BRINP1

gene
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Also known as FAM5A

Summary

BRINP1 (BMP/retinoic acid inducible neural specific 1, HGNC:2687) is a protein-coding gene on chromosome 9q33.1, encoding BMP/retinoic acid-inducible neural-specific protein 1 (O60477). Plays a role in neurogenesis and brain development.

This gene is located within a chromosomal region that shows loss of heterozygosity in some bladder cancers. It contains a 5’ CpG island that may be a frequent target of hypermethylation, and it may undergo hypermethylation-based silencing in some bladder cancers.

Source: NCBI Gene 1620 — RefSeq curated summary.

At a glance

  • GWAS associations: 15
  • Clinical variants (ClinVar): 13 total
  • MANE Select transcript: NM_014618

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2687
Approved symbolBRINP1
NameBMP/retinoic acid inducible neural specific 1
Location9q33.1
Locus typegene with protein product
StatusApproved
AliasesFAM5A
Ensembl geneENSG00000078725
Ensembl biotypeprotein_coding
OMIM602865
Entrez1620

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000265922, ENST00000373964, ENST00000482797, ENST00000936748, ENST00000936749, ENST00000958983

RefSeq mRNA: 1 — MANE Select: NM_014618 NM_014618

CCDS: CCDS6822

Canonical transcript exons

ENST00000265922 — 8 exons

ExonStartEnd
ENSE00000723362119238655119238760
ENSE00000723367119242047119242216
ENSE00000723371119248960119249150
ENSE00000926953119208719119208941
ENSE00000926954119213919119214155
ENSE00001168324119166629119168224
ENSE00001168335119313138119313405
ENSE00003342941119369056119369435

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 96.95.

FANTOM5 (CAGE): breadth broad, TPM avg 3.8192 / max 193.2541, expressed in 507 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1022673.5626492
1022680.170390
1022660.086349

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277196.95gold quality
Brodmann (1909) area 23UBERON:001355496.44gold quality
entorhinal cortexUBERON:000272896.07gold quality
primary visual cortexUBERON:000243695.75gold quality
postcentral gyrusUBERON:000258194.90gold quality
occipital lobeUBERON:000202193.88gold quality
superior frontal gyrusUBERON:000266193.83gold quality
parietal lobeUBERON:000187293.76gold quality
Brodmann (1909) area 46UBERON:000648392.94gold quality
prefrontal cortexUBERON:000045192.79gold quality
frontal poleUBERON:000279592.76gold quality
frontal cortexUBERON:000187092.14gold quality
buccal mucosa cellCL:000233692.07gold quality
dorsolateral prefrontal cortexUBERON:000983491.98gold quality
orbitofrontal cortexUBERON:000416791.95gold quality
right frontal lobeUBERON:000281091.72gold quality
temporal lobeUBERON:000187191.59gold quality
Brodmann (1909) area 10UBERON:001354191.48gold quality
cerebral cortexUBERON:000095691.42gold quality
Brodmann (1909) area 9UBERON:001354091.37gold quality
neocortexUBERON:000195091.36gold quality
paraflocculusUBERON:000535190.99gold quality
lateral nuclear group of thalamusUBERON:000273690.94gold quality
telencephalonUBERON:000189390.51gold quality
Ammon’s hornUBERON:000195490.29gold quality
cerebellumUBERON:000203790.22gold quality
cerebellar hemisphereUBERON:000224590.02gold quality
cerebellar cortexUBERON:000212990.01gold quality
right hemisphere of cerebellumUBERON:001489089.69gold quality
cortical plateUBERON:000534389.63gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.38

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): REST

miRNA regulators (miRDB)

81 targeting BRINP1, 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-6867-5P100.0082.213464
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-5193100.0067.261744
HSA-MIR-7110-3P100.0073.182486
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-223-3P99.9970.141140
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-433-3P99.9869.371203
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-314899.9775.066478
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-568899.9673.234504
HSA-MIR-493-5P99.9672.472382
HSA-MIR-495-3P99.9672.814197

Literature-anchored findings (GeneRIF, showing 10)

  • DBCCR1 is involved in the process of bladder tumorigenesis (PMID:12442002)
  • the prevalent inactivation of DBCCR1 seen at the expression level in astrocytomas is not primarily caused by genomic loss of the gene. (PMID:15643521)
  • likely tumor suppressor for NSCLC;silencing through homozygous deletion or methylation of its promoter promotes progression (PMID:15746151)
  • hypermethylation of the DBC1 promoter region is a frequent event during the development of lymphoproliferative malignancies (PMID:18264085)
  • High DBC1 expression is associated with breast and lung cancer.. (PMID:20429629)
  • Rxpression of DBC1 and SIRT1 is a significant prognostic indicator for breast carcinoma patients. (PMID:21056897)
  • the stress-induced DBC1-SIRT1 interaction is important for cell fate determination following genotoxic stress. (PMID:22465953)
  • we found that the SIRT1 modulators AROS and DBC1 have an impact on hsp70 transcription, HSF1 acetylation status, and HSF1 recruitment to the hsp70 promoter (PMID:23349863)
  • DBC1 modulates the stability and function of the nuclear receptor Rev-erb-alpha. (PMID:23398316)
  • Results found that the expression of DBCCR1 is significantly lower in the lung cancer tissues compared with adjacent non-tumor tissues of patients, and correlates with more advanced stages of cancer, and shorter survival of patients. Interestingly, DBCCR1 attenuates the expression of DNMT1, suggesting a reciprocal regulation between genetic silencing of cancer suppressor genes and activating DNA methylation. (PMID:28427182)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriobrinp1ENSDARG00000078302
mus_musculusBrinp1ENSMUSG00000028351
rattus_norvegicusBrinp1ENSRNOG00000005561

Paralogs (2): BRINP3 (ENSG00000162670), BRINP2 (ENSG00000198797)

Protein

Protein identifiers

BMP/retinoic acid-inducible neural-specific protein 1O60477 (reviewed: O60477)

Alternative names: Deleted in bladder cancer protein 1

All UniProt accessions (1): O60477

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in neurogenesis and brain development. May suppress cell cycle progression in postmitotic neurons by inhibiting G1/S transition.

Subcellular location. Cytoplasm.

Tissue specificity. Highly expressed in brain. Weakly expressed in heart, lung, skeletal muscle, kidney, thymus, prostate, testis and small intestine.

Miscellaneous. Silenced by methylation in 50% of bladder cancer cell lines.

Similarity. Belongs to the BRINP family.

Isoforms (3)

UniProt IDNamesCanonical?
O60477-11yes
O60477-22
O60477-33

RefSeq proteins (1): NP_055433* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR020864MACPFDomain
IPR033237BRINPFamily
IPR057450BRINP_EGFDomain
IPR057671BRINP_CDomain

Pfam: PF01823, PF19052, PF25415

UniProt features (17 total): glycosylation site 7, sequence variant 4, splice variant 3, signal peptide 1, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O60477-F177.880.22

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 (7): 156, 433, 443, 553, 599, 631, 677

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 184 (showing top): GOBP_MEMORY, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, GOBP_COGNITION, GOBP_BEHAVIOR, GOBP_CELLULAR_RESPONSE_TO_LIPID, LI_WILMS_TUMOR, GCANCTGNY_MYOD_Q6, GOBP_POSITIVE_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, CAGCTG_AP4_Q5, GOBP_NEGATIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_MULTICELLULAR_ORGANISMAL_RESPONSE_TO_STRESS

GO Biological Process (21): behavioral fear response (GO:0001662), brain development (GO:0007420), short-term memory (GO:0007614), cell population proliferation (GO:0008283), gene expression (GO:0010467), proteasomal protein catabolic process (GO:0010498), central nervous system neuron differentiation (GO:0021953), central nervous system neuron development (GO:0021954), social behavior (GO:0035176), exploration behavior (GO:0035640), maternal behavior (GO:0042711), positive regulation of neuron differentiation (GO:0045666), negative regulation of mitotic cell cycle (GO:0045930), homeostasis of number of cells within a tissue (GO:0048873), negative regulation of neurogenesis (GO:0050768), protein stabilization (GO:0050821), cellular response to retinoic acid (GO:0071300), vocalization behavior (GO:0071625), nervous system development (GO:0007399), neurogenesis (GO:0022008), regulation of cell cycle (GO:0051726)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): cytoplasm (GO:0005737), dendrite (GO:0030425), neuronal cell body (GO:0043025), glutamatergic synapse (GO:0098978), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
behavior3
central nervous system development2
neuron differentiation2
behavioral defense response1
fear response1
animal organ development1
head development1
memory1
cellular process1
macromolecule biosynthetic process1
protein catabolic process1
central nervous system neuron differentiation1
neuron development1
biological process involved in intraspecies interaction between organisms1
parental behavior1
positive regulation of cell differentiation1
regulation of neuron differentiation1
mitotic cell cycle1
regulation of mitotic cell cycle1
negative regulation of cell cycle1
tissue homeostasis1
homeostasis of number of cells1
negative regulation of cell development1
neurogenesis1
regulation of neurogenesis1
negative regulation of nervous system development1
regulation of protein stability1
response to retinoic acid1
cellular response to lipid1
cellular response to oxygen-containing compound1
system development1
nervous system development1
cell differentiation1
binding1
intracellular anatomical structure1
cellular anatomical structure1
neuron projection1
dendritic tree1
somatodendritic compartment1
cell body1

Protein interactions and networks

STRING

1426 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BRINP1SMPDL3AQ92484975
BRINP1PRF1P14222730
BRINP1ASTN1O14525530
BRINP1ABCC4O15439492
BRINP1C2orf80Q0P641491
BRINP1ASTN2O75129476
BRINP1FHIP1AQ05DH4457
BRINP1CNEP1R1Q8N9A8449
BRINP1CCL14Q16627435
BRINP1ALDH1A1P00352429
BRINP1GPR26Q8NDV2429
BRINP1ALOX15P16050425
BRINP1WACQ9BTA9423
BRINP1BMPR1BP78366418
BRINP1SMPD1P17405411

IntAct

13 interactions, top by confidence:

ABTypeScore
ZNF326BRINP1psi-mi:“MI:0914”(association)0.580
ZNF326BRINP1psi-mi:“MI:0915”(physical association)0.580
BRINP1ZNF326psi-mi:“MI:0915”(physical association)0.580
BRINP1HNRNPA1psi-mi:“MI:0914”(association)0.460
BRINP1SIRT1psi-mi:“MI:0915”(physical association)0.400
BRINP1CCND1psi-mi:“MI:0915”(physical association)0.370
BRINP1RAC1psi-mi:“MI:0915”(physical association)0.370
BRINP1HSPA5psi-mi:“MI:0914”(association)0.350
HNRNPA1NUDT21psi-mi:“MI:0914”(association)0.350
GPC3PXDNLpsi-mi:“MI:0914”(association)0.350

BioGRID (51): PBXIP1 (Affinity Capture-MS), BRINP1 (Protein-peptide), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS), BRINP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0F7YYX3, A0A182IRF8, A0A1S4GYH9, A0A1S4GYJ6, A0A1S4HE90, B0X6Z1, B6DDQ8, F5HK49, G5EBL2, G5ECL4, M1JMQ7, O10309, O55183, O60477, P0CJ08, P0DQE5, P18153, P18301, P22815, P34404, P43648, P52823, P54194, P85831, P97574, Q06KA2, Q08264, Q09288, Q0IF93, Q10128, Q11077, Q16S34, Q24738, Q5E9L2, Q5MIW7, Q6P9Z6, Q7PJ76, Q7PN86, Q7PNF2, Q7ZZR3

Diamond homologs: O60477, Q499E0, Q5E9L2, Q5RDR5, Q6DFY8, Q76B58, Q7ZZR3, Q8K1M7, Q8K1M8, Q920P3, Q925T8, Q9C0B6, Q90X85

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance8
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2047 predictions. Top by Δscore:

VariantEffectΔscore
9:119176732:T:TAdonor_gain1.0000
9:119195652:T:TAdonor_gain1.0000
9:119208714:CTTA:Cdonor_loss1.0000
9:119208715:TTA:Tdonor_loss1.0000
9:119208716:TA:Tdonor_loss1.0000
9:119208717:A:ACdonor_gain1.0000
9:119208718:C:CAdonor_loss1.0000
9:119208718:C:CCdonor_gain1.0000
9:119208718:CCT:Cdonor_gain1.0000
9:119208718:CCTCT:Cdonor_gain1.0000
9:119208937:CTCAT:Cacceptor_gain1.0000
9:119208939:CAT:Cacceptor_gain1.0000
9:119238650:CCTA:Cdonor_loss1.0000
9:119238651:CTAC:Cdonor_loss1.0000
9:119238652:TA:Tdonor_loss1.0000
9:119238653:ACCT:Adonor_loss1.0000
9:119242041:CTGTA:Cdonor_loss1.0000
9:119242042:TGTA:Tdonor_loss1.0000
9:119242043:GTAC:Gdonor_loss1.0000
9:119242044:TAC:Tdonor_loss1.0000
9:119242045:A:Cdonor_loss1.0000
9:119242046:C:Adonor_loss1.0000
9:119242212:CTCCC:Cacceptor_gain1.0000
9:119242214:CCC:Cacceptor_gain1.0000
9:119242215:CC:Cacceptor_gain1.0000
9:119242215:CCC:Cacceptor_gain1.0000
9:119242216:CC:Cacceptor_gain1.0000
9:119242216:CCTG:Cacceptor_loss1.0000
9:119242217:C:CCacceptor_gain1.0000
9:119242217:CT:Cacceptor_loss1.0000

AlphaMissense

5080 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:119167206:A:GC722R1.000
9:119167271:C:GR700P1.000
9:119167394:C:TG659E1.000
9:119167395:C:AG659W1.000
9:119167609:C:AW587C1.000
9:119167609:C:GW587C1.000
9:119167611:A:GW587R1.000
9:119167611:A:TW587R1.000
9:119167645:C:AW575C1.000
9:119167645:C:GW575C1.000
9:119167647:A:GW575R1.000
9:119167647:A:TW575R1.000
9:119167659:G:CH571D1.000
9:119167675:G:CN565K1.000
9:119167675:G:TN565K1.000
9:119167793:A:GL526P1.000
9:119167849:G:CS507R1.000
9:119167849:G:TS507R1.000
9:119167851:T:GS507R1.000
9:119167988:C:GC461S1.000
9:119167989:A:GC461R1.000
9:119167989:A:TC461S1.000
9:119168020:G:CC450W1.000
9:119168021:C:TC450Y1.000
9:119168022:A:GC450R1.000
9:119168029:G:CC447W1.000
9:119168030:C:GC447S1.000
9:119168030:C:TC447Y1.000
9:119168031:A:GC447R1.000
9:119168031:A:TC447S1.000

dbSNP variants (sampled 300 via entrez): RS1000009629 (9:119363277 A>G), RS1000022107 (9:119343870 T>A,C), RS1000024338 (9:119277358 T>A), RS1000041104 (9:119301523 A>C,T), RS1000048569 (9:119292857 A>T), RS1000051869 (9:119346379 T>C), RS1000069647 (9:119168185 G>C), RS1000090088 (9:119209466 G>A,T), RS1000090128 (9:119205858 C>A,T), RS1000117150 (9:119299502 A>G,T), RS1000117474 (9:119289295 T>G), RS1000125546 (9:119261483 C>T), RS1000140849 (9:119308281 C>G), RS1000179184 (9:119178781 C>T), RS1000179769 (9:119326110 A>T)

Disease associations

OMIM: gene MIM:602865 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

15 associations (top):

StudyTraitp-value
GCST002932_25Manganese levels1.000000e-06
GCST004790_2Change in LVEF in response to paclitaxel and trastuzumab in HER2+ breast cancer6.000000e-07
GCST006606_12Response to TNF inhibitor in rheumatoid arthritis (change in swollen 28-joint count)9.000000e-08
GCST007327_32Smoking status (ever vs never smokers)7.000000e-09
GCST007628_4Impulsivity (motor)1.000000e-06
GCST008162_2Hip circumference1.000000e-06
GCST008477_18Emphysema annual change measurement in smokers (adjusted lung density)7.000000e-06
GCST008477_5Emphysema annual change measurement in smokers (adjusted lung density)7.000000e-06
GCST008526_71Coffee consumption5.000000e-06
GCST008647_43Urinary sodium excretion3.000000e-09
GCST009524_123Household income (MTAG)3.000000e-08
GCST011741_17LDL cholesterol levels in HIV infection5.000000e-06
GCST011741_2LDL cholesterol levels in HIV infection5.000000e-06
GCST011742_56Triglyceride levels in HIV infection4.000000e-06
GCST012316_4ghrelin levels7.000000e-08

EFO canonical traits (13, from GWAS)

EFO IDTrait name
EFO:0008204left ventricular diastolic function measurement
EFO:0008347response to trastuzumab
EFO:0004653response to TNF antagonist
EFO:0005413joint damage measurement
EFO:0004318smoking behavior
EFO:0006946behavioural disinhibition measurement
EFO:0007626emphysema imaging measurement
EFO:0006781coffee consumption measurement
EFO:0009282sodium measurement
EFO:0009695household income
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004530triglyceride measurement
EFO:0600001ghrelin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, affects cotreatment, increases expression8
monomethylarsonous acidaffects acetylation, affects methylation, decreases expression3
bisphenol Adecreases expression, increases methylation2
trichostatin Aaffects cotreatment, affects methylation, decreases reaction, increases expression2
entinostatincreases expression, affects cotreatment2
Decitabinedecreases reaction, affects expression, affects cotreatment, affects methylation2
Panobinostataffects cotreatment, increases expression2
Benzo(a)pyreneaffects methylation, decreases methylation2
Aflatoxin B1decreases methylation, increases methylation2
aristolochic acid Idecreases expression1
methylmercuric chlorideincreases expression1
methyleugenoldecreases expression1
arseniteincreases methylation1
sodium arsenitedecreases reaction, affects acetylation, decreases expression, affects cotreatment, affects methylation1
perfluorooctanoic aciddecreases expression1
benzo(e)pyreneincreases methylation1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
incobotulinumtoxinAincreases expression1
NSC668394increases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Arsenic Trioxideincreases expression1
Calcitriolincreases expression1
Cisplatinaffects expression1
Methapyrileneincreases methylation1
Plant Extractsaffects cotreatment, decreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.