NIBAN3

Summary

NIBAN3 (niban apoptosis regulator 3, HGNC:24130) is a protein-coding gene on chromosome 19p13.11, encoding Protein Niban 3 (Q86XR2).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 154 total
• MANE Select transcript: NM_001321827

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24130
Approved symbol	NIBAN3
Name	niban apoptosis regulator 3
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39802, BCNP1
Ensembl gene	ENSG00000167483
Ensembl biotype	protein_coding
OMIM	609967
Entrez	199786

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000332386, ENST00000335393, ENST00000449408, ENST00000595601, ENST00000595684, ENST00000597887, ENST00000599124, ENST00000599164, ENST00000599819, ENST00000600519, ENST00000600871, ENST00000601861, ENST00000651880

RefSeq mRNA: 6 — MANE Select: NM_001321827 NM_001098524, NM_001321826, NM_001321827, NM_001321828, NM_001363609, NM_173544

CCDS: CCDS12362, CCDS42521, CCDS82314, CCDS82315, CCDS82317, CCDS86723

Canonical transcript exons

ENST00000599164 — 15 exons

Exon	Start	End
ENSE00001113458	17530755	17530885
ENSE00001113459	17540392	17540582
ENSE00001113460	17539603	17539765
ENSE00001113461	17543317	17543433
ENSE00001113463	17543524	17543631
ENSE00001234576	17549444	17549527
ENSE00001296095	17546686	17546797
ENSE00003048458	17527267	17527395
ENSE00003160026	17551786	17553640
ENSE00003515247	17533587	17533701
ENSE00003541088	17542136	17542294
ENSE00003546164	17539150	17539265
ENSE00003658383	17532263	17532388
ENSE00003675702	17539347	17539451
ENSE00003684433	17537376	17537543

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 93.71.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 5.5711 / max 787.0167, expressed in 112 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174525	5.0796	107
174524	0.4674	53
174526	0.0241	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
spleen	UBERON:0002106	93.71	gold quality
granulocyte	CL:0000094	91.93	gold quality
lymph node	UBERON:0000029	91.44	gold quality
ileal mucosa	UBERON:0000331	87.50	gold quality
vermiform appendix	UBERON:0001154	86.88	gold quality
blood	UBERON:0000178	86.08	gold quality
buccal mucosa cell	CL:0002336	85.87	gold quality
bone marrow	UBERON:0002371	82.05	gold quality
caecum	UBERON:0001153	80.33	gold quality
leukocyte	CL:0000738	80.11	gold quality
monocyte	CL:0000576	79.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.69	silver quality
bone marrow cell	CL:0002092	77.22	gold quality
superficial temporal artery	UBERON:0001614	76.44	gold quality
epithelium of nasopharynx	UBERON:0001951	75.81	gold quality
tendon of biceps brachii	UBERON:0008188	75.49	gold quality
trabecular bone tissue	UBERON:0002483	73.68	gold quality
small intestine Peyer’s patch	UBERON:0003454	73.45	gold quality
tonsil	UBERON:0002372	72.45	gold quality
mucosa of transverse colon	UBERON:0004991	70.54	gold quality
small intestine	UBERON:0002108	69.32	gold quality
gall bladder	UBERON:0002110	66.91	gold quality
epithelial cell of pancreas	CL:0000083	65.20	gold quality
sperm	CL:0000019	63.48	gold quality
ventricular zone	UBERON:0003053	62.62	gold quality
superior surface of tongue	UBERON:0007371	62.49	gold quality
cortical plate	UBERON:0005343	62.15	gold quality
oviduct epithelium	UBERON:0004804	61.08	gold quality
medial globus pallidus	UBERON:0002477	61.01	silver quality
lower lobe of lung	UBERON:0008949	60.69	silver quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 13.

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	1125.83
E-CURD-122	yes	433.17
E-MTAB-8498	yes	409.41
E-MTAB-8911	yes	372.38
E-HCAD-4	yes	111.05
E-CURD-112	yes	42.99
E-HCAD-10	yes	20.79
E-MTAB-9067	yes	19.80
E-ANND-3	yes	17.18
E-MTAB-6701	yes	13.99
E-MTAB-9467	yes	13.21
E-MTAB-6678	yes	6.44
E-MTAB-10042	yes	5.65
E-MTAB-11011	no	2080.14
E-CURD-77	no	993.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting NIBAN3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4795-5P	99.11	66.90	876
HSA-MIR-4477A	98.83	69.75	2952

Literature-anchored findings (GeneRIF, showing 2)

• Isolation and sequencing. Prediction of transmembrane domains, with three alternatively spliced final exons. (PMID:12886250)
• PI3K inhibition and p38 MAPK activation leads to reduction in phosphorylation of BCNP1 at serine residues. (PMID:27680505)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Niban3	ENSMUSG00000043243
rattus_norvegicus	Niban3	ENSRNOG00000039357

Paralogs (2): NIBAN1 (ENSG00000135842), NIBAN2 (ENSG00000136830)

Protein

Protein identifiers

Protein Niban 3 — Q86XR2 (reviewed: Q86XR2)

Alternative names: B-cell novel protein 1, Niban-like protein 2, Protein FAM129C

All UniProt accessions (6): M0QX95, Q86XR2, M0QXK3, M0QZV9, M0R0A8, M0R0E0

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Specifically expressed in B-lymphocytes.

Similarity. Belongs to the Niban family.

Isoforms (7)

UniProt ID	Names	Canonical?
Q86XR2-1	1, 3	yes
Q86XR2-2	2, 1
Q86XR2-3	3, 2
Q86XR2-4	4
Q86XR2-5	5
Q86XR2-6	6
Q86XR2-7	7

RefSeq proteins (6): NP_001091994, NP_001308755, NP_001308756, NP_001308757, NP_001350538, NP_775815 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001849	PH_domain	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR026088	Niban-like	Family
IPR059060	Niban_1/2/3_dom	Domain

Pfam: PF26086, PF26089

UniProt features (16 total): splice variant 9, sequence variant 4, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86XR2-F1	78.15	0.57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 108 (showing top): RACCACAR_AML_Q6, CADWELL_ATG16L1_TARGETS_DN, BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP, BOYLAN_MULTIPLE_MYELOMA_C_D_UP, LEE_RECENT_THYMIC_EMIGRANT, OSF2_Q6, chr19p13, PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MARTENS_BOUND_BY_PML_RARA_FUSION, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_UP, DACH1_TARGET_GENES, HHEX_TARGET_GENES, LMTK3_TARGET_GENES, MAML1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

476 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NIBAN3	FRMD3	A2A2Y4	596
NIBAN3	MS4A1	P08984	566
NIBAN3	BANK1	Q8NDB2	548
NIBAN3	MS4A2	Q01362	545
NIBAN3	CLEC17A	Q6ZS10	511
NIBAN3	FCRLA	Q7L513	436
NIBAN3	C10orf62	Q5T681	433
NIBAN3	STAP1	Q9ULZ2	393
NIBAN3	CFAP141	Q5VU69	392
NIBAN3	ARMCX6	Q7L4S7	389
NIBAN3	VPREB3	Q9UKI3	351
NIBAN3	OR5M3	Q8NGP4	349
NIBAN3	TEX26	Q8N6G2	348
NIBAN3	FAM241B	Q96D05	348
NIBAN3	ARHGAP15	Q53QZ3	329

IntAct

11 interactions, top by confidence:

A	B	Type	Score
NIBAN3	MDFI	psi-mi:“MI:0915”(physical association)	0.560
BAG3	NIBAN3	psi-mi:“MI:0915”(physical association)	0.560
NIBAN3	MDFI	psi-mi:“MI:0915”(physical association)	0.000
BAG3	NIBAN3	psi-mi:“MI:0915”(physical association)	0.000
NIBAN3		psi-mi:“MI:0915”(physical association)	0.000
	NIBAN3	psi-mi:“MI:0915”(physical association)	0.000
NIBAN3	gcvP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): FAM129C (Two-hybrid), FAM129C (Two-hybrid), FAM129C (Proximity Label-MS), FAM129C (Affinity Capture-RNA)

ESM2 similar proteins: A4FV37, A4IFI1, A5D8V7, A6NC98, A6NFT4, A6NGB0, A6QQM8, A9UQN0, B0BMJ2, B0BNK9, D3Z5T1, D6REC4, J3QPZ5, O00411, O60826, O94812, P0C7Q1, P0CW27, P86182, Q0P5D1, Q13515, Q15834, Q17Q97, Q1RMI8, Q2M329, Q3V3V9, Q494R4, Q4QRL3, Q571B6, Q58EX7, Q5BK61, Q5FVL4, Q5ND29, Q5SPX1, Q66H85, Q6F5E8, Q6NTM6, Q6PDY0, Q7TMK6, Q80ZJ8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	128
Likely benign	9
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3026 predictions. Top by Δscore:

Variant	Effect	Δscore
19:17523417:GAT:G	donor_gain	1.0000
19:17527393:GGG:G	donor_gain	1.0000
19:17527394:GG:G	donor_gain	1.0000
19:17527394:GGG:G	donor_gain	1.0000
19:17527395:GG:G	donor_gain	1.0000
19:17527396:G:GG	donor_gain	1.0000
19:17530863:G:GT	donor_gain	1.0000
19:17530881:GCAAA:G	donor_gain	1.0000
19:17530886:G:GG	donor_gain	1.0000
19:17532259:GCA:G	acceptor_loss	1.0000
19:17532260:CAG:C	acceptor_loss	1.0000
19:17532261:A:AG	acceptor_gain	1.0000
19:17532261:AGA:A	acceptor_loss	1.0000
19:17532262:G:GA	acceptor_gain	1.0000
19:17532262:GA:G	acceptor_gain	1.0000
19:17532262:GAA:G	acceptor_gain	1.0000
19:17532262:GAAGC:G	acceptor_gain	1.0000
19:17532385:GGAG:G	donor_gain	1.0000
19:17532386:G:GT	donor_gain	1.0000
19:17532386:GAGGT:G	donor_loss	1.0000
19:17532389:G:GC	donor_loss	1.0000
19:17532390:T:A	donor_loss	1.0000
19:17537485:G:GT	donor_gain	1.0000
19:17537486:G:T	donor_gain	1.0000
19:17537537:GGCA:G	donor_gain	1.0000
19:17539148:A:AG	acceptor_gain	1.0000
19:17539149:G:GG	acceptor_gain	1.0000
19:17539262:CGAG:C	donor_loss	1.0000
19:17539266:G:GA	donor_loss	1.0000
19:17539267:T:A	donor_loss	1.0000

AlphaMissense

3933 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:17532374:T:C	F131L	0.976
19:17532376:C:A	F131L	0.976
19:17532376:C:G	F131L	0.976
19:17543341:T:C	F483L	0.960
19:17543343:C:A	F483L	0.960
19:17543343:C:G	F483L	0.960
19:17539185:T:C	F242L	0.954
19:17539187:C:A	F242L	0.954
19:17539187:C:G	F242L	0.954
19:17539660:T:C	F323L	0.935
19:17539662:C:A	F323L	0.935
19:17539662:C:G	F323L	0.935
19:17532338:T:C	F119L	0.933
19:17532340:C:A	F119L	0.933
19:17532340:C:G	F119L	0.933
19:17542244:T:C	F458L	0.933
19:17542246:T:A	F458L	0.933
19:17542246:T:G	F458L	0.933
19:17542238:T:C	F456L	0.929
19:17542240:T:A	F456L	0.929
19:17542240:T:G	F456L	0.929
19:17543596:T:C	F538L	0.922
19:17543598:T:A	F538L	0.922
19:17543598:T:G	F538L	0.922
19:17530781:T:C	F59L	0.905
19:17530783:C:A	F59L	0.905
19:17530783:C:G	F59L	0.905
19:17537450:T:C	F199L	0.903
19:17537452:C:A	F199L	0.903
19:17537452:C:G	F199L	0.903

dbSNP variants (sampled 300 via entrez): RS1000019230 (19:17538373 G>A), RS1000024503 (19:17548219 G>A), RS1000093083 (19:17549681 C>G,T), RS1000126535 (19:17542476 G>A,T), RS1000152465 (19:17554237 T>C), RS1000175735 (19:17526143 C>T), RS1000210078 (19:17554537 A>G), RS1000442419 (19:17522545 C>T), RS1000479394 (19:17548443 G>A,C), RS1000540928 (19:17553389 G>C), RS1000542892 (19:17542054 T>A,C,G), RS1000778783 (19:17521373 G>T), RS1000797827 (19:17531753 C>T), RS1000881445 (19:17525763 C>T), RS1000909728 (19:17525333 CCCTT>C,CCCTTCCTT)

Disease associations

OMIM: gene MIM:609967 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90002388_363	Lymphocyte count	3.000000e-18

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004587	lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, increases expression	2
Benzo(a)pyrene	affects methylation, increases mutagenesis	2
aristolochic acid I	increases expression	1
licochalcone B	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Diethylhexyl Phthalate	decreases expression	1
Nickel	increases expression	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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