POMZP3

Summary

POMZP3 (POM121 and ZP3 fusion, HGNC:9203) is a protein-coding gene on chromosome 7q11.23, encoding POM121 and ZP3 fusion protein (Q6PJE2).

This gene appears to have resulted from a fusion of DNA sequences derived from 2 distinct loci, specifically through the duplication of two internal exons from the POM121 gene and four 3’ exons from the ZP3 gene. The 5’ end of this gene is similar to the 5` coding region of the POM121 gene which encodes an integral nuclear pore membrane protein. However, the protein encoded by this gene lacks the nuclear pore localization motif. The 3’ end of this gene is similar to the last 4 exons of the zona pellucida glycoprotein 3 (ZP3) gene and the encoded protein retains one zona pellucida domain. Multiple protein isoforms are encoded by transcript variants of this gene.

Source: NCBI Gene 22932 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_012230

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9203
Approved symbol	POMZP3
Name	POM121 and ZP3 fusion
Location	7q11.23
Locus type	gene with protein product
Status	Approved
Aliases	POM-ZP3, POM121
Ensembl gene	ENSG00000146707
Ensembl biotype	protein_coding
OMIM	600587
Entrez	22932

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 nonsense_mediated_decay

ENST00000275569, ENST00000310842, ENST00000424818, ENST00000441393, ENST00000454397, ENST00000879744, ENST00000879745, ENST00000879746, ENST00000879747, ENST00000936948, ENST00000960016

RefSeq mRNA: 2 — MANE Select: NM_012230 NM_012230, NM_152992

CCDS: CCDS43606, CCDS5590

Canonical transcript exons

ENST00000310842 — 7 exons

Exon	Start	End
ENSE00001815655	76626708	76627279
ENSE00002452471	76626000	76626215
ENSE00002475922	76625522	76625683
ENSE00003466845	76609986	76610215
ENSE00003537628	76618183	76618300
ENSE00003552604	76611454	76611591
ENSE00003791055	76611722	76611813

Expression profiles

Bgee: expression breadth ubiquitous, 141 present calls, max score 89.78.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	89.78	gold quality
right testis	UBERON:0004534	88.85	gold quality
testis	UBERON:0000473	88.81	gold quality
lower esophagus mucosa	UBERON:0035834	88.41	gold quality
apex of heart	UBERON:0002098	88.36	gold quality
skeletal muscle tissue	UBERON:0001134	87.00	gold quality
cortical plate	UBERON:0005343	86.97	gold quality
mucosa of stomach	UBERON:0001199	86.80	gold quality
right coronary artery	UBERON:0001625	86.60	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.42	gold quality
lower esophagus	UBERON:0013473	86.40	gold quality
embryo	UBERON:0000922	86.02	gold quality
ganglionic eminence	UBERON:0004023	86.02	gold quality
gastrocnemius	UBERON:0001388	85.99	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.96	gold quality
skeletal muscle organ	UBERON:0014892	85.81	gold quality
muscle of leg	UBERON:0001383	85.77	gold quality
popliteal artery	UBERON:0002250	85.75	gold quality
tibial artery	UBERON:0007610	85.75	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.73	gold quality
right ovary	UBERON:0002118	85.58	gold quality
muscle tissue	UBERON:0002385	85.57	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.50	gold quality
left ovary	UBERON:0002119	85.36	gold quality
ascending aorta	UBERON:0001496	85.25	gold quality
thoracic aorta	UBERON:0001515	85.08	gold quality
cerebellum	UBERON:0002037	85.00	gold quality
ovary	UBERON:0000992	84.99	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.99	gold quality
cerebellar cortex	UBERON:0002129	84.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.80
E-MTAB-6142	no	61.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting POMZP3, 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-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-589-5P	98.72	66.96	927
HSA-MIR-138-1-3P	98.25	67.89	867
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-6748-3P	97.20	65.66	836

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	zp3e	ENSDARG00000016908
danio_rerio	zp3b	ENSDARG00000039828
danio_rerio	zp3a.1	ENSDARG00000042129
danio_rerio	zp3a.2	ENSDARG00000042130
danio_rerio	zp3.2	ENSDARG00000090768
danio_rerio	zp3	ENSDARG00000114958
danio_rerio	zp3.2	ENSDARG00000115457
mus_musculus	Zp3	ENSMUSG00000004948
rattus_norvegicus	Zp3	ENSRNOG00000001434

Paralogs (1): ZP3 (ENSG00000188372)

Protein

Protein identifiers

POM121 and ZP3 fusion protein — Q6PJE2 (reviewed: Q6PJE2)

All UniProt accessions (4): Q6PJE2, C9J370, C9JER0, H7C4D5

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in spleen, thymus, pancreas, testis, ovary, small intestine, colon and lymphocytes.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PJE2-4	1	yes
Q6PJE2-5	2

RefSeq proteins (2): NP_036362, NP_694537 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR042235	ZP-C_dom	Homologous_superfamily
IPR055355	ZP-C	Domain

Pfam: PF00100

UniProt features (5 total): chain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PJE2-F1	73.49	0.39

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 321 (showing top): MORF_DNMT1, REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GCANCTGNY_MYOD_Q6, REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MORF_RRM1, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, MORF_UBE2N, GENTILE_RESPONSE_CLUSTER_D3, MORF_HDAC2, RIZKI_TUMOR_INVASIVENESS_3D_DN, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleoplasm (GO:0005654), nuclear membrane (GO:0031965)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	1
cellular anatomical structure	1
nucleus	1
nuclear envelope	1
organelle membrane	1

Protein interactions and networks

STRING

280 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POMZP3	OR4L1	Q8NH43	507
POMZP3	FRG2B	Q96QU4	474
POMZP3	ZP1	P60852	445
POMZP3	DNAAF8	Q8IYS4	431
POMZP3	ZP4	Q12836	404
POMZP3	ZP2	Q05996	387
POMZP3	OR5A2	Q8NGI9	379
POMZP3	ZNF708	P17019	375
POMZP3	ZAR1	Q86SH2	375
POMZP3	FAM171B	Q6P995	372
POMZP3	CLEC2L	P0C7M8	370
POMZP3	HRCT1	Q6UXD1	370
POMZP3	HSD17B12	Q53GQ0	352
POMZP3	FBRSL1	Q9HCM7	350
POMZP3	C4BPB	P20851	349

IntAct

6 interactions, top by confidence:

A	B	Type	Score
POMZP3	ADORA2A	psi-mi:“MI:0915”(physical association)	0.370
POMZP3	NMI	psi-mi:“MI:0915”(physical association)	0.370
KPNA2	POM121C	psi-mi:“MI:0914”(association)	0.350
POMZP3	PRRC2A	psi-mi:“MI:0914”(association)	0.350
SLC25A25	HAX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (11): POMZP3 (Two-hybrid), NMI (Two-hybrid), POMZP3 (Proximity Label-MS), POMZP3 (Two-hybrid), ATXN3 (Affinity Capture-MS), PRRC2A (Affinity Capture-MS), POMZP3 (Affinity Capture-MS), POMZP3 (Affinity Capture-MS), POMZP3 (Affinity Capture-RNA), APP (Reconstituted Complex), POMZP3 (Two-hybrid)

ESM2 similar proteins: A0A0D9SF12, A0A1Z2R986, A2AWH2, A6QNY1, C3VD30, D3ZF92, E7F5F0, E7FKV8, M3WHG5, O55034, O70303, O75509, O76081, O88393, O94966, P26342, P35054, P35125, P49763, P79209, P97946, Q03167, Q0VFL4, Q3T191, Q3UPF5, Q4TUC0, Q503Y8, Q5EB20, Q5M889, Q5XI33, Q62005, Q6B9Z1, Q6PJE2, Q6UWQ7, Q6UWV7, Q7TP54, Q7Z2W4, Q810F8, Q91V27, Q91ZV2

Diamond homologs: A6NF01, A6NNC1, A8CG34, P52591, Q3SYA9, Q6PJE2, Q8K3Z9, Q96HA1, Q96KW2, P10761, P21754, P23491, P42098, P48830, P48831, P48832, P48833, P53785, P53786, P79762, P97708, G5E8D7, Q60997, Q8CIZ5, Q95218, Q8N7R1, Q5SW25

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

847 predictions. Top by Δscore:

Variant	Effect	Δscore
7:76610213:TCA:T	acceptor_gain	1.0000
7:76610214:CA:C	acceptor_gain	1.0000
7:76610214:CACTG:C	acceptor_gain	1.0000
7:76610216:C:CC	acceptor_gain	1.0000
7:76611587:ACCAG:A	acceptor_gain	1.0000
7:76611588:CCAG:C	acceptor_gain	1.0000
7:76611588:CCAGC:C	acceptor_gain	1.0000
7:76611589:CAG:C	acceptor_gain	1.0000
7:76611589:CAGC:C	acceptor_gain	1.0000
7:76611590:A:T	acceptor_gain	1.0000
7:76611592:C:CC	acceptor_gain	1.0000
7:76611717:CTCA:C	donor_loss	1.0000
7:76611718:TCA:T	donor_loss	1.0000
7:76611719:CAC:C	donor_loss	1.0000
7:76611720:ACC:A	donor_loss	1.0000
7:76611721:C:T	donor_loss	1.0000
7:76611811:TAT:T	acceptor_gain	1.0000
7:76611813:TCTGC:T	acceptor_loss	1.0000
7:76611814:C:CC	acceptor_gain	1.0000
7:76611814:CT:C	acceptor_loss	1.0000
7:76611815:T:A	acceptor_loss	1.0000
7:76618177:TCTTA:T	donor_loss	1.0000
7:76618178:CTTAC:C	donor_loss	1.0000
7:76618179:TTA:T	donor_loss	1.0000
7:76618180:TA:T	donor_loss	1.0000
7:76618298:CAG:C	acceptor_gain	1.0000
7:76618298:CAGCT:C	acceptor_gain	1.0000
7:76618301:C:CC	acceptor_gain	1.0000
7:76618302:T:C	acceptor_gain	1.0000
7:76618302:T:TC	acceptor_gain	1.0000

AlphaMissense

1236 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:76611739:G:C	F140L	0.971
7:76611739:G:T	F140L	0.971
7:76611741:A:G	F140L	0.971
7:76611751:C:A	K136N	0.971
7:76611751:C:G	K136N	0.971
7:76618261:G:C	F89L	0.970
7:76618261:G:T	F89L	0.970
7:76618263:A:G	F89L	0.970
7:76618210:G:C	F106L	0.969
7:76618210:G:T	F106L	0.969
7:76618212:A:G	F106L	0.969
7:76618204:A:C	F108L	0.962
7:76618204:A:T	F108L	0.962
7:76618206:A:G	F108L	0.962
7:76618226:A:G	F101S	0.961
7:76611588:C:A	W147C	0.946
7:76611588:C:G	W147C	0.946
7:76618225:G:C	F101L	0.946
7:76618225:G:T	F101L	0.946
7:76618227:A:G	F101L	0.946
7:76618205:A:C	F108C	0.928
7:76618262:A:C	F89C	0.926
7:76611590:A:G	W147R	0.924
7:76611590:A:T	W147R	0.924
7:76611794:A:G	L122P	0.921
7:76611744:A:G	S139P	0.918
7:76611746:C:G	C138S	0.917
7:76611747:A:T	C138S	0.917
7:76618226:A:C	F101C	0.904
7:76611801:A:G	C120R	0.900

dbSNP variants (sampled 300 via entrez): RS1000170647 (7:76623101 G>C), RS1000431024 (7:76627404 G>T), RS1000484378 (7:76613439 G>A), RS1001087092 (7:76618698 T>C), RS1001181895 (7:76624124 G>A), RS1001212920 (7:76623830 A>C,G), RS1001601998 (7:76618555 AG>A,AGG), RS1002201698 (7:76619328 CA>C), RS1002244778 (7:76624761 A>G), RS1002990483 (7:76610818 C>G,T), RS1003094735 (7:76621155 G>A,T), RS1003295990 (7:76625769 C>A,G,T), RS1003432590 (7:76610523 A>G), RS1003675661 (7:76626055 T>C), RS1004036691 (7:76611889 A>C,G)

Disease associations

OMIM: gene MIM:600587 | 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

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

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
bisphenol A	increases expression	1
cobaltous chloride	decreases expression	1
CGP 52608	affects binding, increases reaction	1
JP8 aviation fuel	decreases expression	1
abrine	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	increases expression	1
Doxorubicin	decreases expression	1
Endosulfan	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Etoposide	affects response to substance	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Mitoxantrone	affects response to substance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Paclitaxel	affects response to substance	1
Copper Sulfate	increases expression	1
Lactic Acid	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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