NBPF9

Summary

NBPF9 (NBPF member 9, HGNC:31991) is a protein-coding gene on chromosome 1q21.2, encoding NBPF family member NBPF9 (P0DPF3). It is a common-essential gene (DepMap: required in 100.0% of cancer 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 400818 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 17 total
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_001388367

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31991
Approved symbol	NBPF9
Name	NBPF member 9
Location	1q21.2
Locus type	gene with protein product
Status	Approved
Aliases	AE01
Ensembl gene	ENSG00000269713
Ensembl biotype	protein_coding
OMIM	613999
Entrez	400818

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 20 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000483630, ENST00000610300, ENST00000611593, ENST00000613595, ENST00000615421, ENST00000621074, ENST00000621645, ENST00000698196, ENST00000698197, ENST00000698832, ENST00000906712, ENST00000906713, ENST00000932857, ENST00000932858, ENST00000952563, ENST00000952564, ENST00000952565, ENST00000952566, ENST00000952567, ENST00000952568, ENST00000952569, ENST00000952570

RefSeq mRNA: 20 — MANE Select: NM_001388367 NM_001037675, NM_001277444, NM_001388366, NM_001388367, NM_001388368, NM_001388369, NM_001388370, NM_001388371, NM_001388372, NM_001388373, NM_001388374, NM_001388375, NM_001388376, NM_001388377, NM_001388378, NM_001388379, NM_001388381, NM_001388382, NM_001388383, NM_001388384

CCDS: CCDS72895, CCDS72896

Canonical transcript exons

ENST00000698832 — 30 exons

Exon	Start	End
ENSE00002692265	149098438	149098706
ENSE00003479286	149056512	149056620
ENSE00003492177	149065526	149065689
ENSE00003521163	149058164	149058215
ENSE00003534406	149064431	149064482
ENSE00003540670	149077208	149077419
ENSE00003543628	149057335	149057507
ENSE00003545887	149070934	149071139
ENSE00003565186	149080053	149080155
ENSE00003587472	149077883	149077955
ENSE00003602114	149071604	149071676
ENSE00003604343	149062862	149062913
ENSE00003617006	149081965	149082174
ENSE00003633487	149079007	149079221
ENSE00003635679	149063633	149063805
ENSE00003636686	149052186	149055899
ENSE00003651056	149069594	149069645
ENSE00003679529	149058925	149059097
ENSE00003686503	149075655	149075864
ENSE00003695807	149062093	149062265
ENSE00003698554	149059700	149059808
ENSE00003701628	149060523	149060695
ENSE00003702427	149061332	149061383
ENSE00003718987	149073768	149073870
ENSE00003735193	149072718	149072932
ENSE00003740187	149101262	149101379
ENSE00003744719	149102729	149102847
ENSE00003748139	149090753	149090894
ENSE00003749449	149103301	149103551
ENSE00003931055	149082272	149082430

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 97.60.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9935 / max 15.2469, expressed in 670 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
201703	0.9935	670

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	97.60	gold quality
stromal cell of endometrium	CL:0002255	95.63	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.70	gold quality
colonic epithelium	UBERON:0000397	94.15	gold quality
bone marrow cell	CL:0002092	93.96	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.79	gold quality
cerebellar cortex	UBERON:0002129	93.76	gold quality
cerebellum	UBERON:0002037	93.72	gold quality
cerebellar hemisphere	UBERON:0002245	93.70	gold quality
right lobe of thyroid gland	UBERON:0001119	93.36	gold quality
left lobe of thyroid gland	UBERON:0001120	92.97	gold quality
liver	UBERON:0002107	92.97	gold quality
thyroid gland	UBERON:0002046	92.89	gold quality
ventricular zone	UBERON:0003053	92.61	gold quality
uterine cervix	UBERON:0000002	92.47	gold quality
skin of leg	UBERON:0001511	92.36	gold quality
zone of skin	UBERON:0000014	92.34	gold quality
skin of abdomen	UBERON:0001416	92.27	gold quality
tonsil	UBERON:0002372	92.23	gold quality
right lobe of liver	UBERON:0001114	92.08	gold quality
mucosa of stomach	UBERON:0001199	91.96	gold quality
right uterine tube	UBERON:0001302	91.78	gold quality
body of pancreas	UBERON:0001150	91.47	gold quality
right ovary	UBERON:0002118	91.44	gold quality
right lung	UBERON:0002167	91.27	gold quality
endocervix	UBERON:0000458	91.22	gold quality
subcutaneous adipose tissue	UBERON:0002190	91.16	gold quality
tibial nerve	UBERON:0001323	91.03	gold quality
calcaneal tendon	UBERON:0003701	91.02	gold quality
popliteal artery	UBERON:0002250	90.98	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	1346.99
E-GEOD-84465	yes	942.54
E-GEOD-125970	yes	22.49
E-CURD-112	yes	18.24
E-ENAD-27	yes	6.54
E-ANND-3	yes	5.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting NBPF9, 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-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-1323	99.83	69.89	2471
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-12124	99.68	69.17	2700
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-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-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
HSA-MIR-1912-3P	99.32	67.40	936

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Cross-species orthologs

0 orthologs

Paralogs (14): NBPF3 (ENSG00000142794), NBPF20 (ENSG00000162825), NBPF6 (ENSG00000186086), NBPF4 (ENSG00000196427), NBPF1 (ENSG00000219481), NBPF11 (ENSG00000263956), NBPF15 (ENSG00000266338), NBPF12 (ENSG00000268043), NBPF8 (ENSG00000270231), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF9 — P0DPF3 (reviewed: P0DPF3)

Alternative names: Neuroblastoma breakpoint family member 9

All UniProt accessions (4): P0DPF3, A0A087WVG0, A0A087WZE1, A0A087X0Y3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in a 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.

Isoforms (2)

UniProt ID	Names	Canonical?
P0DPF3-1	1	yes
P0DPF3-2	2

RefSeq proteins (20): NP_001032764, NP_001264373, NP_001375295, NP_001375296, NP_001375297, NP_001375298, NP_001375299, NP_001375300, NP_001375301, NP_001375302, NP_001375303, NP_001375304, NP_001375305, NP_001375306, NP_001375307, NP_001375308, NP_001375310, NP_001375311, NP_001375312, NP_001375313 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (30 total): domain 9, sequence conflict 7, region of interest 5, compositionally biased region 5, coiled-coil region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DPF3-F1	45.46	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, DODD_NASOPHARYNGEAL_CARCINOMA_UP, chr1q21, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, JOHNSTONE_PARVB_TARGETS_2_DN, DACH1_TARGET_GENES, SKIL_TARGET_GENES, ZFP91_TARGET_GENES, MIR3529_3P, MIR141_3P, MIR200A_3P, MIR580_3P, MIR4692, MIR4514, MIR4478

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

398 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NBPF9	C1orf167	Q5SNV9	595
NBPF9	SPDYE5	A6NIY4	479
NBPF9	NOTCH2NLB	P0DPK3	445
NBPF9	TYW1B	Q6NUM6	431
NBPF9	VSIG10L	Q86VR7	376
NBPF9	CNTNAP3B	Q96NU0	376
NBPF9	DBNDD1	Q9H9R9	352
NBPF9	ADAM30	Q9UKF2	351
NBPF9	LIX1L	Q8IVB5	336
NBPF9	SLAIN1	Q8ND83	327
NBPF9	GABPB2	Q8TAK5	323
NBPF9	MYO1H	Q8N1T3	315
NBPF9	GUCA1C	O95843	313
NBPF9	EFCAB7	A8K855	307
NBPF9	ZNF92	Q03936	302
NBPF9	ANKRD49	Q8WVL7	302

IntAct

0 interactions, top by confidence:

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	14
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3493 predictions. Top by Δscore:

Variant	Effect	Δscore
1:149056619:GAA:G	acceptor_gain	1.0000
1:149057330:CTCA:C	donor_loss	1.0000
1:149057331:T:G	donor_loss	1.0000
1:149057331:TCA:T	donor_loss	1.0000
1:149057332:CA:C	donor_loss	1.0000
1:149057332:G:GG	donor_gain	1.0000
1:149057332:GTGA:G	donor_loss	1.0000
1:149057333:A:AC	donor_gain	1.0000
1:149057333:A:T	donor_loss	1.0000
1:149057333:ACCT:A	donor_gain	1.0000
1:149057333:ACCTC:A	donor_gain	1.0000
1:149057334:C:CA	donor_loss	1.0000
1:149057334:C:CC	donor_gain	1.0000
1:149057334:CCT:C	donor_gain	1.0000
1:149057334:CCTC:C	donor_gain	1.0000
1:149057334:CCTCC:C	donor_gain	1.0000
1:149057335:GAG:G	donor_gain	1.0000
1:149057335:GAGG:G	donor_gain	1.0000
1:149057336:GGAG:G	donor_gain	1.0000
1:149057336:GGAGG:G	donor_gain	1.0000
1:149057337:GGGAG:G	donor_gain	1.0000
1:149057389:G:GT	donor_gain	1.0000
1:149057390:T:TA	donor_gain	1.0000
1:149057503:TGAGC:T	acceptor_gain	1.0000
1:149057506:G:GT	acceptor_gain	1.0000
1:149057506:GC:G	acceptor_gain	1.0000
1:149057506:GG:G	acceptor_gain	1.0000
1:149057506:GGCTC:G	acceptor_gain	1.0000
1:149057507:A:AC	acceptor_loss	1.0000
1:149057507:A:AG	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS10399744 (1:149099293 C>G,T), RS1043478 (1:149055675 T>A,C,G), RS1043480 (1:149055601 C>A,G,T), RS10607874 (1:149052262 TAA>T,TA), RS1065139 (1:149054528 G>A), RS1065202 (1:149054271 C>A,G), RS10907357 (1:149105549 A>G), RS111295005 (1:149072498 C>A), RS111348851 (1:149064225 T>C), RS111393524 (1:149072983 C>A,G,T), RS111437406 (1:149073130 C>T), RS111615420 (1:149075552 T>A,C), RS111734804 (1:149078030 A>G), RS111740471 (1:149064704 C>A,T), RS111844469 (1:149073603 T>C)

Disease associations

OMIM: gene MIM:613999 | 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
GCST90000025_766	Appendicular lean mass	6.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004980	appendicular lean mass

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
Air Pollutants	affects expression, increases abundance, decreases expression	2
Ozone	affects cotreatment, increases oxidation, affects expression, increases abundance	2
aristolochic acid I	increases expression	1
methacrylaldehyde	increases oxidation, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
bisphenol S	decreases expression	1
bisphenol AF	decreases expression	1
Acrolein	affects cotreatment, increases oxidation	1
Doxorubicin	decreases expression	1
Pesticides	decreases expression	1
Smoke	increases abundance, decreases expression	1
Tobacco Smoke Pollution	increases methylation	1
Aflatoxin B1	increases methylation	1
Lactic Acid	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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