NBPF14

Summary

NBPF14 (NBPF member 14, HGNC:25232) is a protein-coding gene on chromosome 1q21.2, encoding NBPF family member NBPF14 (Q5TI25). 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 25832 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 12 total
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_001395631

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25232
Approved symbol	NBPF14
Name	NBPF member 14
Location	1q21.2
Locus type	gene with protein product
Status	Approved
Aliases	DJ328E19.C1.1
Ensembl gene	ENSG00000270629
Ensembl biotype	protein_coding
OMIM	614003
Entrez	25832

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000606877, ENST00000611826, ENST00000614999, ENST00000616120, ENST00000619423, ENST00000621066, ENST00000621070

RefSeq mRNA: 2 — MANE Select: NM_001395631 NM_001395631, NM_015383

CCDS: CCDS91039

Canonical transcript exons

ENST00000619423 — 71 exons

Exon	Start	End
ENSE00003460569	148587301	148587403
ENSE00003460738	148576410	148576461
ENSE00003477007	148589184	148589393
ENSE00003479616	148585141	148585213
ENSE00003491316	148575639	148575811
ENSE00003498069	148595543	148595752
ENSE00003500762	148590757	148590968
ENSE00003527998	148583141	148583192
ENSE00003540128	148586255	148586469
ENSE00003544219	148551153	148551261
ENSE00003566047	148577183	148577355
ENSE00003599309	148579074	148579237
ENSE00003618413	148577983	148578034
ENSE00003624656	148593598	148593700
ENSE00003625831	148584471	148584676
ENSE00003667412	148592552	148592766
ENSE00003686778	148551976	148552148
ENSE00003688061	148591432	148591504
ENSE00003688833	148552779	148552830
ENSE00003711949	148568482	148568533
ENSE00003714020	148566143	148566315
ENSE00003714278	148554309	148554360
ENSE00003715637	148537011	148537119
ENSE00003715920	148559021	148559072
ENSE00003717733	148556690	148556862
ENSE00003718137	148550372	148550544
ENSE00003718210	148558252	148558424
ENSE00003718416	148571682	148571733
ENSE00003719561	148546445	148546553
ENSE00003719831	148573230	148573338
ENSE00003721231	148542554	148542726
ENSE00003722865	148570042	148570150
ENSE00003723339	148557491	148557542
ENSE00003725603	148548832	148549004
ENSE00003727003	148538649	148538700
ENSE00003727356	148564539	148564711
ENSE00003729288	148569255	148569427
ENSE00003730852	148567713	148567885
ENSE00003731305	148570865	148571037
ENSE00003731359	148560584	148560692
ENSE00003732642	148563766	148563817
ENSE00003733881	148547268	148547440
ENSE00003735043	148536224	148536396
ENSE00003736335	148559793	148559965
ENSE00003740040	148531385	148533248
ENSE00003740124	148544124	148544296
ENSE00003743869	148562997	148563169
ENSE00003743896	148574878	148574929
ENSE00003743960	148572443	148572615
ENSE00003744233	148549601	148549652
ENSE00003744995	148535453	148535504
ENSE00003745017	148545664	148545836
ENSE00003745025	148533861	148533969
ENSE00003745445	148561407	148561579
ENSE00003746426	148555080	148555252
ENSE00003746919	148565320	148565428
ENSE00003747118	148540950	148541122
ENSE00003747137	148541731	148541839
ENSE00003748807	148540179	148540230
ENSE00003748882	148566952	148567003
ENSE00003748994	148548071	148548122
ENSE00003749913	148574053	148574225
ENSE00003750239	148553540	148553712
ENSE00003750327	148537834	148538006
ENSE00003751256	148595855	148596011
ENSE00003751493	148543363	148543414
ENSE00003752237	148555867	148555975
ENSE00003752392	148544893	148544944
ENSE00003752493	148539410	148539582
ENSE00003753215	148534684	148534856
ENSE00003754278	148562236	148562287

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.68.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8998 / max 41.9765, expressed in 469 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
201701	0.8998	469

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	98.68	gold quality
ventricular zone	UBERON:0003053	97.13	gold quality
monocyte	CL:0000576	96.65	gold quality
bone marrow cell	CL:0002092	96.40	gold quality
leukocyte	CL:0000738	96.38	gold quality
calcaneal tendon	UBERON:0003701	94.89	gold quality
stromal cell of endometrium	CL:0002255	94.75	gold quality
granulocyte	CL:0000094	94.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.31	gold quality
skin of abdomen	UBERON:0001416	94.25	gold quality
zone of skin	UBERON:0000014	94.07	gold quality
descending thoracic aorta	UBERON:0002345	93.91	gold quality
bone marrow	UBERON:0002371	93.89	gold quality
skin of leg	UBERON:0001511	93.84	gold quality
colonic epithelium	UBERON:0000397	93.65	gold quality
tonsil	UBERON:0002372	93.47	gold quality
thoracic aorta	UBERON:0001515	93.32	gold quality
ascending aorta	UBERON:0001496	93.19	gold quality
ganglionic eminence	UBERON:0004023	93.05	gold quality
blood	UBERON:0000178	92.87	gold quality
ovary	UBERON:0000992	92.47	gold quality
left ovary	UBERON:0002119	92.30	gold quality
popliteal artery	UBERON:0002250	92.30	gold quality
tibial artery	UBERON:0007610	92.30	gold quality
uterine cervix	UBERON:0000002	92.28	gold quality
right ovary	UBERON:0002118	92.24	gold quality
right coronary artery	UBERON:0001625	92.19	gold quality
esophagus mucosa	UBERON:0002469	92.14	gold quality
vagina	UBERON:0000996	92.11	gold quality
smooth muscle tissue	UBERON:0001135	91.64	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	69.90
E-GEOD-125970	yes	22.24
E-HCAD-25	yes	21.23
E-GEOD-93593	yes	15.60
E-GEOD-83139	yes	11.53
E-ANND-3	yes	11.32
E-ENAD-27	yes	6.96
E-CURD-119	yes	5.58
E-MTAB-7303	no	2411.16
E-MTAB-9689	no	278.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

65 targeting NBPF14, 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-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
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-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-6740-3P	99.48	68.49	1392
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

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), NBPF9 (ENSG00000269713), NBPF8 (ENSG00000270231), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF14 — Q5TI25 (reviewed: Q5TI25)

Alternative names: Neuroblastoma breakpoint family member 14

All UniProt accessions (7): A0A075B7F7, A0A087WTW4, A0A087WV19, A0A087WVE3, A0A087WYI5, A0A087WZJ2, Q5TI25

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in spleen and fetal liver.

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?
Q5TI25-1	1	yes
Q5TI25-2	2

RefSeq proteins (2): NP_001382560, NP_056198 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (83 total): domain 32, sequence conflict 16, region of interest 14, compositionally biased region 14, splice variant 4, chain 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q5TI25 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MITSIADES_RESPONSE_TO_APLIDIN_DN, SENESE_HDAC1_TARGETS_UP, RIGGINS_TAMOXIFEN_RESISTANCE_DN, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, chr1q21, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP, LU_EZH2_TARGETS_DN, KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3, PECE_MAMMARY_STEM_CELL_DN, ZNF213_TARGET_GENES, MIR3529_3P, MIR141_3P, MIR200A_3P, MIR580_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

478 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NBPF14	PPIAL4D	F5H284	477
NBPF14	C2orf78	A6NCI8	447
NBPF14	SPDYE5	A6NIY4	446
NBPF14	PPIAL4E	A0A075B759	402
NBPF14	ABRACL	Q9P1F3	399
NBPF14	PRR20A	P86496	398
NBPF14	ZNF716	A6NP11	395
NBPF14	RBPMS2	Q6ZRY4	374
NBPF14	ZNF839	A8K0R7	371
NBPF14	ZNF627	Q7L945	370
NBPF14	ACP6	Q9NPH0	370
NBPF14	PPIAL4A	Q9Y536	351
NBPF14	FAM72B	Q86X60	344
NBPF14	ADAM30	Q9UKF2	343
NBPF14	FMO5	P49326	341

IntAct

3 interactions, top by confidence:

A	B	Type	Score
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
MYB	NBPF14	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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	12
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4916 predictions. Top by Δscore:

Variant	Effect	Δscore
1:148534682:A:AC	donor_gain	1.0000
1:148534682:ACTGT:A	donor_gain	1.0000
1:148534683:C:CT	donor_gain	1.0000
1:148534683:CTGT:C	donor_gain	1.0000
1:148534683:CTGTC:C	donor_gain	1.0000
1:148534857:C:CC	acceptor_gain	1.0000
1:148534857:C:CG	acceptor_loss	1.0000
1:148537829:CTCA:C	donor_loss	1.0000
1:148537831:CACC:C	donor_loss	1.0000
1:148537832:A:AC	donor_gain	1.0000
1:148537832:ACCT:A	donor_gain	1.0000
1:148537832:ACCTC:A	donor_gain	1.0000
1:148537833:C:CC	donor_gain	1.0000
1:148537833:C:CG	donor_loss	1.0000
1:148537833:CCT:C	donor_gain	1.0000
1:148537833:CCTC:C	donor_gain	1.0000
1:148537833:CCTCC:C	donor_gain	1.0000
1:148537889:T:TA	donor_gain	1.0000
1:148538002:TGAGC:T	acceptor_gain	1.0000
1:148538005:GC:G	acceptor_gain	1.0000
1:148538006:CC:C	acceptor_gain	1.0000
1:148538006:CCTGG:C	acceptor_loss	1.0000
1:148538007:C:CA	acceptor_loss	1.0000
1:148538007:C:CC	acceptor_gain	1.0000
1:148538008:T:C	acceptor_loss	1.0000
1:148538644:GTTAC:G	donor_loss	1.0000
1:148538645:TTA:T	donor_loss	1.0000
1:148538646:TACC:T	donor_loss	1.0000
1:148538647:A:AG	donor_loss	1.0000
1:148538648:C:CA	donor_loss	1.0000

AlphaMissense

19461 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1043761 (1:148533043 G>A), RS1043762 (1:148533041 G>A,C,T), RS111214282 (1:148535979 C>A,T), RS111255093 (1:148544049 G>C), RS111290205 (1:148545196 A>C), RS111940957 (1:148539395 C>T), RS112117679 (1:148540461 C>G), RS112500278 (1:148587974 A>C,T), RS113100780 (1:148578776 G>A,T), RS113206251 (1:148571274 C>A,G), RS113244910 (1:148545441 C>G,T), RS113271014 (1:148588305 C>G,T), RS113295798 (1:148536478 A>T), RS113367975 (1:148540314 G>A), RS113794407 (1:148536939 C>G)

Disease associations

OMIM: gene MIM:614003 | 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
GCST001060_2	AIDS progression	2.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, decreases expression	2
Cadmium Chloride	increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression, affects cotreatment	1
2-butenal	decreases expression	1
sodium arsenite	increases expression	1
manganese chloride	decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Cannabidiol	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance	1
Ozone	affects expression, increases abundance	1
Pesticides	decreases expression	1
Smoke	decreases expression, increases abundance	1
Tetrachlorodibenzodioxin	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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