BRINP3

gene
On this page

Also known as DBCCR1LDBCCR1L1

Summary

BRINP3 (BMP/retinoic acid inducible neural specific 3, HGNC:22393) is a protein-coding gene on chromosome 1q31.1, encoding BMP/retinoic acid-inducible neural-specific protein 3 (Q76B58). Inhibits neuronal cell proliferation by negative regulation of the cell cycle transition.

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.

Source: NCBI Gene 339479 — RefSeq curated summary.

At a glance

  • GWAS associations: 24
  • Clinical variants (ClinVar): 113 total
  • MANE Select transcript: NM_199051

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:22393
Approved symbolBRINP3
NameBMP/retinoic acid inducible neural specific 3
Location1q31.1
Locus typegene with protein product
StatusApproved
AliasesDBCCR1L, DBCCR1L1
Ensembl geneENSG00000162670
Ensembl biotypeprotein_coding
OMIM618390
Entrez339479

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000367462, ENST00000445957, ENST00000463404, ENST00000631494, ENST00000633243, ENST00000956272

RefSeq mRNA: 2 — MANE Select: NM_199051 NM_001317188, NM_199051

CCDS: CCDS1373

Canonical transcript exons

ENST00000367462 — 8 exons

ExonStartEnd
ENSE00001370507190281560190281750
ENSE00003494147190226082190226318
ENSE00003564460190097658190099134
ENSE00003639993190454655190454940
ENSE00003663090190160668190160890
ENSE00003669051190234372190234477
ENSE00003676709190264865190265055
ENSE00003781667190477448190477864

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 87.78.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0536 / max 167.6098, expressed in 213 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter IDTPM avgSamples expressed
164000.8528138
163930.4766125
164020.169472
163990.106249
163970.098650
164010.063443
163980.060332
163920.047832
163960.046722
163950.039010

Top tissues by expression

279 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.78gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.73gold quality
endothelial cellCL:000011584.04gold quality
prefrontal cortexUBERON:000045183.99gold quality
primary visual cortexUBERON:000243683.96gold quality
right frontal lobeUBERON:000281083.51gold quality
amygdalaUBERON:000187683.21gold quality
dorsolateral prefrontal cortexUBERON:000983482.94gold quality
cingulate cortexUBERON:000302782.09gold quality
Brodmann (1909) area 9UBERON:001354081.98gold quality
anterior cingulate cortexUBERON:000983581.95gold quality
neocortexUBERON:000195081.56gold quality
frontal cortexUBERON:000187081.45gold quality
hypothalamusUBERON:000189880.72gold quality
cortical plateUBERON:000534380.51gold quality
cerebral cortexUBERON:000095679.99gold quality
cerebellar hemisphereUBERON:000224579.94gold quality
cerebellar cortexUBERON:000212979.89gold quality
nucleus accumbensUBERON:000188279.75gold quality
right hemisphere of cerebellumUBERON:001489079.53gold quality
Brodmann (1909) area 23UBERON:001355479.23gold quality
caudate nucleusUBERON:000187379.07gold quality
telencephalonUBERON:000189379.06gold quality
occipital lobeUBERON:000202178.70gold quality
cerebellumUBERON:000203778.45gold quality
temporal lobeUBERON:000187178.43gold quality
rectumUBERON:000105277.70gold quality
colonic epitheliumUBERON:000039776.68gold quality
mucosa of transverse colonUBERON:000499176.53gold quality
putamenUBERON:000187475.90gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-HCAD-35yes81.07
E-HCAD-25yes20.83
E-GEOD-93593yes5.18
E-ANND-3no4.02

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

79 targeting BRINP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-3646100.0073.565283
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-1212199.9966.64255
HSA-MIR-428299.9975.366408
HSA-MIR-1213699.9872.815713
HSA-MIR-480399.9871.993117
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-548N99.9871.944170
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345

Literature-anchored findings (GeneRIF, showing 14)

  • BRINP3 is a mitochondrially localized protein that is selectively up-regulated in human gonadotropinomas; its actions to increase proliferation, migration, and invasion suggest it may play an important role in pituitary tumorigenesis (PMID:17138656)
  • These data implicate FAM5C alleles in the risk of myocardial infarction and suggest further functional studies of FAM5C are required to identify the gene’s contribution to atherosclerosis (PMID:18430236)
  • Loss of FAM5C is associated with tongue squamous cell carcinoma. (PMID:19787213)
  • FAM5C mRNA expression was significantly higher in aggressive periodontitis diseased versus healthy sites, and was found to be correlated to the IL-1beta, IL-17A, IL-4 and RANKL mRNA levels. (PMID:20383335)
  • 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 (PMID:22013132)
  • expression does not contribute to chronic periodontitis (PMID:22355820)
  • 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. (PMID:22377736)
  • Under expression of BRINP3 is associated with the pathogenesis of ulcerative colitis. (PMID:25171508)
  • 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). (PMID:25251368)
  • 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. (PMID:25887438)
  • FAM5C is a risk factor for cerebral infarction in type 2 diabetic patients. (PMID:26717922)
  • 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. (PMID:27461004)
  • 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. (PMID:27836731)
  • The results demonstrated that FAM5C is an N-glycosylated protein, and N-glycosylation by UGGT1 is necessary for the secretion of FAM5C. (PMID:28351617)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriobrinp3a.2ENSDARG00000061051
mus_musculusBrinp3ENSMUSG00000035131
rattus_norvegicusBrinp3ENSRNOG00000002811

Paralogs (2): BRINP1 (ENSG00000078725), BRINP2 (ENSG00000198797)

Protein

Protein identifiers

BMP/retinoic acid-inducible neural-specific protein 3Q76B58 (reviewed: Q76B58)

Alternative names: DBCCR1-like protein 1

All UniProt accessions (3): A0A0J9YVN8, B1AMP1, Q76B58

UniProt curated annotations — full annotation on UniProt →

Function. Inhibits neuronal cell proliferation by negative regulation of the cell cycle transition. Promotes pituitary gonadotrope cell proliferation, migration and invasion, when overexpressed. May play a role in cell pituitary tumor development.

Subcellular location. Secreted. Mitochondrion.

Tissue specificity. Strongly expressed in oral keratinocytes compared to the weak expression in tongue squamous cell carcinoma (SCC). Expressed in endothelial and aortic smooth muscle cells. Overexpressed in gonadotropinomas compared to normal pituitarie tissues.

Similarity. Belongs to the BRINP family.

Isoforms (2)

UniProt IDNamesCanonical?
Q76B58-11yes
Q76B58-22

RefSeq proteins (2): NP_001304117, NP_950252* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009030Growth_fac_rcpt_cys_sfHomologous_superfamily
IPR020864MACPFDomain
IPR033237BRINPFamily
IPR057450BRINP_EGFDomain
IPR057671BRINP_CDomain

Pfam: PF01823, PF19052, PF25415

UniProt features (13 total): glycosylation site 6, splice variant 2, sequence conflict 2, signal peptide 1, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q76B58-F177.130.21

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (6): 168, 337, 456, 562, 609, 641

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 188 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOBP_BEHAVIOR, TGCGCANK_UNKNOWN, GOBP_CELLULAR_RESPONSE_TO_LIPID, TTTGTAG_MIR520D, GOBP_POSITIVE_REGULATION_OF_NEURON_DIFFERENTIATION, MORF_BRCA1, GOBP_GROWTH, TATTATA_MIR374, GOBP_NEUROGENESIS, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, CAGCTG_AP4_Q5, MORF_RAD51L3, CTCTAGA_MIR526C_MIR518F_MIR526A, GOBP_CELLULAR_RESPONSE_TO_RETINOIC_ACID

GO Biological Process (10): central nervous system neuron differentiation (GO:0021953), social behavior (GO:0035176), multicellular organism growth (GO:0035264), exploration behavior (GO:0035640), positive regulation of neuron differentiation (GO:0045666), negative regulation of mitotic cell cycle (GO:0045930), cellular response to retinoic acid (GO:0071300), nervous system development (GO:0007399), negative regulation of cell cycle (GO:0045786), regulation of cell cycle (GO:0051726)

GO Molecular Function (0):

GO Cellular Component (5): extracellular region (GO:0005576), cytoplasm (GO:0005737), mitochondrion (GO:0005739), dendrite (GO:0030425), neuronal cell body (GO:0043025)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
neuron differentiation2
behavior2
cell cycle2
cellular anatomical structure2
central nervous system development1
biological process involved in intraspecies interaction between organisms1
multicellular organismal process1
developmental growth1
positive regulation of cell differentiation1
regulation of neuron differentiation1
mitotic cell cycle1
regulation of mitotic cell cycle1
negative regulation of cell cycle1
response to retinoic acid1
cellular response to lipid1
cellular response to oxygen-containing compound1
system development1
negative regulation of cellular process1
regulation of cell cycle1
regulation of cellular process1
intracellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1
neuron projection1
dendritic tree1
somatodendritic compartment1
cell body1

Protein interactions and networks

STRING

1136 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BRINP3SLIT3O75094523
BRINP3RRP15Q9Y3B9438
BRINP3KCTD3Q9Y597429
BRINP3GPATCH2Q9NW75407
BRINP3ASTN1O14525405
BRINP3ZNF684Q5T5D7398
BRINP3CCDC17Q96LX7395
BRINP3ANP32DO95626392
BRINP3SLIT1O75093390
BRINP3OGNP20774370
BRINP3ADGRL4Q9HBW9367
BRINP3OR5M11Q96RB7361
BRINP3TMEM236Q5W0B7358
BRINP3CCDC126Q96EE4355
BRINP3OR5AR1Q8NGP9355

IntAct

9 interactions, top by confidence:

ABTypeScore
STIM2PRKAB2psi-mi:“MI:0914”(association)0.640
BRINP3BUB1psi-mi:“MI:0914”(association)0.530
PDGFRAGXYLT2psi-mi:“MI:0914”(association)0.350
PSCAMETTL15psi-mi:“MI:0914”(association)0.350
SCGB2A2RTL8Cpsi-mi:“MI:0914”(association)0.350
C1orf54AGRNpsi-mi:“MI:0914”(association)0.350

BioGRID (40): BRINP3 (Reconstituted Complex), BRINP3 (Affinity Capture-MS), BRINP2 (Affinity Capture-MS), DHFRL1 (Affinity Capture-MS), TXNDC15 (Affinity Capture-MS), BUB1 (Affinity Capture-MS), TUBA4A (Affinity Capture-MS), KIAA0232 (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), CBWD1 (Affinity Capture-MS), NRP2 (Affinity Capture-MS), ATG2B (Affinity Capture-MS), EDEM2 (Affinity Capture-MS), DNAJB9 (Affinity Capture-MS), LRP5 (Affinity Capture-MS)

ESM2 similar proteins: A0A0A6YXX9, A0A1Z2R986, A2RTF1, C6KI89, E9Q355, F5HFJ7, O36400, P03425, P04853, P09258, P09728, P0DP43, P12554, P12556, P16772, P19758, P21526, P22229, P28907, P35740, P35771, Q04547, Q2TAV2, Q2YDM0, Q3TBN1, Q499E0, Q4R6B2, Q5BKX0, Q5E9L2, Q5RDR5, Q66000, Q66001, Q68FB2, Q6AY76, Q6DFY8, Q6ZRH7, Q76B58, Q77MP7, Q77NN4, Q783Y1

Diamond homologs: O60477, Q499E0, Q5E9L2, Q5RDR5, Q6DFY8, Q76B58, Q7ZZR3, Q8K1M7, Q8K1M8, Q920P3, Q925T8, Q9C0B6, Q90X85, A2VEC9, B3EWZ3, B3EWZ8, C5IAW9, D3YXG0, D3ZTD8, E9Q6D8, G5ECS8, O08721, O95450, P07357, P07358, P10643, P13671, P55314, P61134, P61135, P79331, P98136, P98137, P98167, Q13591, Q29RQ1, Q29RU4, Q5RAD0, Q62217, Q700K0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

113 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance107
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3398 predictions. Top by Δscore:

VariantEffectΔscore
1:190160663:CTTA:Cdonor_loss1.0000
1:190160665:TA:Tdonor_loss1.0000
1:190160666:A:ATdonor_loss1.0000
1:190160667:C:CTdonor_loss1.0000
1:190160887:TCAT:Tacceptor_gain1.0000
1:190160888:CAT:Cacceptor_gain1.0000
1:190160888:CATC:Cacceptor_gain1.0000
1:190226076:TCTTA:Tdonor_loss1.0000
1:190226077:CTTA:Cdonor_loss1.0000
1:190226078:TTA:Tdonor_loss1.0000
1:190226079:TAC:Tdonor_loss1.0000
1:190226080:A:ACdonor_gain1.0000
1:190226080:A:ATdonor_loss1.0000
1:190226081:C:Adonor_loss1.0000
1:190226081:C:CTdonor_gain1.0000
1:190226081:CCTG:Cdonor_gain1.0000
1:190226081:CCTGA:Cdonor_gain1.0000
1:190226314:AAGCC:Aacceptor_gain1.0000
1:190226315:AGCC:Aacceptor_gain1.0000
1:190226316:GCC:Gacceptor_gain1.0000
1:190226317:CC:Cacceptor_gain1.0000
1:190226317:CCC:Cacceptor_gain1.0000
1:190226318:CCT:Cacceptor_gain1.0000
1:190226319:C:CCacceptor_gain1.0000
1:190226319:C:Tacceptor_gain1.0000
1:190226319:CTT:Cacceptor_loss1.0000
1:190226320:T:Cacceptor_gain1.0000
1:190226320:T:TCacceptor_gain1.0000
1:190226328:C:CTacceptor_gain1.0000
1:190226329:A:Tacceptor_gain1.0000

AlphaMissense

5088 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:190098026:A:GC765R1.000
1:190098141:G:CC726W1.000
1:190098143:A:GC726R1.000
1:190098211:A:GL703P1.000
1:190098271:A:GL683P1.000
1:190098310:C:TG670D1.000
1:190098433:A:GL629P1.000
1:190098451:T:AE623V1.000
1:190098581:G:CH580D1.000
1:190098582:G:CS579R1.000
1:190098582:G:TS579R1.000
1:190098584:T:GS579R1.000
1:190098597:A:CN574K1.000
1:190098597:A:TN574K1.000
1:190098645:G:CC558W1.000
1:190098647:A:GC558R1.000
1:190098705:C:AK538N1.000
1:190098705:C:GK538N1.000
1:190098771:G:CS516R1.000
1:190098771:G:TS516R1.000
1:190098773:T:GS516R1.000
1:190098898:C:GC474S1.000
1:190098899:A:TC474S1.000
1:190226248:G:CC265W1.000
1:190226249:C:TC265Y1.000
1:190226250:A:GC265R1.000
1:190234445:G:CC217W1.000
1:190234446:C:GC217S1.000
1:190234446:C:TC217Y1.000
1:190234447:A:GC217R1.000

dbSNP variants (sampled 300 via entrez): RS1000000976 (1:190148185 C>T), RS1000002036 (1:190422012 G>C), RS1000008107 (1:190244035 C>A), RS1000018133 (1:190187819 C>A,G), RS1000025429 (1:190304223 A>C), RS1000027406 (1:190406559 A>G), RS1000036656 (1:190181358 T>G), RS1000039607 (1:190268667 GACAA>G), RS1000040482 (1:190111037 G>T), RS1000043869 (1:190254909 G>T), RS1000054728 (1:190311678 AGTGT>A), RS1000055238 (1:190321885 T>G), RS1000063625 (1:190457939 T>C), RS1000067844 (1:190192647 C>G,T), RS1000084449 (1:190231107 A>G)

Disease associations

OMIM: gene MIM:618390 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

24 associations (top):

StudyTraitp-value
GCST000110_7Echocardiographic traits6.000000e-06
GCST000635_21Response to statin therapy4.000000e-06
GCST002337_78Amyotrophic lateral sclerosis (sporadic)8.000000e-06
GCST002783_404Body mass index9.000000e-07
GCST002783_530Body mass index1.000000e-06
GCST002934_3Zinc levels8.000000e-07
GCST002974_2Suicide ideation score in major depressive disorder1.000000e-06
GCST003808_5Non-response to selective serotonin reuptake inhibitors and depression2.000000e-06
GCST004571_12Iron status biomarkers (total iron binding capacity)4.000000e-07
GCST004571_14Iron status biomarkers (total iron binding capacity)4.000000e-08
GCST004572_24Iron status biomarkers (transferrin saturation)4.000000e-07
GCST004572_26Iron status biomarkers (transferrin saturation)4.000000e-08
GCST004904_109Body mass index3.000000e-13
GCST004904_220Body mass index3.000000e-10
GCST006041_33Major depressive disorder1.000000e-06
GCST006617_1Uterine fibroid size (maximum volume)8.000000e-08
GCST007324_153Adventurousness1.000000e-12
GCST007325_273General risk tolerance (MTAG)1.000000e-13
GCST007576_23Chronotype2.000000e-10
GCST007576_311Chronotype6.000000e-10
GCST008158_24Body mass index5.000000e-06
GCST010988_264Adult body size6.000000e-15
GCST012033_2Sleep (1/3-day periodicity)2.000000e-12
GCST012034_2Sleep (1/2-day periodicity)1.000000e-08

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0004294left atrial function
EFO:0004298cardiovascular measurement
EFO:0004340body mass index
EFO:0007619suicide ideation measurement
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0006334total iron binding capacity
EFO:0009410uterine fibroid measurement
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression2
Aflatoxin B1decreases methylation, increases methylation2
bisphenol Fincreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
hydroxyhydroquinonedecreases expression1
arseniteincreases methylation1
sulforaphanedecreases expression1
benzo(e)pyrenedecreases methylation1
perfluoro-n-nonanoic aciddecreases expression1
Venlafaxine Hydrochlorideincreases expression1
Resveratroldecreases expression, affects cotreatment1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Doxorubicindecreases expression1
Estradioldecreases expression1
Methapyrilenedecreases methylation1
Plant Extractsaffects cotreatment, decreases expression1
Rotenonedecreases expression1
Cyclosporinedecreases expression1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): mood disorder