NBPF15

Summary

NBPF15 (NBPF member 15, HGNC:28791) is a protein-coding gene on chromosome 1q21.1, encoding NBPF family member NBPF15 (Q8N660).

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 284565 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 154 total — 1 pathogenic
• MANE Select transcript: NM_001385408

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28791
Approved symbol	NBPF15
Name	NBPF member 15
Location	1q21.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC8902
Ensembl gene	ENSG00000266338
Ensembl biotype	protein_coding
OMIM	610414
Entrez	284565

Gene structure

Transcript identifiers

Ensembl transcripts: 69 — 68 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000478419, ENST00000488031, ENST00000577412, ENST00000579734, ENST00000581897, ENST00000584793, ENST00000614785, ENST00000869020, ENST00000869021, ENST00000869022, ENST00000869023, ENST00000869024, ENST00000869025, ENST00000869026, ENST00000869027, ENST00000869028, ENST00000869029, ENST00000869030, ENST00000869031, ENST00000869032, ENST00000869033, ENST00000869034, ENST00000912883, ENST00000912884, ENST00000912885, ENST00000912886, ENST00000912887, ENST00000912888, ENST00000912889, ENST00000912890, ENST00000912891, ENST00000912892, ENST00000912893, ENST00000912894, ENST00000969975, ENST00000969976, ENST00000969977, ENST00000969978, ENST00000969979, ENST00000969980, ENST00000969981, ENST00000969982, ENST00000969983, ENST00000969984, ENST00000969985, ENST00000969986, ENST00000969987, ENST00000969988, ENST00000969989, ENST00000969990, ENST00000969991, ENST00000969992, ENST00000969993, ENST00000969994, ENST00000969995, ENST00000969996, ENST00000969997, ENST00000969998, ENST00000969999, ENST00000970000, ENST00000970002, ENST00000970003, ENST00000970004, ENST00000970006, ENST00000970008, ENST00000970010, ENST00000970011, ENST00000970013, ENST00000970015

RefSeq mRNA: 54 — MANE Select: NM_001385408 NM_001170755, NM_001385373, NM_001385374, NM_001385375, NM_001385376, NM_001385377, NM_001385378, NM_001385403, NM_001385404, NM_001385405, NM_001385406, NM_001385407, NM_001385408, NM_001385409, NM_001385410, NM_001385411, NM_001385412, NM_001385413, NM_001385414, NM_001385415, NM_001385416, NM_001385417, NM_001385418, NM_001385419, NM_001385420, NM_001385421, NM_001385422, NM_001385423, NM_001385424, NM_001385425, NM_001385426, NM_001385427, NM_001385428, NM_001385429, NM_001385430, NM_001385431, NM_001385432, NM_001385433, NM_001385434, NM_001385435, NM_001385436, NM_001385437, NM_001385438, NM_001385439, NM_001385440, NM_001385441, NM_001385442, NM_001385443, NM_001385444, NM_001385445, NM_001385446, NM_001385447, NM_001385448, NM_173638

CCDS: CCDS72852, CCDS91031

Canonical transcript exons

ENST00000581897 — 22 exons

Exon	Start	End
ENSE00002687127	144461381	144461669
ENSE00002691863	144440141	144440295
ENSE00002698832	144459366	144459483
ENSE00002703206	144460843	144460961
ENSE00002726155	144423870	144423975
ENSE00003463961	144429700	144429863
ENSE00003483704	144427818	144427990
ENSE00003487468	144424690	144424862
ENSE00003494864	144421390	144423256
ENSE00003499111	144428606	144428657
ENSE00003536781	144437945	144438047
ENSE00003540135	144433773	144433824
ENSE00003546054	144426278	144426450
ENSE00003551884	144425517	144425568
ENSE00003561956	144450772	144450870
ENSE00003608457	144435111	144435316
ENSE00003618516	144436895	144437109
ENSE00003624239	144435781	144435853
ENSE00003681603	144427047	144427098
ENSE00003718194	144456537	144456805
ENSE00003718754	144448775	144448916
ENSE00003937989	144439829	144440038

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 93.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2878 / max 5.0569, expressed in 132 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14114	0.2878	132

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	93.98	gold quality
cerebellar hemisphere	UBERON:0002245	93.74	gold quality
cerebellar cortex	UBERON:0002129	93.73	gold quality
cerebellum	UBERON:0002037	93.66	gold quality
thymus	UBERON:0002370	93.64	silver quality
right hemisphere of cerebellum	UBERON:0014890	93.50	gold quality
stromal cell of endometrium	CL:0002255	91.72	gold quality
thyroid gland	UBERON:0002046	90.95	gold quality
ganglionic eminence	UBERON:0004023	90.86	gold quality
right lobe of thyroid gland	UBERON:0001119	90.71	gold quality
left lobe of thyroid gland	UBERON:0001120	90.68	gold quality
right lobe of liver	UBERON:0001114	90.65	gold quality
right lung	UBERON:0002167	90.19	gold quality
mucosa of stomach	UBERON:0001199	90.04	gold quality
right uterine tube	UBERON:0001302	89.86	gold quality
lower esophagus muscularis layer	UBERON:0035833	89.75	gold quality
lower esophagus	UBERON:0013473	89.74	gold quality
spleen	UBERON:0002106	89.70	gold quality
body of pancreas	UBERON:0001150	89.58	gold quality
body of uterus	UBERON:0009853	89.50	gold quality
cortical plate	UBERON:0005343	89.49	gold quality
muscle layer of sigmoid colon	UBERON:0035805	89.34	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	89.31	gold quality
tibial artery	UBERON:0007610	89.27	gold quality
popliteal artery	UBERON:0002250	89.25	gold quality
endometrium	UBERON:0001295	89.13	gold quality
liver	UBERON:0002107	89.09	gold quality
left ovary	UBERON:0002119	89.09	gold quality
myometrium	UBERON:0001296	88.92	gold quality
lymph node	UBERON:0000029	88.86	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.25
E-MTAB-5061	no	3.08

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1, ESR2, NR1I2

miRNA regulators (miRDB)

71 targeting NBPF15, 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-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-5093	99.67	69.26	2291
HSA-MIR-580-3P	99.67	69.23	1841
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-942-5P	99.41	68.40	1977
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662

Literature-anchored findings (GeneRIF, showing 1)

• We suggest that the entanglements between the mosaic disorder-ordered segments in NBPF15 N terminus have triggered the multiple types of aggregates and phase transition of NBPF15 proteins, which could be associated with Olduvai-related cognitive dysfunction diseases (PMID:31808794)

Cross-species orthologs

0 orthologs

Paralogs (14): NBPF3 (ENSG00000142794), NBPF20 (ENSG00000162825), NBPF6 (ENSG00000186086), NBPF4 (ENSG00000196427), NBPF1 (ENSG00000219481), NBPF11 (ENSG00000263956), NBPF12 (ENSG00000268043), NBPF9 (ENSG00000269713), NBPF8 (ENSG00000270231), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF15 — Q8N660 (reviewed: Q8N660)

Alternative names: Neuroblastoma breakpoint family member 15, Neuroblastoma breakpoint family member 16

All UniProt accessions (3): Q8N660, A0A087WVG8, A0A8I5KV21

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Ubiquitously expressed with a higher expression observed in breast and liver. Also expressed in neuroblastoma cell line.

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 (54): NP_001164226, NP_001372302, NP_001372303, NP_001372304, NP_001372305, NP_001372306, NP_001372307, NP_001372332, NP_001372333, NP_001372334, NP_001372335, NP_001372336, NP_001372337, NP_001372338, NP_001372339, NP_001372340, NP_001372341, NP_001372342, NP_001372343, NP_001372344, NP_001372345, NP_001372346, NP_001372347, NP_001372348, NP_001372349, NP_001372350, NP_001372351, NP_001372352, NP_001372353, NP_001372354, NP_001372355, NP_001372356, NP_001372357, NP_001372358, NP_001372359, NP_001372360, NP_001372361, NP_001372362, NP_001372363, NP_001372364, NP_001372365, NP_001372366, NP_001372367, NP_001372368, NP_001372369, NP_001372370, NP_001372371, NP_001372372, NP_001372373, NP_001372374, NP_001372375, NP_001372376, NP_001372377, NP_775909 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (19 total): domain 6, sequence conflict 4, compositionally biased region 3, region of interest 3, chain 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N660-F1	46.94	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, chr1q21, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, PECE_MAMMARY_STEM_CELL_DN, DACH1_TARGET_GENES, SKIL_TARGET_GENES, ZFP91_TARGET_GENES, MIR3529_3P, MIR33A_3P, MIR141_3P, MIR200A_3P, MIR5093, MIR580_3P, MIR4692, MIR4514

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

510 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NBPF15	NOTCH2NLB	P0DPK3	540
NBPF15	FAM72B	Q86X60	461
NBPF15	PPIAL4D	F5H284	449
NBPF15	USP17L11	C9JVI0	447
NBPF15	GOLGA8CP	A6NN73	447
NBPF15	SPDYE5	A6NIY4	418
NBPF15	OR4F17	Q8NGA8	417
NBPF15	PRAMEF15	P0DUQ1	399
NBPF15	PPIAL4E	A0A075B759	378
NBPF15	FAM72C	H0Y354	368
NBPF15	SRGAP2B	P0DMP2	350
NBPF15	OR4M2	Q8NGB6	348
NBPF15	PPIAL4A	Q9Y536	324
NBPF15	FAM72D	Q6L9T8	322
NBPF15	ZNF492	Q9P255	322

IntAct

7 interactions, top by confidence:

A	B	Type	Score
NBPF15	F2RL1	psi-mi:“MI:0915”(physical association)	0.370
NBPF15	FXR1	psi-mi:“MI:0915”(physical association)	0.370
NBPF15	PACS2	psi-mi:“MI:0915”(physical association)	0.370
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
FMR1	NBPF15	psi-mi:“MI:0915”(physical association)	0.000
leuD	NBPF15	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): NBPF15 (Affinity Capture-MS), NBPF15 (Two-hybrid), NBPF15 (Proximity Label-MS), NBPF15 (Phenotypic Suppression), NBPF15 (Two-hybrid), NBPF15 (Negative Genetic), NBPF15 (Negative Genetic), NBPF15 (Negative Genetic), NBPF15 (Affinity Capture-RNA), KDM1A (Two-hybrid)

ESM2 similar proteins: A0A087WUL8, A0A0J9YWL9, A0A0J9YY54, A0A0U1RQI7, A6NJ88, A6QL64, B4DH59, D3ZVV1, E9Q6E9, F1LWT0, O04492, O88799, P0DKJ7, P0DKJ8, P0DKL2, P0DPF3, P18583, P53353, Q08AG5, Q0P6D6, Q2EG98, Q3BBV2, Q4ZJZ1, Q5HY64, Q5JPF3, Q5QGU6, Q5TAG4, Q5TI25, Q5XHX6, Q6P3W6, Q6P902, Q6XPR3, Q6ZQX7, Q86T75, Q86VE3, Q86VQ3, Q8N2N9, Q8N660, Q8N693, Q96EQ9

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	128
Likely benign	17
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4682496	GRCh37/hg19 1q21.1-21.2(chr1:146125775-148884815)x1	Pathogenic

SpliceAI

2184 predictions. Top by Δscore:

Variant	Effect	Δscore
1:144423866:T:G	donor_loss	1.0000
1:144423869:AGGTA:A	donor_loss	1.0000
1:144423871:CCAGG:C	donor_loss	1.0000
1:144423872:CCCAG:C	donor_loss	1.0000
1:144424685:CTCA:C	donor_loss	1.0000
1:144424686:TCACC:T	donor_loss	1.0000
1:144424687:CACCT:C	donor_loss	1.0000
1:144424688:A:AC	donor_gain	1.0000
1:144424688:A:T	donor_loss	1.0000
1:144424688:ACCT:A	donor_gain	1.0000
1:144424688:ACCTC:A	donor_gain	1.0000
1:144424689:C:CT	donor_gain	1.0000
1:144424689:CCT:C	donor_gain	1.0000
1:144424689:CCTC:C	donor_gain	1.0000
1:144424689:CCTCC:C	donor_gain	1.0000
1:144426276:A:AC	donor_gain	1.0000
1:144426276:ACTGT:A	donor_gain	1.0000
1:144426277:C:CA	donor_gain	1.0000
1:144426277:CTGT:C	donor_gain	1.0000
1:144426277:CTGTC:C	donor_gain	1.0000
1:144426450:CCTGG:C	acceptor_loss	1.0000
1:144426451:C:CA	acceptor_loss	1.0000
1:144426451:C:CC	acceptor_gain	1.0000
1:144437941:T:G	donor_loss	1.0000
1:144437941:TCA:T	donor_loss	1.0000
1:144437942:G:A	donor_loss	1.0000
1:144437943:A:AG	donor_loss	1.0000
1:144437943:GG:G	donor_loss	1.0000
1:144437944:AGGT:A	donor_loss	1.0000
1:144437945:CAG:C	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1043751 (1:144423198 T>A,C), RS1058107 (1:144443041 T>C,G), RS1058121 (1:144442773 A>G), RS1058122 (1:144442757 A>C,G), RS1058126 (1:144442587 C>A,T), RS1065451 (1:144440948 A>G), RS111234729 (1:144453143 T>A), RS111338061 (1:144462367 A>C), RS111389537 (1:144459618 A>G), RS111406432 (1:144422050 A>AAC), RS111507951 (1:144423797 A>G), RS111615504 (1:144460784 T>TAGAC), RS111628885 (1:144428106 T>G), RS111661293 (1:144423837 C>G), RS111689283 (1:144446953 C>T)

Disease associations

OMIM: gene MIM:610414 | 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

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	increases expression	1
triphenyl phosphate	affects expression	1
ethyl-p-hydroxybenzoate	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
Resveratrol	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Pesticides	decreases expression	1
Plant Extracts	increases expression, affects cotreatment	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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