NBPF1

Summary

NBPF1 (NBPF member 1, HGNC:26088) is a protein-coding gene on chromosome 1p36.13, encoding NBPF family member NBPF1 (Q3BBV0).

This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes.

Source: NCBI Gene 55672 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 108 total
• MANE Select transcript: NM_001405666

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26088
Approved symbol	NBPF1
Name	NBPF member 1
Location	1p36.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20719, KIAA1693
Ensembl gene	ENSG00000219481
Ensembl biotype	protein_coding
OMIM	610501
Entrez	55672

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 protein_coding

ENST00000392963, ENST00000420513, ENST00000430580, ENST00000449853, ENST00000599069, ENST00000599908

RefSeq mRNA: 32 — MANE Select: NM_001405666 NM_001405666, NM_001405667, NM_001405668, NM_001405669, NM_001405670, NM_001405671, NM_001405672, NM_001405673, NM_001405674, NM_001405675, NM_001405676, NM_001405677, NM_001405678, NM_001405679, NM_001405680, NM_001405681, NM_001405682, NM_001405683, NM_001405684, NM_001405685, NM_001405686, NM_001405687, NM_001405692, NM_001405693, NM_001405694, NM_001405695, NM_001405696, NM_001405697, NM_001405698, NM_001405699, NM_001405700, NM_017940

Canonical transcript exons

ENST00000430580 — 29 exons

Exon	Start	End
ENSE00001644846	16613338	16613487
ENSE00001649442	16594592	16594661
ENSE00001657332	16608508	16608779
ENSE00001765538	16592159	16592313
ENSE00001784848	16585489	16585698
ENSE00002247206	16591847	16592056
ENSE00002263810	16564807	16564918
ENSE00002303921	16562319	16564186
ENSE00003220237	16594931	16595009
ENSE00003459005	16569073	16569236
ENSE00003477087	16588849	16589063
ENSE00003484999	16573142	16573193
ENSE00003512760	16565633	16565805
ENSE00003524682	16589899	16590001
ENSE00003524745	16576267	16576481
ENSE00003537312	16587050	16587261
ENSE00003541840	16580745	16580956
ENSE00003542558	16574487	16574692
ENSE00003551708	16593441	16593567
ENSE00003571026	16583594	16583696
ENSE00003605444	16577317	16577419
ENSE00003610699	16582544	16582758
ENSE00003611950	16575157	16575229
ENSE00003637631	16587725	16587797
ENSE00003641270	16579193	16579402
ENSE00003667368	16566408	16566459
ENSE00003679120	16581420	16581492
ENSE00003737522	16567979	16568030
ENSE00003748891	16567179	16567351

Expression profiles

Bgee: expression breadth ubiquitous, 213 present calls, max score 96.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.2471 / max 162.8225, expressed in 1737 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
10544	11.7758	1733
10543	0.4712	253

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	96.51	gold quality
secondary oocyte	CL:0000655	96.38	gold quality
cortical plate	UBERON:0005343	95.23	gold quality
right adrenal gland	UBERON:0001233	94.73	gold quality
ventricular zone	UBERON:0003053	94.68	gold quality
right adrenal gland cortex	UBERON:0035827	94.62	gold quality
left adrenal gland cortex	UBERON:0035825	94.52	gold quality
left adrenal gland	UBERON:0001234	94.33	gold quality
ganglionic eminence	UBERON:0004023	94.07	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.04	gold quality
adrenal gland	UBERON:0002369	93.54	gold quality
adrenal cortex	UBERON:0001235	93.00	gold quality
oocyte	CL:0000023	92.69	gold quality
colonic epithelium	UBERON:0000397	92.29	gold quality
rectum	UBERON:0001052	92.26	gold quality
spinal cord	UBERON:0002240	92.17	gold quality
smooth muscle tissue	UBERON:0001135	90.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.50	gold quality
cerebellar hemisphere	UBERON:0002245	90.49	gold quality
cerebellar cortex	UBERON:0002129	90.46	gold quality
stromal cell of endometrium	CL:0002255	89.98	gold quality
right ovary	UBERON:0002118	89.27	gold quality
cerebellum	UBERON:0002037	88.92	gold quality
endocervix	UBERON:0000458	88.78	gold quality
transverse colon	UBERON:0001157	88.56	gold quality
left ovary	UBERON:0002119	88.23	gold quality
calcaneal tendon	UBERON:0003701	88.12	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.83	gold quality
ovary	UBERON:0000992	87.64	gold quality
ileal mucosa	UBERON:0000331	87.48	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	10.88
E-ANND-3	yes	7.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1, ESR2

miRNA regulators (miRDB)

73 targeting NBPF1, 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-4692	100.00	67.32	2066
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4762-5P	99.57	68.54	1424
HSA-MIR-549A-3P	99.54	68.17	825
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-520F-5P	99.34	70.40	1632
HSA-MIR-1912-3P	99.32	67.40	936

Literature-anchored findings (GeneRIF, showing 6)

• Chibby and clusterin were co-immunoprecipitated with NBPF1. (PMID:20096688)
• We demonstrated that NBPF1 exerts different tumor suppressive effects, depending on the cell line analyzed, and provide new clues into the molecular mechanism of the enigmatic NBPF proteins. (PMID:25958384)
• NBPF1 overexpression may be a suppressor for cervical cancer via affecting cell invasion and apoptosis through regulating PI3K/mTOR signaling pathway. (PMID:26802646)
• Upregulation of NBPF1 might promote apoptosis of A431 squamous carcinoma cells and block cell cycle via inhibiting the activation of Akt-p53-Cyclin signaling pathway (PMID:31058534)
• NBPF1 independently determine the risk stratification and prognosis of patients with neuroblastoma. (PMID:32619576)
• Oncogene or tumor suppressor gene: An integrated pan-cancer analysis of NBPF1. (PMID:36060966)

Cross-species orthologs

0 orthologs

Paralogs (14): NBPF3 (ENSG00000142794), NBPF20 (ENSG00000162825), NBPF6 (ENSG00000186086), NBPF4 (ENSG00000196427), NBPF11 (ENSG00000263956), NBPF15 (ENSG00000266338), NBPF12 (ENSG00000268043), NBPF9 (ENSG00000269713), NBPF8 (ENSG00000270231), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF1 — Q3BBV0 (reviewed: Q3BBV0)

Alternative names: Neuroblastoma breakpoint family member 1

All UniProt accessions (2): Q3BBV0, S4R2Z6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Widely expressed. The only tissue which shows a weak expression is kidney.

Miscellaneous. Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the chromosome 1.

Similarity. Belongs to the NBPF family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q3BBV0-1	1	yes
Q3BBV0-2	2

RefSeq proteins (32): NP_001392595, NP_001392596, NP_001392597, NP_001392598, NP_001392599, NP_001392600, NP_001392601, NP_001392602, NP_001392603, NP_001392604, NP_001392605, NP_001392606, NP_001392607, NP_001392608, NP_001392609, NP_001392610, NP_001392611, NP_001392612, NP_001392613, NP_001392614, NP_001392615, NP_001392616, NP_001392621, NP_001392622, NP_001392623, NP_001392624, NP_001392625, NP_001392626, NP_001392627, NP_001392628, NP_001392629, NP_060410 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (52 total): sequence conflict 17, sequence variant 10, domain 8, compositionally biased region 7, region of interest 5, coiled-coil region 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3BBV0-F1	47.77	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 87 (showing top): MITSIADES_RESPONSE_TO_APLIDIN_DN, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, chr1p36, KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3, DMRT1_TARGET_GENES, FOXR2_TARGET_GENES, H1_6_TARGET_GENES, HHEX_TARGET_GENES, HOXB6_TARGET_GENES, HOXC6_TARGET_GENES, ID2_TARGET_GENES, NFKBIA_TARGET_GENES, NPAT_TARGET_GENES, SMCHD1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

606 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NBPF1	HYDIN	Q4G0P3	861
NBPF1	SRGAP2	O75044	850
NBPF1	GPRIN2	O60269	841
NBPF1	SRGAP3	O43295	839
NBPF1	UGT2B17	O75795	830
NBPF1	NPEPPS	P55786	829
NBPF1	DRD5	P21918	812
NBPF1	GTF2I	P78347	763
NBPF1	EVI5	O60447	657
NBPF1	ZNF674	Q2M3X9	513
NBPF1	TBC1D1	Q86TI0	502
NBPF1	UGT2B28	Q9BY64	491
NBPF1	CDK11B	P21127	447
NBPF1	LILRB2	Q8N423	424
NBPF1	UGT2B15	P23765	422

IntAct

23 interactions, top by confidence:

A	B	Type	Score
KDM1A	NBPF1	psi-mi:“MI:0915”(physical association)	0.560
NBPF3	NBPF1	psi-mi:“MI:0915”(physical association)	0.400
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350
TSGA10IP	BRCA2	psi-mi:“MI:0914”(association)	0.350
BRAF	NBPF1	psi-mi:“MI:2364”(proximity)	0.270
FBXW7	NBPF1	psi-mi:“MI:2364”(proximity)	0.270
SMAD4	NBPF1	psi-mi:“MI:2364”(proximity)	0.270
NBPF1	SMARCA4	psi-mi:“MI:2364”(proximity)	0.270
SMARCA4	NBPF1	psi-mi:“MI:2364”(proximity)	0.270
NBPF1	PTEN	psi-mi:“MI:2364”(proximity)	0.270
NBPF1	PTPN11	psi-mi:“MI:2364”(proximity)	0.270
KDM1A	NBPF1	psi-mi:“MI:0915”(physical association)	0.000
	NBPF1	psi-mi:“MI:0915”(physical association)	0.000
NBPF1		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): NBPF1 (Affinity Capture-MS), NBPF1 (Affinity Capture-MS), NBPF1 (Affinity Capture-RNA), NBPF1 (Affinity Capture-RNA), NBPF1 (Proximity Label-MS), NBPF1 (Affinity Capture-MS), NBPF1 (Affinity Capture-MS), NBPF1 (Affinity Capture-MS), NBPF1 (Affinity Capture-MS), NBPF1 (Affinity Capture-RNA), NBPF1 (Proximity Label-MS), NBPF1 (Proximity Label-MS), NBPF1 (Affinity Capture-RNA), NBPF1 (Proximity Label-MS), NBPF1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A087WUL8, A0A0J9YWL9, A0A0U1RQI7, A0A1D9BZF0, A6NJU9, A6NKU9, A6NNC1, A6QL64, A8MRT5, B2SU53, B4DH59, B5DUH6, C9JG80, E5RHQ5, F8W0I5, P01068, P02895, P06916, P07907, P0DKL2, P0DPF3, P0DRJ4, P13208, P14417, P32072, P83060, Q26755, Q3BBV0, Q3BBV2, Q4ZJY7, Q4ZJZ0, Q4ZJZ1, Q4ZJZ3, Q5TAG4, Q5TI25, Q6P3W6, Q6RY98, Q7T3L1, Q86SG3, Q86T75

Diamond homologs: A0A087WUL8, B4DH59, P0C2Y1, P0DPF2, P0DPF3, Q32LC2, Q3BBV0, Q3BBV2, Q5TAG4, Q5TI25, Q5VU43, Q5VWK0, Q6P3W6, Q86T75, Q86XG9, Q8N660, Q96M43, Q9H094, A0A096LNW5, A2RUV0, G3I6Z6, O35516, P0DPK3, P0DPK4, P10040, P21783, P46530, P46531, Q01705, Q04721, Q04756, Q07008, Q20911, Q7Z3S9, Q80YT7, Q99466, Q9QW30, Q9UM47, Q19UN5, Q8K389

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4385 predictions. Top by Δscore:

Variant	Effect	Δscore
1:16564802:GTTA:G	donor_loss	1.0000
1:16564803:T:A	donor_loss	1.0000
1:16564803:TTACC:T	donor_loss	1.0000
1:16564804:G:GA	donor_loss	1.0000
1:16564804:TA:T	donor_loss	1.0000
1:16564805:A:C	donor_loss	1.0000
1:16564805:GGTA:G	donor_loss	1.0000
1:16564806:AGGT:A	donor_loss	1.0000
1:16564807:CAGG:C	donor_loss	1.0000
1:16564808:CCAGG:C	donor_loss	1.0000
1:16564914:AATTT:A	acceptor_gain	1.0000
1:16564915:ATTT:A	acceptor_gain	1.0000
1:16564916:TTT:T	acceptor_gain	1.0000
1:16564917:G:GA	acceptor_gain	1.0000
1:16564917:GA:G	acceptor_gain	1.0000
1:16564917:GAA:G	acceptor_gain	1.0000
1:16564917:GAAA:G	acceptor_gain	1.0000
1:16564917:GAAAT:G	acceptor_gain	1.0000
1:16564917:TT:T	acceptor_gain	1.0000
1:16564918:A:AG	acceptor_gain	1.0000
1:16564918:AG:A	acceptor_loss	1.0000
1:16564918:TC:T	acceptor_loss	1.0000
1:16564919:C:CA	acceptor_loss	1.0000
1:16564919:C:CC	acceptor_gain	1.0000
1:16564919:CA:C	acceptor_loss	1.0000
1:16564920:GCAG:G	acceptor_loss	1.0000
1:16564921:TGCA:T	acceptor_loss	1.0000
1:16564923:A:AG	acceptor_gain	1.0000
1:16564924:A:AC	acceptor_gain	1.0000
1:16564931:C:CT	acceptor_gain	1.0000

AlphaMissense

7544 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1001170094 (1:16609781 A>G), RS1001262061 (1:16610510 T>C), RS1001894014 (1:16582922 G>A), RS1002800308 (1:16562010 T>G), RS1003165900 (1:16598523 T>G), RS1003196 (1:16602757 T>C,G), RS1003282530 (1:16600072 C>T), RS1005631315 (1:16601440 G>A), RS1008388880 (1:16574920 A>G,T), RS1008587879 (1:16609454 T>C,G), RS1008786433 (1:16583117 C>T), RS1009175889 (1:16579740 G>A,C,T), RS1009207034 (1:16575518 C>A,G,T), RS1012054529 (1:16599512 C>G,T), RS1014058100 (1:16580095 T>A,G)

Disease associations

OMIM: gene MIM:610501 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	5
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	3
Arsenic	affects methylation, affects cotreatment, decreases expression, increases abundance	2
Estradiol	increases expression	2
Formaldehyde	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
afimoxifene	decreases reaction, increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
beta-methylcholine	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
monomethylarsonous acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Irinotecan	decreases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants, Occupational	affects expression	1
Benzo(a)pyrene	affects methylation	1
Calcitriol	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Coumestrol	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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