NBPF8

Summary

NBPF8 (NBPF member 8, HGNC:31990) is a protein-coding gene on chromosome 1p11.2, encoding NBPF family member NBPF8 (Q3BBV2). It is a selective cancer dependency (DepMap: 60.0% of cell lines).

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 728841 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 60.0% of screened cell lines
• MANE Select transcript: NM_001037501

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31990
Approved symbol	NBPF8
Name	NBPF member 8
Location	1p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000270231
Ensembl biotype	protein_coding
OMIM	613998
Entrez	728841

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000652355, ENST00000698216, ENST00000860584, ENST00000860585

RefSeq mRNA: 1 — MANE Select: NM_001037501 NM_001037501

CCDS: CCDS91029

Canonical transcript exons

ENST00000698216 — 23 exons

Exon	Start	End
ENSE00003972980	120461254	120461426
ENSE00003972981	120463676	120463727
ENSE00003972982	120465978	120469676
ENSE00003972983	120464376	120464548
ENSE00003972984	120415035	120415304
ENSE00003972985	120441278	120441489
ENSE00003972986	120462794	120462966
ENSE00003972987	120438544	120438646
ENSE00003972988	120455409	120455460
ENSE00003972989	120440742	120440814
ENSE00003972990	120452117	120452331
ENSE00003972991	120462146	120462197
ENSE00003972992	120465263	120465371
ENSE00003972993	120453372	120453444
ENSE00003972994	120427706	120427847
ENSE00003972995	120453909	120454114
ENSE00003972996	120459367	120459530
ENSE00003972997	120439476	120439690
ENSE00003972998	120449193	120449402
ENSE00003972999	120460573	120460624
ENSE00003973000	120436232	120436697
ENSE00003973001	120451180	120451282
ENSE00003973002	120419850	120420118

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.94.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	91.94	gold quality
right lobe of thyroid gland	UBERON:0001119	90.01	gold quality
left lobe of thyroid gland	UBERON:0001120	89.62	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.55	gold quality
thyroid gland	UBERON:0002046	89.20	gold quality
cerebellar hemisphere	UBERON:0002245	88.93	gold quality
cerebellar cortex	UBERON:0002129	88.82	gold quality
cerebellum	UBERON:0002037	88.62	gold quality
liver	UBERON:0002107	87.45	gold quality
granulocyte	CL:0000094	87.35	gold quality
lower esophagus	UBERON:0013473	86.79	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.79	gold quality
body of pancreas	UBERON:0001150	86.78	gold quality
left uterine tube	UBERON:0001303	86.00	gold quality
left ovary	UBERON:0002119	85.82	gold quality
right ovary	UBERON:0002118	85.66	gold quality
stromal cell of endometrium	CL:0002255	85.56	gold quality
mucosa of stomach	UBERON:0001199	85.26	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.06	gold quality
spleen	UBERON:0002106	84.97	gold quality
ovary	UBERON:0000992	84.76	gold quality
endocervix	UBERON:0000458	84.63	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.25	gold quality
fundus of stomach	UBERON:0001160	84.13	gold quality
ventricular zone	UBERON:0003053	84.01	gold quality
right uterine tube	UBERON:0001302	83.47	gold quality
body of uterus	UBERON:0009853	83.44	gold quality
myometrium	UBERON:0001296	83.26	gold quality
vermiform appendix	UBERON:0001154	83.05	gold quality
lymph node	UBERON:0000029	82.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting NBPF8, 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-3646	100.00	73.56	5283
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-549A-3P	99.54	68.17	825
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-6507-3P	99.35	67.32	1059

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 60.0% of screened cell lines.

Cross-species orthologs

0 orthologs

Paralogs (14): NBPF3 (ENSG00000142794), NBPF20 (ENSG00000162825), NBPF6 (ENSG00000186086), NBPF4 (ENSG00000196427), NBPF1 (ENSG00000219481), NBPF11 (ENSG00000263956), NBPF15 (ENSG00000266338), NBPF12 (ENSG00000268043), NBPF9 (ENSG00000269713), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF8 — Q3BBV2 (reviewed: Q3BBV2)

Alternative names: Neuroblastoma breakpoint family member 8

All UniProt accessions (1): Q3BBV2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in the mammary gland.

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.

RefSeq proteins (1): NP_001032590* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (19 total): domain 7, compositionally biased region 5, region of interest 4, coiled-coil region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3BBV2-F1	47.29	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, chr1p11, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN, MIR3529_3P, MIR141_3P, MIR200A_3P, MIR4692, MIR4514, MIR4478, MIR4443, MIR6818_3P, MIR6852_3P, MIR4520_2_3P, MIR6499_3P

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

5 interactions, top by confidence:

A	B	Type	Score
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
ESR2		psi-mi:“MI:0914”(association)	0.350
NS	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
tcaA1	NBPF8	psi-mi:“MI:0915”(physical association)	0.000

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

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1711136	GRCh37/hg19 1q21.1(chr1:143950572-144462929)x3	Pathogenic

SpliceAI

74 predictions. Top by Δscore:

Variant	Effect	Δscore
1:120463724:CCAG:C	donor_loss	1.0000
1:120463725:CAGG:C	donor_loss	1.0000
1:120463726:AG:A	donor_loss	1.0000
1:120463727:GGTAA:G	donor_loss	1.0000
1:120463728:G:T	donor_loss	1.0000
1:120463729:T:G	donor_loss	1.0000
1:120463662:T:TA	acceptor_gain	0.9900
1:120463666:T:G	acceptor_gain	0.9900
1:120463671:TGCA:T	acceptor_loss	0.9900
1:120463673:CA:C	acceptor_loss	0.9900
1:120463674:A:AG	acceptor_gain	0.9900
1:120463674:A:AT	acceptor_loss	0.9900
1:120463674:AG:A	acceptor_gain	0.9900
1:120463675:G:GT	acceptor_gain	0.9900
1:120463675:GG:G	acceptor_gain	0.9900
1:120463675:GGA:G	acceptor_gain	0.9900
1:120463669:A:AG	acceptor_gain	0.9800
1:120463675:G:GG	acceptor_gain	0.9800
1:120463675:GGAAT:G	acceptor_gain	0.9800
1:120463666:T:TA	acceptor_gain	0.9700
1:120463675:GGAA:G	acceptor_gain	0.9700
1:120463788:G:T	donor_gain	0.9700
1:120463665:AT:A	acceptor_gain	0.9600
1:120463830:C:T	donor_gain	0.9600
1:120463665:A:AG	acceptor_gain	0.9400
1:120463728:G:GG	donor_gain	0.9300
1:120463670:T:G	acceptor_gain	0.9200
1:120463658:T:TA	acceptor_gain	0.9100
1:120463669:ATT:A	acceptor_gain	0.9000
1:120463671:T:A	acceptor_gain	0.9000

AlphaMissense

6213 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS10399744 (1:149099293 C>G,T), RS10625215 (1:120436638 AAG>A,AAGAG), RS10907357 (1:149105549 A>G), RS10907358 (1:120415822 G>A,C,T), RS10907359 (1:120448624 G>A,C,T), RS111214339 (1:120448252 C>A), RS111256803 (1:120450471 A>G,T), RS111282879 (1:120423386 C>G,T), RS111437702 (1:120430132 A>T), RS111503477 (1:120422364 G>T), RS111537918 (1:120448635 G>A), RS111588993 (1:120415439 A>G,T), RS111636993 (1:120420464 G>A,C), RS111706278 (1:120451563 A>G,T), RS111734804 (1:149078030 A>G)

Disease associations

OMIM: gene MIM:613998 | 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

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
bisphenol A	decreases methylation	1
ICG 001	increases expression	1
abrine	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Temozolomide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Estradiol	increases expression	1
Pesticides	decreases expression	1
Polychlorinated Biphenyls	affects expression	1
Triclosan	decreases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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