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

Gene ID: 339479, updated on 5-Mar-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
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Genomic context

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Location:
1q31.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (190097658..190477864, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (189444081..189824968, complement)
105.20220307 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. A preliminary study on the FAM5C expression in generalized chronic periodontitis. Ribeiro FV, et al. Oral Dis, 2012 Mar. PMID 22355820
  2. 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
  3. 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
  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)

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

Process Evidence Code Pubs
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
  
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 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 nervous system development IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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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