NBPF11

Summary

NBPF11 (NBPF member 11, HGNC:31993) is a protein-coding gene on chromosome 1q21.2, encoding NBPF family member NBPF11 (Q86T75). It is a selective cancer dependency (DepMap: 60.0% of cell lines).

Predicted to be located in cytoplasm.

Source: NCBI Gene 200030 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 8 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 60.0% of screened cell lines
• MANE Select transcript: NM_001385469

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31993
Approved symbol	NBPF11
Name	NBPF member 11
Location	1q21.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000263956
Ensembl biotype	protein_coding
OMIM	614001
Entrez	200030

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 22 protein_coding, 1 nonsense_mediated_decay

ENST00000613531, ENST00000614015, ENST00000614506, ENST00000615281, ENST00000682118, ENST00000906682, ENST00000906683, ENST00000906684, ENST00000917377, ENST00000917378, ENST00000917379, ENST00000917380, ENST00000917381, ENST00000917382, ENST00000917383, ENST00000917384, ENST00000917385, ENST00000917386, ENST00000917387, ENST00000955384, ENST00000955385, ENST00000955386, ENST00000955387

RefSeq mRNA: 15 — MANE Select: NM_001385469 NM_001101663, NM_001385468, NM_001385469, NM_001385470, NM_001385471, NM_001385472, NM_001385473, NM_001385474, NM_001385475, NM_001385476, NM_001385477, NM_001385478, NM_001385479, NM_001385480, NM_183372

CCDS: CCDS41381

Canonical transcript exons

ENST00000682118 — 24 exons

Exon	Start	End
ENSE00002700459	148143415	148143686
ENSE00003458833	148106181	148106232
ENSE00003495285	148135672	148135813
ENSE00003509212	148106942	148107114
ENSE00003558352	148107711	148107762
ENSE00003613400	148137711	148137809
ENSE00003713549	148118620	148118722
ENSE00003715313	148122729	148122801
ENSE00003715969	148116463	148116535
ENSE00003717232	148122055	148122266
ENSE00003724940	148115793	148115998
ENSE00003727797	148105360	148105528
ENSE00003736896	148110378	148110541
ENSE00003739117	148123853	148124067
ENSE00003740090	148102151	148103912
ENSE00003742064	148114437	148114488
ENSE00003742262	148126829	148127038
ENSE00003745668	148108482	148108654
ENSE00003746005	148120501	148120710
ENSE00003751239	148104537	148104645
ENSE00003751887	148109284	148109335
ENSE00003753865	148117572	148117786
ENSE00003754012	148124899	148125001
ENSE00003920278	148151750	148152281

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 85.72.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1809 / max 41.6971, expressed in 636 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
201689	0.8952	469
201688	0.2857	133

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	85.72	gold quality
right lobe of liver	UBERON:0001114	84.02	gold quality
liver	UBERON:0002107	83.95	gold quality
ventricular zone	UBERON:0003053	83.82	gold quality
right uterine tube	UBERON:0001302	83.12	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.36	gold quality
zone of skin	UBERON:0000014	81.21	gold quality
skin of abdomen	UBERON:0001416	81.20	gold quality
skin of leg	UBERON:0001511	81.11	gold quality
endocervix	UBERON:0000458	80.93	gold quality
body of pancreas	UBERON:0001150	80.90	gold quality
sural nerve	UBERON:0015488	80.86	gold quality
spleen	UBERON:0002106	80.72	gold quality
ovary	UBERON:0000992	80.64	gold quality
tonsil	UBERON:0002372	80.62	gold quality
body of stomach	UBERON:0001161	80.48	gold quality
left ovary	UBERON:0002119	80.48	gold quality
body of uterus	UBERON:0009853	80.36	gold quality
right ovary	UBERON:0002118	80.29	gold quality
stromal cell of endometrium	CL:0002255	80.22	gold quality
uterine cervix	UBERON:0000002	80.00	gold quality
thoracic mammary gland	UBERON:0005200	79.98	gold quality
apex of heart	UBERON:0002098	79.95	gold quality
mucosa of stomach	UBERON:0001199	79.81	gold quality
cortex of kidney	UBERON:0001225	79.76	gold quality
subcutaneous adipose tissue	UBERON:0002190	79.74	gold quality
myometrium	UBERON:0001296	79.58	gold quality
small intestine Peyer’s patch	UBERON:0003454	79.44	gold quality
stomach	UBERON:0000945	79.40	gold quality
right lobe of thyroid gland	UBERON:0001119	79.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.59
E-MTAB-7606	no	234.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

77 targeting NBPF11, 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-3646	100.00	73.56	5283
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-3912-5P	99.95	66.11	925
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-10395-5P	99.86	67.35	676
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-4255	99.72	67.70	1541
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-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-4762-5P	99.57	68.54	1424
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-8054	99.48	70.81	2084

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), NBPF15 (ENSG00000266338), NBPF12 (ENSG00000268043), NBPF9 (ENSG00000269713), NBPF8 (ENSG00000270231), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF11 — Q86T75 (reviewed: Q86T75)

Alternative names: Neuroblastoma breakpoint family member 11, Neuroblastoma breakpoint family member 24

All UniProt accessions (3): Q86T75, A0A087WTH4, A0A087WUF5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in spinal cord.

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?
Q86T75-1	1	yes
Q86T75-2	2

RefSeq proteins (15): NP_001095133, NP_001372397, NP_001372398, NP_001372399, NP_001372400, NP_001372401, NP_001372402, NP_001372403, NP_001372404, NP_001372405, NP_001372406, NP_001372407, NP_001372408, NP_001372409, NP_899228 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (20 total): domain 6, compositionally biased region 5, region of interest 4, coiled-coil region 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86T75-F1	49.78	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): BENPORATH_ES_WITH_H3K27ME3, WWTAAGGC_UNKNOWN, AACTTT_UNKNOWN, OSMAN_BLADDER_CANCER_DN, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, chr1q21, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_UP, LU_EZH2_TARGETS_DN, RATTENBACHER_BOUND_BY_CELF1, HMG20B_TARGET_GENES, PTTG1_TARGET_GENES, UBN1_TARGET_GENES, ZFP91_TARGET_GENES, ZNF213_TARGET_GENES, ZNF592_TARGET_GENES

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

446 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NBPF11	ACP6	Q9NPH0	696
NBPF11	FMO5	P49326	654
NBPF11	CHD1L	Q86WJ1	581
NBPF11	PRKAB2	O43741	575
NBPF11	GJA8	P48165	574
NBPF11	NOTCH2NLB	P0DPK3	571
NBPF11	BCL9	O00512	517
NBPF11	GPHRA	B7ZAQ6	507
NBPF11	PPIAL4D	F5H284	478
NBPF11	HYDIN	Q4G0P3	474
NBPF11	NUDT17	P0C025	447
NBPF11	SPDYE5	A6NIY4	446
NBPF11	GJA5	P36382	446
NBPF11	LIX1L	Q8IVB5	445
NBPF11	POLR3GL	Q9BT43	435

IntAct

4 interactions, top by confidence:

A	B	Type	Score
BKRF1	NBPF11	psi-mi:“MI:0915”(physical association)	0.370
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): NBPF11 (Affinity Capture-MS), NBPF11 (Negative Genetic), NBPF11 (Affinity Capture-RNA), CBY1 (Two-hybrid), CBY1 (Affinity Capture-Western), NBPF11 (Affinity Capture-Western), NBPF11 (Two-hybrid), NBPF11 (Reconstituted Complex), NBPF11 (Reconstituted Complex)

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	1
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
565170	GRCh37/hg19 1q21.1-21.2(chr1:145895746-147926347)x1	Pathogenic

SpliceAI

594 predictions. Top by Δscore:

Variant	Effect	Δscore
1:148106177:T:A	donor_loss	1.0000
1:148106178:GTAA:G	donor_loss	1.0000
1:148106179:GGT:G	donor_loss	1.0000
1:148106180:AG:A	donor_loss	1.0000
1:148106181:CAG:C	donor_loss	1.0000
1:148106182:CCAG:C	donor_loss	1.0000
1:148106939:G:GG	donor_gain	1.0000
1:148106943:GACA:G	donor_gain	1.0000
1:148126826:G:GG	donor_gain	1.0000
1:148106231:GG:G	acceptor_gain	0.9900
1:148106231:GGA:G	acceptor_gain	0.9900
1:148106232:A:G	acceptor_loss	0.9900
1:148106232:AG:A	acceptor_gain	0.9900
1:148106235:TGCA:T	acceptor_loss	0.9900
1:148106935:G:C	donor_loss	0.9900
1:148106936:AG:A	donor_loss	0.9900
1:148106937:G:GT	donor_loss	0.9900
1:148106938:TGAGT:T	donor_loss	0.9900
1:148106939:GT:G	donor_loss	0.9900
1:148106940:AG:A	donor_loss	0.9900
1:148106941:CA:C	donor_gain	0.9900
1:148106941:CAG:C	donor_loss	0.9900
1:148106943:GACAG:G	donor_gain	0.9900
1:148106944:GGACA:G	donor_gain	0.9900
1:148107113:G:A	acceptor_loss	0.9900
1:148107113:G:GA	acceptor_gain	0.9900
1:148107113:GG:G	acceptor_gain	0.9900
1:148107114:A:AG	acceptor_gain	0.9900
1:148107114:AG:A	acceptor_gain	0.9900
1:148107114:AGG:A	acceptor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1043522 (1:148103375 T>A,C), RS1043820 (1:148102423 T>C), RS1043825 (1:148102414 G>A), RS1043841 (1:148102384 T>C), RS1043856 (1:148102335 G>C,T), RS1043877 (1:148102275 A>C), RS1061849 (1:148133414 T>C), RS1065169 (1:148102397 G>A), RS1065171 (1:148102394 C>T), RS1065172 (1:148102389 A>C), RS1065200 (1:148102285 C>A,G,T), RS1065203 (1:148102282 A>G), RS10900300 (1:148113082 A>T), RS111239941 (1:148119556 G>A,T), RS111373154 (1:148123027 A>G)

Disease associations

OMIM: gene MIM:614001 | 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

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, increases expression	3
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases expression	1
2-butenal	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Sunitinib	increases expression	1
Coumestrol	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance	1
Ozone	increases abundance, affects expression	1
Pesticides	decreases expression	1
Smoke	increases abundance, increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1

Clinical trials (associated diseases)

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