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    BRINP3 BMP/retinoic acid inducible neural specific 3 [ Homo sapiens (human) ]

    Gene ID: 339479, updated on 10-Dec-2024

    Summary

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    Official Symbol
    BRINP3provided by HGNC
    Official Full Name
    BMP/retinoic acid inducible neural specific 3provided by HGNC
    Primary source
    HGNC:HGNC:22393
    See related
    Ensembl:ENSG00000162670 MIM:618390; AllianceGenome:HGNC:22393
    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
    FAM5C; DBCCR1L; DBCCR1L1
    Summary
    This gene is overexpressed in pituitary tumors but is underexpressed in tongue squamous cell carcinomas, ulcerative colitis, and peri-implantitis. Polymorphisms that increase expression of this gene have been shown to increase vascular inflammation, and an association of this gene with myocardial infarction has been demonstrated. Finally, hypermethylation of this gene may find usefulness as a biomarker for gastric cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
    Expression
    Biased expression in brain (RPKM 4.5), small intestine (RPKM 2.0) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BRINP3 in Genome Data Viewer
    Location:
    1q31.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (190097658..190477864, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (189444081..189824968, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (190066788..190446994, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak549 silencer Neighboring gene long intergenic non-protein coding RNA 1701 Neighboring gene MPRA-validated peak550 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr1:189868671-189869595 Neighboring gene MPRA-validated peak553 silencer Neighboring gene DExH-box helicase 29 pseudogene Neighboring gene MPRA-validated peak555 silencer Neighboring gene MPRA-validated peak561 silencer Neighboring gene uncharacterized LOC105371659 Neighboring gene MPRA-validated peak564 silencer Neighboring gene MPRA-validated peak563 silencer Neighboring gene MPRA-validated peak566 silencer Neighboring gene uncharacterized LOC105371658 Neighboring gene MPRA-validated peak568 silencer Neighboring gene MPRA-validated peak569 silencer Neighboring gene MPRA-validated peak571 silencer Neighboring gene BRINP3 divergent transcript Neighboring gene MPRA-validated peak575 silencer Neighboring gene long intergenic non-protein coding RNA 1720 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:190647894-190649093 Neighboring gene MPRA-validated peak580 silencer

    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. Bone morphogenetic protein and retinoic acid-inducible neural specific protein-3 is expressed in gonadotrope cell pituitary adenomas and induces proliferation, migration, and invasion. Shorts-Cary L, et al. Endocrinology, 2007 Mar. PMID 17138656
    2. A preliminary study on the FAM5C expression in generalized chronic periodontitis. Ribeiro FV, et al. Oral Dis, 2012 Mar. PMID 22355820
    3. The relationships between FAM5C SNP (rs10920501) variability and metabolic syndrome and inflammation in women with coronary heart disease. Cline JL, et al. Biol Res Nurs, 2013 Apr. PMID 22013132, Free PMC Article
    4. Id4 and FABP7 are preferentially expressed in cells with astrocytic features in oligodendrogliomas and oligoastrocytomas. Liang Y, et al. BMC Clin Pathol, 2005 Jul 15. PMID 16018821, Free PMC Article
    5. Interaction of FAM5C with UDP-glucose:glycoprotein glucosyltransferase 1 (UGGT1): Implication of N-glycosylation in FAM5C secretion. Terao Y, et al. Biochem Biophys Res Commun, 2017 May 6. PMID 28351617

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the association of serum OGN and FAM5C levels and muscle mass with bone mineral density (BMD), bone turnover markers, and the presence of vertebral fractures (VFs) in 156 postmenopausal women with type 2 diabetes mellitus, is reported.
      Title: Association of osteoglycin and FAM5C with bone turnover markers, bone mineral density, and vertebral fractures in postmenopausal women with type 2 diabetes mellitus.
    2. Data show that all the six inflammation-related CpG-SNPs genotypes including IL1B rs16944, IL1R2 rs2071008, PLA2G7 rs9395208, FAM5C rs12732361, CD40 rs1800686, and CD36 rs2065666 were associated with coronary heart disease (CHD), suggesting an important role of inflammation in the risk of CHD.
      Title: Association of six CpG-SNPs in the inflammation-related genes with coronary heart disease.
    3. FAM5C is a risk factor for cerebral infarction in type 2 diabetic patients.
      Title: The Expression of microRNA-223 and FAM5C in Cerebral Infarction Patients with Diabetes Mellitus.
    4. The results demonstrated that FAM5C is an N-glycosylated protein, and N-glycosylation by UGGT1 is necessary for the secretion of FAM5C.
      Title: Interaction of FAM5C with UDP-glucose:glycoprotein glucosyltransferase 1 (UGGT1): Implication of N-glycosylation in FAM5C secretion.
    5. study provides evidence that the BRINP3 polymorphic variant rs1342913 and low level of BRINP3 expression are associated with peri-implantitis, independently from the presence of chronic periodontitis.
      Title: Different contribution of BRINP3 gene in chronic periodontitis and peri-implantitis: a cross-sectional study.
    6. Data show that family with sequence similarity 5 member C protein FAM5C-positive endothelium expressed intercellular adhesion molecule-1 (ICAM-1) or vascular cell adhesion molecule-1 (VCAM-1).
      Title: Family with sequence similarity 5, member C (FAM5C) increases leukocyte adhesion molecules in vascular endothelial cells: implication in vascular inflammation.
    7. Under expression of BRINP3 is associated with the pathogenesis of ulcerative colitis.
      Title: Mucosal transcriptomics implicates under expression of BRINP3 in the pathogenesis of ulcerative colitis.
    8. findings suggest a protective effect of T allele in women with a history of myocardial infarction (MI;) genotype of FAM5C rs10920501 explained about 7percent of variability of age of onset of coronary heart disease in women who have had an MI; FAM5C remains a gene of interest in a complex disease process
      Title: The relationships between FAM5C SNP (rs10920501) variability and metabolic syndrome and inflammation in women with coronary heart disease.
    9. expression does not contribute to chronic periodontitis
      Title: A preliminary study on the FAM5C expression in generalized chronic periodontitis.
    10. Hypermethylated FAM5C and MYLK in serum are strongly associated with the development of gastric cancer and can be used as potential biomarkers for diagnosis and pre-warning.
      Title: Hypermethylated FAM5C and MYLK in serum as diagnosis and pre-warning markers for gastric cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study.
    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

    Process Evidence Code Pubs
    involved_in cellular response to retinoic acid IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to retinoic acid ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in central nervous system neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in central nervous system neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of mitotic cell cycle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of mitotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    BMP/retinoic acid-inducible neural-specific protein 3
    Names
    DBCCR1-like protein 1
    bone morphogenetic protein/retinoic acid inducible neural-specific 3
    family with sequence similarity 5, member C
    protein FAM5C

    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_001317188.2 → NP_001304117.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK294365, AL365402, HY113909
      UniProtKB/Swiss-Prot
      Q76B58
      Conserved Domains (1) summary
      cl02616
      Location:39 → 161
      MACPF; MAC/Perforin domain

    2. NM_199051.3 → NP_950252.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_950252.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB111893, AL365402, DA809835, DC330008
      Consensus CDS
      CCDS1373.1
      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58
      Related
      ENSP00000356432.3, ENST00000367462.5
      Conserved Domains (2) summary
      smart00457
      Location:79 → 263
      MACPF; membrane-attack complex / perforin
      pfam19052
      Location:319 → 766
      BRINP; BMP/retinoic acid-inducible neural-specific 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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      190097658..190477864 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001129.2 → XP_016856618.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

      UniProtKB/Swiss-Prot
      Q76B58
      Conserved Domains (1) summary
      cl02616
      Location:39 → 161
      MACPF; MAC/Perforin domain

    2. XM_017001127.2 → XP_016856616.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

      Conserved Domains (1) summary
      smart00457
      Location:50 → 233
      MACPF; membrane-attack complex / perforin

    3. XM_017001126.2 → XP_016856615.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58
      Conserved Domains (2) summary
      smart00457
      Location:79 → 263
      MACPF; membrane-attack complex / perforin
      pfam19052
      Location:319 → 766
      BRINP; BMP/retinoic acid-inducible neural-specific protein

    4. XM_017001125.2 → XP_016856614.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58
      Conserved Domains (2) summary
      smart00457
      Location:79 → 263
      MACPF; membrane-attack complex / perforin
      pfam19052
      Location:319 → 766
      BRINP; BMP/retinoic acid-inducible neural-specific protein

    5. XM_047419250.1 → XP_047275206.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58

    6. XM_017001128.2 → XP_016856617.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

      Conserved Domains (1) summary
      smart00457
      Location:50 → 233
      MACPF; membrane-attack complex / perforin

    7. XM_011509476.3 → XP_011507778.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

      See identical proteins and their annotated locations for XP_011507778.1

      UniProtKB/Swiss-Prot
      Q76B58
      Conserved Domains (1) summary
      cl02616
      Location:39 → 161
      MACPF; MAC/Perforin domain

    8. XM_047419245.1 → XP_047275201.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58

    9. XM_011509472.3 → XP_011507774.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011507774.1

      Conserved Domains (1) summary
      smart00457
      Location:50 → 233
      MACPF; membrane-attack complex / perforin

    10. XM_011509475.3 → XP_011507777.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X3

      Conserved Domains (1) summary
      smart00457
      Location:37 → 220
      MACPF; membrane-attack complex / perforin

    11. XM_017001133.2 → XP_016856622.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X6

    12. XM_017001132.2 → XP_016856621.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      189444081..189824968 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336262.1 → XP_054192237.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58

    2. XM_054336270.1 → XP_054192245.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

    3. XM_054336266.1 → XP_054192241.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

    4. XM_054336261.1 → XP_054192236.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58

    5. XM_054336264.1 → XP_054192239.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58

    6. XM_054336263.1 → XP_054192238.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58

    7. XM_054336267.1 → XP_054192242.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

    8. XM_054336269.1 → XP_054192244.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

    9. XM_054336265.1 → XP_054192240.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

    10. XM_054336260.1 → XP_054192235.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KVP1, B7Z260, O95726, Q2M330, Q76B58

    11. XM_054336268.1 → XP_054192243.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X3

    12. XM_054336272.1 → XP_054192247.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X6

    13. XM_054336271.1 → XP_054192246.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q76B58.1 GenPept UniProtKB/Swiss-Prot:Q76B58

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