NBPF10

Summary

NBPF10 (NBPF member 10, HGNC:31992) is a protein-coding gene on chromosome 1q21.1, encoding NBPF family member NBPF10 (Q6P3W6).

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. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 100132406 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 57 total
• MANE Select transcript: NM_001302371

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31992
Approved symbol	NBPF10
Name	NBPF member 10
Location	1q21.1
Locus type	gene with protein product
Status	Approved
Aliases	AG1
Ensembl gene	ENSG00000271425
Ensembl biotype	protein_coding
OMIM	614000
Entrez	100132406

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000583866, ENST00000612520

RefSeq mRNA: 2 — MANE Select: NM_001302371 NM_001039703, NM_001302371

CCDS: CCDS76206

Canonical transcript exons

ENST00000583866 — 90 exons

Exon	Start	End
ENSE00003472278	146139809	146140020
ENSE00003474136	146132186	146132237
ENSE00003498311	146128119	146128282
ENSE00003510593	146104224	146104396
ENSE00003517572	146135307	146135521
ENSE00003528013	146134193	146134265
ENSE00003543790	146107344	146107516
ENSE00003560035	146105043	146105094
ENSE00003577608	146141604	146141818
ENSE00003605653	146140484	146140556
ENSE00003612291	146105804	146105976
ENSE00003632188	146106573	146106624
ENSE00003669623	146138236	146138445
ENSE00003673766	146103401	146103509
ENSE00003682172	146127028	146127079
ENSE00003685309	146133523	146133728
ENSE00003685758	146136353	146136455
ENSE00003690924	146142650	146142752
ENSE00003694822	146073500	146073551
ENSE00003694870	146080605	146080777
ENSE00003695039	146101855	146101906
ENSE00003695169	146110512	146110684
ENSE00003695184	146084518	146084626
ENSE00003695267	146075869	146076041
ENSE00003695325	146109751	146109802
ENSE00003695421	146071968	146072019
ENSE00003695737	146126236	146126408
ENSE00003695755	146121498	146121670
ENSE00003695825	146100325	146100376
ENSE00003695853	146081436	146081487
ENSE00003695891	146111281	146111332
ENSE00003696087	146113652	146113824
ENSE00003696093	146091642	146091814
ENSE00003696134	146097904	146098076
ENSE00003696136	146102626	146102798
ENSE00003696441	146092411	146092462
ENSE00003696461	146095603	146095654
ENSE00003696539	146117547	146117655
ENSE00003696728	146099502	146099674
ENSE00003696760	146070324	146070432
ENSE00003697051	146090881	146090932
ENSE00003697132	146123927	146123978
ENSE00003697184	146079782	146079890
ENSE00003697356	146093182	146093354
ENSE00003697387	146094780	146094952
ENSE00003697437	146115230	146115402
ENSE00003697529	146123106	146123278
ENSE00003698133	146085341	146085513
ENSE00003698425	146108942	146109114
ENSE00003698504	146115999	146116050
ENSE00003698508	146072729	146072901
ENSE00003698518	146093957	146094065
ENSE00003698709	146096364	146096536
ENSE00003699232	146067180	146067288
ENSE00003699255	146069543	146069715
ENSE00003699257	146088464	146088636
ENSE00003699298	146077467	146077639
ENSE00003699330	146074271	146074443
ENSE00003699471	146078236	146078287
ENSE00003699783	146119956	146120128
ENSE00003699827	146089239	146089347
ENSE00003699832	146118370	146118542
ENSE00003699979	146083737	146083909
ENSE00003700203	146097133	146097184
ENSE00003700282	146079007	146079179
ENSE00003700343	146068003	146068175
ENSE00003700345	146124688	146124860
ENSE00003700382	146082966	146083017
ENSE00003700414	146125465	146125516
ENSE00003700629	146122283	146122391
ENSE00003700671	146119195	146119246
ENSE00003700759	146086164	146086215
ENSE00003700788	146071147	146071319
ENSE00003701012	146114469	146114520
ENSE00003701055	146090062	146090234
ENSE00003701360	146108119	146108227
ENSE00003701508	146082197	146082369
ENSE00003701714	146098679	146098787
ENSE00003701930	146101086	146101258
ENSE00003701958	146068772	146068823
ENSE00003702076	146112829	146112937
ENSE00003702093	146087693	146087744
ENSE00003702118	146086924	146087096
ENSE00003702263	146120725	146120776
ENSE00003714032	146075046	146075154
ENSE00003734795	146112054	146112226
ENSE00003742299	146076706	146076757
ENSE00003748572	146116772	146116944
ENSE00003751938	146064711	146066561
ENSE00003847712	146144595	146144804

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 99.66.

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

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

Tissue	Anatomy ID	Expression score	Quality
nipple	UBERON:0002030	99.66	gold quality
buccal mucosa cell	CL:0002336	99.54	gold quality
visceral pleura	UBERON:0002401	99.47	gold quality
upper leg skin	UBERON:0004262	99.47	gold quality
trabecular bone tissue	UBERON:0002483	99.42	gold quality
skin of hip	UBERON:0001554	99.37	gold quality
caput epididymis	UBERON:0004358	99.36	gold quality
tibia	UBERON:0000979	99.35	gold quality
trigeminal ganglion	UBERON:0001675	99.20	gold quality
mammalian vulva	UBERON:0000997	99.16	gold quality
parietal pleura	UBERON:0002400	99.15	gold quality
corpus epididymis	UBERON:0004359	99.08	gold quality
urethra	UBERON:0000057	99.03	gold quality
pleura	UBERON:0000977	99.02	gold quality
superior surface of tongue	UBERON:0007371	98.97	gold quality
dorsal root ganglion	UBERON:0000044	98.93	gold quality
synovial joint	UBERON:0002217	98.89	gold quality
oviduct epithelium	UBERON:0004804	98.87	gold quality
mammary duct	UBERON:0001765	98.85	gold quality
tongue squamous epithelium	UBERON:0006919	98.84	gold quality
pylorus	UBERON:0001166	98.83	gold quality
epithelium of mammary gland	UBERON:0003244	98.79	gold quality
oral cavity	UBERON:0000167	98.78	gold quality
cauda epididymis	UBERON:0004360	98.76	gold quality
cardia of stomach	UBERON:0001162	98.75	gold quality
pharyngeal mucosa	UBERON:0000355	98.74	gold quality
penis	UBERON:0000989	98.72	gold quality
trachea	UBERON:0003126	98.71	gold quality
layer of synovial tissue	UBERON:0007616	98.71	gold quality
renal medulla	UBERON:0000362	98.68	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	527.27
E-ENAD-27	yes	6.17
E-ANND-3	yes	6.02
E-MTAB-8060	no	1080.41

Regulation

Is transcription factor: no

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), NBPF14 (ENSG00000270629), (ENSG00000271254), NBPF19 (ENSG00000271383), NBPF26 (ENSG00000273136)

Protein

Protein identifiers

NBPF family member NBPF10 — Q6P3W6 (reviewed: Q6P3W6)

Alternative names: Neuroblastoma breakpoint family member 10

All UniProt accessions (2): A0A087X002, Q6P3W6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Similarity. Belongs to the NBPF family.

RefSeq proteins (2): NP_001034792, NP_001289300* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010630	Olduvai_dom	Domain
IPR055306	NBPF	Family

Pfam: PF06758

UniProt features (80 total): domain 42, region of interest 18, compositionally biased region 17, coiled-coil region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q6P3W6 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, chr1q21, LU_EZH2_TARGETS_DN, BCAT_BILD_ET_AL_DN, GSE10856_CTRL_VS_TNFRSF6B_IN_MACROPHAGE_UP, GSE12366_GC_VS_NAIVE_BCELL_DN, GSE12845_IGD_POS_BLOOD_VS_NAIVE_TONSIL_BCELL_UP, GSE14000_4H_VS_16H_LPS_DC_TRANSLATED_RNA_DN, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_UP, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_RUXOLITINIB_UP, GSE1432_1H_VS_24H_IFNG_MICROGLIA_UP, GSE1432_6H_VS_24H_IFNG_MICROGLIA_UP, GSE1460_DP_THYMOCYTE_VS_NAIVE_CD4_TCELL_ADULT_BLOOD_DN, FAN_EMBRYONIC_CTX_BRAIN_MYELOID, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_DN

GO Biological Process (0):

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

640 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NBPF10	NOTCH2NLB	P0DPK3	543
NBPF10	TP53	P04637	506
NBPF10	ADAM30	Q9UKF2	409
NBPF10	NOTCH2NLA	Q7Z3S9	407
NBPF10	ANKRD20A4P	Q4UJ75	406
NBPF10	MDM2	Q00987	393
NBPF10	LIN9	Q5TKA1	373
NBPF10	LIN37	Q96GY3	361
NBPF10	LIX1L	Q8IVB5	349
NBPF10	SPATA31D3	P0C874	324
NBPF10	ACP6	Q9NPH0	323
NBPF10	ELSPBP1	Q96BH3	322
NBPF10	LIN54	Q6MZP7	321
NBPF10	IFNA13	P01562	309
NBPF10	ACTB	P02570	309

IntAct

2 interactions, top by confidence:

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

ESM2 similar proteins: A0A072TK64, A0A072ULZ1, A0A6P8HC43, A5A3E0, B5DUH6, B9G9L9, E9Q0N2, F4HWL4, F4JCB2, O04309, O04492, O95744, O96790, P01068, P0C589, P0CG38, P0CG39, P0DRJ4, P25071, P29127, P32072, P35753, P37842, P58454, Q0J361, Q28201, Q29428, Q43710, Q4UL00, Q54YZ9, Q5GC91, Q5GC92, Q5GC94, Q6P3W6, Q6S8J3, Q6T269, Q70SU7, Q70SU8, Q8AVN9, Q8RXK2

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	46
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

9754 predictions. Top by Δscore:

Variant	Effect	Δscore
1:146067286:TTT:T	acceptor_gain	1.0000
1:146067287:TT:T	acceptor_gain	1.0000
1:146068000:G:GG	donor_gain	1.0000
1:146068002:CA:C	donor_gain	1.0000
1:146068004:GACA:G	donor_gain	1.0000
1:146068004:GACAG:G	donor_gain	1.0000
1:146068005:GGACA:G	donor_gain	1.0000
1:146068174:G:C	acceptor_loss	1.0000
1:146068174:G:GA	acceptor_gain	1.0000
1:146068175:A:AC	acceptor_loss	1.0000
1:146068175:A:AG	acceptor_gain	1.0000
1:146068177:CCAG:C	acceptor_loss	1.0000
1:146068822:GA:G	acceptor_gain	1.0000
1:146071143:T:A	donor_loss	1.0000
1:146071144:G:C	donor_loss	1.0000
1:146071144:G:GG	donor_gain	1.0000
1:146071147:GAG:G	donor_gain	1.0000
1:146071147:GAGG:G	donor_gain	1.0000
1:146071148:GGAG:G	donor_gain	1.0000
1:146071148:GGAGG:G	donor_gain	1.0000
1:146071149:GGGAG:G	donor_gain	1.0000
1:146071201:G:GT	donor_gain	1.0000
1:146071318:G:GT	acceptor_gain	1.0000
1:146071318:GG:G	acceptor_gain	1.0000
1:146071318:GGCTC:G	acceptor_gain	1.0000
1:146071319:A:AG	acceptor_gain	1.0000
1:146071319:AG:A	acceptor_gain	1.0000
1:146071321:CCA:C	acceptor_loss	1.0000
1:146071322:TCCA:T	acceptor_loss	1.0000
1:146071964:T:A	donor_loss	1.0000

AlphaMissense

24706 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1043492 (1:146066165 G>T), RS1043495 (1:146066155 C>A,T), RS1043562 (1:146065596 T>C), RS1043749 (1:146066529 C>A,G,T), RS1043765 (1:146066307 C>A,G,T), RS1043767 (1:146066303 A>C,T), RS1043769 (1:146066264 T>A,C,G), RS10533520 (1:146139265 ATTTTTTTT>A,ATT,ATTTT,ATTTTT,ATTTTTT,ATTTTTTT,ATTTTTTTTT,ATTTTTTTTTT,ATTTTTTTTTTT,ATTTTTTTTTTTT,ATTTTTTTTTTTTT,ATTTTTTTTTTTTTT), RS1065064 (1:146066475 A>C), RS1065072 (1:146066242 G>A), RS10752816 (1:146144187 G>C), RS10752817 (1:146143914 T>C), RS10752818 (1:146143911 A>G), RS10752819 (1:146143903 C>G,T), RS10752820 (1:146143803 G>A,T)

Disease associations

OMIM: gene MIM:614000 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST004950_28	Breast cancer	8.000000e-09
GCST005983_40	Serum uric acid levels	5.000000e-14
GCST007236_63	Breast cancer	2.000000e-07
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

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004761	uric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

41 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression, decreases expression	4
trichostatin A	affects cotreatment, increases expression	3
bisphenol F	increases methylation, affects cotreatment, decreases expression	2
bisphenol A	increases methylation, affects cotreatment, decreases expression	2
entinostat	decreases expression, affects cotreatment	2
bisphenol S	decreases expression, affects cotreatment	2
Estradiol	increases expression	2
Valproic Acid	decreases methylation, increases expression	2
Cadmium Chloride	increases abundance, increases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
cinnamaldehyde	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
manganese chloride	decreases expression, increases abundance	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
Fulvestrant	affects methylation	1
Vorinostat	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Cadmium	increases abundance, increases expression	1
Calcitriol	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Fluorouracil	increases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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