NBPF20

Summary

NBPF20 (NBPF member 20, HGNC:32000) is a protein-coding gene on chromosome 1q21.1, encoding NBPF family member NBPF20 (P0DPF2). It is a selective cancer dependency (DepMap: 20.0% 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 100288142 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 6 total
• Cancer dependency (DepMap): dependent in 20.0% of screened cell lines
• MANE Select transcript: NM_001397211

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32000
Approved symbol	NBPF20
Name	NBPF member 20
Location	1q21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000162825
Ensembl biotype	protein_coding
OMIM	614007
Entrez	100288142

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000369373, ENST00000698833

RefSeq mRNA: 2 — MANE Select: NM_001397211 NM_001278267, NM_001397211

CCDS: CCDS91033

Canonical transcript exons

ENST00000698833 — 143 exons

Exon	Start	End
ENSE00001607547	145328945	145328996
ENSE00001651170	145329706	145329878
ENSE00001693842	145327291	145327399
ENSE00001765235	145328114	145328286
ENSE00003461234	145399049	145399100
ENSE00003480023	145385194	145385366
ENSE00003549193	145402167	145402381
ENSE00003555856	145386013	145386064
ENSE00003582888	145393884	145393935
ENSE00003617163	145387547	145387598
ENSE00003639845	145401059	145401131
ENSE00003668570	145386774	145386946
ENSE00003676602	145388318	145388490
ENSE00003695047	145394978	145395141
ENSE00003696717	145381257	145381308
ENSE00003697977	145374865	145374973
ENSE00003698850	145382018	145382190
ENSE00003701859	145375688	145375860
ENSE00003702429	145384371	145384479
ENSE00003712555	145321740	145321912
ENSE00003712561	145318604	145318776
ENSE00003713367	145351917	145352089
ENSE00003714048	145314665	145314716
ENSE00003715053	145366180	145366352
ENSE00003715222	145367003	145367054
ENSE00003715440	145312208	145312380
ENSE00003715511	145392303	145392354
ENSE00003715780	145339215	145339387
ENSE00003715879	145405098	145405307
ENSE00003716419	145332058	145332166
ENSE00003716722	145365357	145365465
ENSE00003716873	145297139	145297247
ENSE00003717557	145303533	145303584
ENSE00003718197	145293204	145293376
ENSE00003718497	145320196	145320368
ENSE00003718528	145299548	145299720
ENSE00003718851	145295567	145295618
ENSE00003720118	145389121	145389229
ENSE00003720284	145383570	145383742
ENSE00003720650	145371751	145371802
ENSE00003720791	145403216	145403318
ENSE00003720918	145336013	145336185
ENSE00003721107	145346322	145346430
ENSE00003721814	145313009	145313117
ENSE00003721875	145340767	145340939
ENSE00003721948	145338454	145338505
ENSE00003722222	145393074	145393246
ENSE00003722613	145359802	145359974
ENSE00003722755	145378814	145378986
ENSE00003723863	145367764	145367936
ENSE00003724195	145332881	145333053
ENSE00003724379	145370940	145371112
ENSE00003725110	145353503	145353675
ENSE00003725253	145319435	145319486
ENSE00003725696	145301901	145302009
ENSE00003725882	145301100	145301272
ENSE00003726171	145360603	145360711
ENSE00003726456	145294782	145294954
ENSE00003726627	145373293	145373344
ENSE00003726733	145304294	145304466
ENSE00003727235	145317781	145317889
ENSE00003727792	145311437	145311488
ENSE00003728273	145342387	145342559
ENSE00003728309	145352742	145352793
ENSE00003728357	145315426	145315598
ENSE00003729217	145324185	145324236
ENSE00003729337	145390769	145390820
ENSE00003729821	145343969	145344141
ENSE00003729962	145331257	145331429
ENSE00003732134	145292381	145292489
ENSE00003732660	145296338	145296510
ENSE00003733629	145335242	145335293
ENSE00003733984	145308253	145308361
ENSE00003734257	145334459	145334631
ENSE00003734594	145355856	145355964
ENSE00003734905	145310658	145310830
ENSE00003735449	145306716	145306767
ENSE00003735476	145347978	145348029
ENSE00003735842	145309897	145309948
ENSE00003736056	145297962	145298134
ENSE00003736218	145363785	145363836
ENSE00003736593	145316207	145316258
ENSE00003737127	145355055	145355227
ENSE00003737890	145344750	145344801
ENSE00003738109	145324946	145325118
ENSE00003739064	145389944	145390116
ENSE00003739110	145374064	145374236
ENSE00003739141	145361426	145361598
ENSE00003739284	145294021	145294072
ENSE00003739614	145364556	145364728
ENSE00003739658	145341564	145341672
ENSE00003739852	145326490	145326662
ENSE00003739959	145305893	145306065
ENSE00003740515	145322543	145322651
ENSE00003740550	145350291	145350463
ENSE00003740974	145372512	145372684
ENSE00003741183	145330486	145330537
ENSE00003741397	145339996	145340047
ENSE00003741606	145363004	145363176
ENSE00003742463	145382799	145382850
ENSE00003742731	145359031	145359082
ENSE00003744206	145368545	145368596
ENSE00003744261	145336814	145336922
ENSE00003744408	145376505	145376556
ENSE00003744624	145305070	145305178
ENSE00003745022	145348739	145348911
ENSE00003745570	145316978	145317150
ENSE00003745939	145313832	145314004
ENSE00003746290	145391530	145391702
ENSE00003746638	145325719	145325770
ENSE00003747862	145309076	145309248
ENSE00003748083	145377266	145377438
ENSE00003748127	145333698	145333749
ENSE00003748288	145302724	145302896
ENSE00003748362	145380440	145380612
ENSE00003748614	145357490	145357541
ENSE00003749006	145298787	145298838
ENSE00003749084	145356679	145356851
ENSE00003749169	145351094	145351202
ENSE00003749258	145323366	145323538
ENSE00003749286	145307477	145307649
ENSE00003749317	145378043	145378094
ENSE00003749500	145345521	145345693
ENSE00003750586	145343208	145343259
ENSE00003750859	145320969	145321020
ENSE00003751249	145349520	145349571
ENSE00003751425	145347145	145347317
ENSE00003752063	145379617	145379725
ENSE00003753102	145370117	145370225
ENSE00003753105	145300329	145300380
ENSE00003753127	145337637	145337809
ENSE00003753372	145358251	145358423
ENSE00003753937	145354284	145354335
ENSE00003754554	145362243	145362294
ENSE00003754788	145369316	145369488
ENSE00003974914	145420488	145420756
ENSE00003974915	145412749	145412890
ENSE00003974916	145423314	145423431
ENSE00003974917	145400389	145400594
ENSE00003974918	145405410	145405564
ENSE00003974919	145290005	145291769
ENSE00003974920	145425323	145425603
ENSE00003974921	145424780	145424898

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 92.58.

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	92.58	gold quality
cerebellar cortex	UBERON:0002129	91.11	gold quality
cerebellum	UBERON:0002037	91.07	gold quality
cerebellar hemisphere	UBERON:0002245	90.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.37	gold quality
stromal cell of endometrium	CL:0002255	87.34	gold quality
tonsil	UBERON:0002372	86.41	gold quality
bone marrow cell	CL:0002092	85.05	gold quality
liver	UBERON:0002107	84.44	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.11	gold quality
right lobe of liver	UBERON:0001114	82.19	gold quality
ventricular zone	UBERON:0003053	82.10	gold quality
ganglionic eminence	UBERON:0004023	81.80	gold quality
cortical plate	UBERON:0005343	81.48	gold quality
calcaneal tendon	UBERON:0003701	79.69	gold quality
bone marrow	UBERON:0002371	79.05	gold quality
islet of Langerhans	UBERON:0000006	78.97	gold quality
body of pancreas	UBERON:0001150	78.76	gold quality
pancreas	UBERON:0001264	78.66	gold quality
adrenal tissue	UBERON:0018303	78.15	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.85	gold quality
lower esophagus	UBERON:0013473	77.83	gold quality
right adrenal gland cortex	UBERON:0035827	77.72	gold quality
superior frontal gyrus	UBERON:0002661	77.63	gold quality
adrenal gland	UBERON:0002369	77.51	gold quality
testis	UBERON:0000473	77.21	gold quality
right adrenal gland	UBERON:0001233	76.91	gold quality
granulocyte	CL:0000094	76.90	gold quality
left adrenal gland	UBERON:0001234	76.90	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	17.85
E-ANND-3	yes	5.16
E-MTAB-8060	no	904.83
E-MTAB-6386	no	92.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting NBPF20, 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-4778-3P	99.93	70.40	1818
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-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-1912-3P	99.32	67.40	936
HSA-MIR-329-5P	99.27	68.11	1597

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 20.0% of screened cell lines.

Cross-species orthologs

0 orthologs

Paralogs (14): NBPF3 (ENSG00000142794), NBPF6 (ENSG00000186086), NBPF4 (ENSG00000196427), NBPF1 (ENSG00000219481), NBPF11 (ENSG00000263956), NBPF15 (ENSG00000266338), NBPF12 (ENSG00000268043), NBPF9 (ENSG00000269713), NBPF8 (ENSG00000270231), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF10 (ENSG00000271425), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF20 — P0DPF2 (reviewed: P0DPF2)

Alternative names: Neuroblastoma breakpoint family member 20

All UniProt accessions (2): A0A8V8TMC1, H7BY70

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

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 (2): NP_001265196, NP_001384140* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (137 total): domain 64, region of interest 42, compositionally biased region 30, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for P0DPF2 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): chr1q21, MIR3529_3P, MIR141_3P, MIR200A_3P, MIR4778_3P, MIR580_3P, MIR4478, MIR4443, MIR6818_3P, MIR6852_3P, MIR4520_2_3P, MIR6499_3P, MIR152_5P, MIR6832_5P, MIR3929

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

422 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NBPF20	NOTCH2NLB	P0DPK3	507
NBPF20	CLLU1-AS1	Q5K130	473
NBPF20	LIX1L	Q8IVB5	445
NBPF20	PPIAL4C	A0A0B4J2A2	435
NBPF20	FAM47A	Q5JRC9	419
NBPF20	ZNF431	Q8TF32	412
NBPF20	ZNF19	P17023	373
NBPF20	ACP6	Q9NPH0	370
NBPF20	GPHRA	B7ZAQ6	368
NBPF20	FMO5	P49326	351
NBPF20	PEX11B	O96011	322
NBPF20	NUDT17	P0C025	321
NBPF20	ZNF814	B7Z6K7	321
NBPF20	ZNF714	Q96N38	318
NBPF20	NOTCH2NLA	Q7Z3S9	313

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A087WUL8, A6NJU9, A6NKU9, A6NNC1, A8MRT5, B2SU53, B5DUH6, C9JG80, E5RHQ5, F8W0I5, P01068, P02849, P02895, P07907, P08519, P0DPF2, P0DPF3, P0DUT2, P13208, P14417, P16881, P20465, P32072, P83060, P96886, Q06602, Q06811, Q13117, Q1HVI8, Q26678, Q26755, Q27905, Q3BBV0, Q4ZJY7, Q5TAG4, Q5TI25, Q60997, Q6P3W6, Q6RY98, Q7T3L1

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2887 predictions. Top by Δscore:

Variant	Effect	Δscore
1:145292378:G:A	donor_loss	1.0000
1:145292379:GGTAA:G	donor_loss	1.0000
1:145292381:CAGGT:C	donor_loss	1.0000
1:145292383:CCCAG:C	donor_loss	1.0000
1:145292409:C:A	donor_gain	1.0000
1:145292487:TTT:T	acceptor_gain	1.0000
1:145292488:TT:T	acceptor_gain	1.0000
1:145293199:CTCA:C	donor_loss	1.0000
1:145293201:CACC:C	donor_loss	1.0000
1:145293202:A:AC	donor_gain	1.0000
1:145293202:ACCT:A	donor_gain	1.0000
1:145293202:ACCTC:A	donor_gain	1.0000
1:145293203:C:CC	donor_gain	1.0000
1:145293203:CCT:C	donor_gain	1.0000
1:145293203:CCTC:C	donor_gain	1.0000
1:145293203:CCTCC:C	donor_gain	1.0000
1:145298017:T:TA	donor_gain	1.0000
1:145298130:TGAGC:T	acceptor_gain	1.0000
1:145298133:GC:G	acceptor_gain	1.0000
1:145298134:CC:C	acceptor_gain	1.0000
1:145298135:C:CC	acceptor_gain	1.0000
1:145298782:GTTAC:G	donor_loss	1.0000
1:145298783:TTAC:T	donor_loss	1.0000
1:145298784:TACC:T	donor_loss	1.0000
1:145298785:ACCT:A	donor_loss	1.0000
1:145298786:CCTG:C	donor_loss	1.0000
1:145299546:A:AC	donor_gain	1.0000
1:145299546:ACTGT:A	donor_gain	1.0000
1:145299547:C:CA	donor_gain	1.0000
1:145299547:CTGT:C	donor_gain	1.0000

AlphaMissense

36607 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:145297978:A:C	F4841L	0.996
1:145297978:A:T	F4841L	0.996
1:145297980:A:G	F4841L	0.996
1:145313848:A:C	F4109L	0.995
1:145313848:A:T	F4109L	0.995
1:145313850:A:G	F4109L	0.995
1:145321786:A:C	F3705L	0.995
1:145321786:A:T	F3705L	0.995
1:145321788:A:G	F3705L	0.995
1:145293220:A:C	F5085L	0.994
1:145293220:A:T	F5085L	0.994
1:145293222:A:G	F5085L	0.994
1:145313878:A:C	F4099L	0.993
1:145313878:A:T	F4099L	0.993
1:145313880:A:G	F4099L	0.993
1:145317024:A:C	F3949L	0.992
1:145317024:A:T	F3949L	0.992
1:145317026:A:G	F3949L	0.992
1:145293250:A:C	F5075L	0.991
1:145293250:A:T	F5075L	0.991
1:145293252:A:G	F5075L	0.991
1:145313922:A:G	C4085R	0.990
1:145317831:T:A	R3890S	0.990
1:145317831:T:G	R3890S	0.990
1:145298008:A:C	F4831L	0.989
1:145298008:A:T	F4831L	0.989
1:145298010:A:G	F4831L	0.989
1:145313849:A:G	F4109S	0.989
1:145291553:G:C	F5199L	0.988
1:145291553:G:T	F5199L	0.988

dbSNP variants (sampled 300 via entrez): RS1043882 (1:145290108 T>A,C), RS1043890 (1:145290097 G>A), RS1058123 (1:145407853 G>A,C), RS1058124 (1:145407850 G>A,T), RS1058125 (1:145407819 G>A,T), RS1064412 (1:145407846 G>C,T), RS1065210 (1:145290100 G>C), RS111226928 (1:145396046 A>G), RS111242368 (1:145411320 T>C), RS111254438 (1:145388710 G>A), RS111383096 (1:145388893 T>C), RS111388002 (1:145397329 C>T), RS111402912 (1:145408255 G>C), RS111403893 (1:145396710 T>A,G), RS111466428 (1:145400981 G>A,C)

Disease associations

OMIM: gene MIM:614007 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST005983_40	Serum uric acid levels	5.000000e-14
GCST007725_40	Serum uric acid levels	6.000000e-14
GCST007733_48	Serum uric acid levels	6.000000e-14
GCST007733_68	Serum uric acid levels	1.000000e-29
GCST008971_100	Urate levels	2.000000e-51
GCST008971_99	Urate levels	5.000000e-08
GCST008972_115	Urate levels	9.000000e-15
GCST008972_151	Urate levels	1.000000e-69
GCST008972_92	Urate levels	8.000000e-11

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004761	uric acid measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
beta-lapachone	increases expression	1
manganese chloride	decreases expression, increases abundance	1
aflatoxin B2	increases methylation	1
entinostat	decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
abrine	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Estradiol	increases expression	1
Manganese	decreases expression, increases abundance	1
Pesticides	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases methylation	1
beta-Naphthoflavone	increases expression	1

Clinical trials (associated diseases)

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