925

See all (42) 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)

Genotypes

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 
part_of 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_2023_10

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

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