PATE3

Summary

PATE3 (prostate and testis expressed 3, HGNC:35426) is a protein-coding gene on chromosome 11q24.2, encoding Prostate and testis expressed protein 3 (B3GLJ2).

Predicted to be located in extracellular region.

Source: NCBI Gene 100169851 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 14 total
• MANE Select transcript: NM_001129883

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:35426
Approved symbol	PATE3
Name	prostate and testis expressed 3
Location	11q24.2
Locus type	gene with protein product
Status	Approved
Aliases	PATE-DJ, HEL-127
Ensembl gene	ENSG00000236027
Ensembl biotype	protein_coding
Entrez	100169851

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000445202

RefSeq mRNA: 1 — MANE Select: NM_001129883 NM_001129883

CCDS: CCDS44764

Canonical transcript exons

ENST00000445202 — 3 exons

Exon	Start	End
ENSE00001646264	125789386	125789508
ENSE00001679252	125790478	125791600
ENSE00001749513	125788127	125788200

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 97.56.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1453 / max 219.1486, expressed in 5 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
117475	0.0792	5
117472	0.0179	3
117473	0.0150	2
117471	0.0145	3
117474	0.0112	2
206490	0.0076	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	97.56	gold quality
colonic epithelium	UBERON:0000397	41.91	gold quality
sural nerve	UBERON:0015488	41.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.93	gold quality
mucosa of stomach	UBERON:0001199	33.16	gold quality
bone marrow	UBERON:0002371	32.96	gold quality
corpus callosum	UBERON:0002336	32.48	gold quality
muscle tissue	UBERON:0002385	32.20	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
primary visual cortex	UBERON:0002436	30.59	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
adrenal tissue	UBERON:0018303	29.60	gold quality
liver	UBERON:0002107	29.47	gold quality
monocyte	CL:0000576	29.00	gold quality
urinary bladder	UBERON:0001255	28.90	gold quality
tonsil	UBERON:0002372	28.88	gold quality
leukocyte	CL:0000738	28.87	gold quality
duodenum	UBERON:0002114	28.14	gold quality
placenta	UBERON:0001987	27.66	gold quality
lymph node	UBERON:0000029	27.57	gold quality
calcaneal tendon	UBERON:0003701	27.21	gold quality
superior frontal gyrus	UBERON:0002661	27.08	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.15	gold quality
gall bladder	UBERON:0002110	25.98	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting PATE3, 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-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-4519	99.48	66.10	859
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-3688-5P	99.12	69.67	1091
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-154-5P	98.92	66.65	733
HSA-MIR-3611	98.76	68.76	1290
HSA-MIR-302F	98.44	69.02	1776
HSA-MIR-1265	98.36	66.46	598
HSA-MIR-147A	98.33	66.40	795
HSA-MIR-6810-5P	98.29	66.21	975

Literature-anchored findings (GeneRIF, showing 1)

• analysis of PATE, expressed primarily in prostate and less in testis, and additional PATE-like genes PATE-M, PATE-DJ, and PATE-B (PMID:18387948)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pate3	ENSMUSG00000094995
rattus_norvegicus	Pate3	ENSRNOG00000087356

Paralogs (4): ACRV1 (ENSG00000134940), PATE1 (ENSG00000171053), PATE2 (ENSG00000196844), PATE4 (ENSG00000237353)

Protein

Protein identifiers

Prostate and testis expressed protein 3 — B3GLJ2 (reviewed: B3GLJ2)

Alternative names: Acrosomal vesicle protein HEL-127, PATE-like protein DJ

All UniProt accessions (1): B3GLJ2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Tissue specificity. Specifically expressed in prostate and testis.

Similarity. Belongs to the PATE family.

RefSeq proteins (1): NP_001123355* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016054	LY6_UPA_recep-like	Domain

Pfam: PF00021

UniProt features (9 total): disulfide bond 4, signal peptide 1, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B3GLJ2-F1	90.23	0.71

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (4): 23–50, 26–35, 42–68, 72–88

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 6 (showing top): chr11q24, MIR10527_5P, MIR6825_5P, MIR577, MIR6851_5P, MIR3689D

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

122 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PATE3	PATE2	Q6UY27	848
PATE3	PATE4	P0C8F1	822
PATE3	PATE1	Q8WXA2	797
PATE3	LY6L	H3BQJ8	761
PATE3	PINLYP	A6NC86	697
PATE3	LYPD5	Q6UWN5	666
PATE3	LY6G5B	Q8NDX9	641
PATE3	GLB1L3	Q8NCI6	626
PATE3	LYPD4	Q6UWN0	625
PATE3	SPACA4	Q8TDM5	620
PATE3	LY6G6F	Q5SQ64	604
PATE3	LYPD2	Q6UXB3	598
PATE3	LY6G5C	Q5SRR4	598
PATE3	GLB1L2	Q8IW92	595
PATE3	GLB1L	Q6UWU2	594

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A346CIB0, B3GLJ2, B3GLJ3, C1IC49, O42255, O42256, O73857, O93471, O93472, P01442, P0C8F1, P15818, P43445, P58370, P60301, P60302, P60303, P60304, P60310, P60814, P79810, P81827, P81828, P82935, P83121, Q00996, Q09098, Q2VBN2, Q2VBP1, Q2VBP3, Q3UN54, Q3UW31, Q53B47, Q6UY27, Q70WS8, Q7ZT13, Q802B3, Q8AY52, Q8AY53, Q98958

Diamond homologs: B3GLJ2, B3GLJ3, P50289, P53353, Q8WXA2, P26436, P83106, P83107, Q06990

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

289 predictions. Top by Δscore:

Variant	Effect	Δscore
11:125788197:GTGG:G	donor_gain	0.9800
11:125789507:GC:G	donor_gain	0.9800
11:125788199:GG:G	donor_gain	0.9700
11:125788200:GG:G	donor_gain	0.9700
11:125788200:GGT:G	donor_loss	0.9700
11:125788201:G:GC	donor_loss	0.9700
11:125788201:G:GG	donor_gain	0.9700
11:125788203:GAG:G	donor_loss	0.9700
11:125789482:C:T	donor_gain	0.9700
11:125788204:AG:A	donor_loss	0.9500
11:125789385:GCA:G	acceptor_gain	0.9500
11:125789509:G:GG	donor_gain	0.9500
11:125790477:GGCA:G	acceptor_gain	0.9500
11:125790476:A:AG	acceptor_gain	0.9300
11:125790477:G:GG	acceptor_gain	0.9300
11:125788151:G:GT	donor_gain	0.9200
11:125790472:TTTTA:T	acceptor_loss	0.9200
11:125790473:TTTA:T	acceptor_loss	0.9200
11:125790475:TAGG:T	acceptor_loss	0.9200
11:125790476:A:T	acceptor_loss	0.9200
11:125790987:T:G	acceptor_gain	0.9100
11:125788148:C:A	donor_gain	0.8800
11:125788200:G:A	donor_gain	0.8800
11:125788198:TGG:T	donor_gain	0.8600
11:125788199:GGG:G	donor_gain	0.8600
11:125788196:TGTGG:T	donor_gain	0.8400
11:125788197:GTGGG:G	donor_gain	0.8400
11:125788198:TGGGT:T	donor_gain	0.8400
11:125788199:GGGTG:G	donor_gain	0.8400
11:125789498:G:GT	donor_gain	0.8400

AlphaMissense

649 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:125790590:C:A	N95K	0.959
11:125790590:C:G	N95K	0.959
11:125789403:T:A	C23S	0.958
11:125789404:G:C	C23S	0.958
11:125790516:T:C	F71L	0.957
11:125790518:C:A	F71L	0.957
11:125790518:C:G	F71L	0.957
11:125789439:T:A	C35S	0.954
11:125789440:G:C	C35S	0.954
11:125790507:T:A	C68S	0.954
11:125790508:G:C	C68S	0.954
11:125789484:T:A	C50S	0.948
11:125789485:G:C	C50S	0.948
11:125789460:T:A	C42S	0.947
11:125789461:G:C	C42S	0.947
11:125789486:C:G	C50W	0.947
11:125789485:G:A	C50Y	0.944
11:125789451:T:C	F39L	0.941
11:125789453:T:A	F39L	0.941
11:125789453:T:G	F39L	0.941
11:125789439:T:C	C35R	0.938
11:125790520:G:A	C72Y	0.936
11:125789412:T:C	C26R	0.934
11:125789403:T:C	C23R	0.932
11:125789412:T:A	C26S	0.932
11:125789413:G:C	C26S	0.932
11:125789484:T:C	C50R	0.932
11:125790519:T:A	C72S	0.931
11:125790520:G:C	C72S	0.931
11:125790550:G:C	R82P	0.930

dbSNP variants (sampled 300 via entrez): RS1000083189 (11:125790474 T>C), RS1000566887 (11:125787093 A>T), RS1002099415 (11:125787522 G>T), RS1002355431 (11:125790485 T>C,G), RS1002857296 (11:125790221 C>A,T), RS1003891837 (11:125789165 G>C), RS1004219547 (11:125790584 C>T), RS1005225213 (11:125789247 C>T), RS1006473482 (11:125788055 G>A), RS1007242125 (11:125786263 C>G), RS1007448344 (11:125791673 T>C), RS1008018062 (11:125791223 C>G), RS1008447747 (11:125790199 G>A), RS1008501529 (11:125789894 C>A,G), RS1009246657 (11:125786995 T>C,G)

Disease associations

OMIM: gene `` | 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
GCST002861_2	Breast cancer (survival)	1.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0000714	survival time

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-palmitoylglycerol	increases expression	1
Benzo(a)pyrene	affects methylation	1
Lactic Acid	decreases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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