PRY2

Summary

PRY2 (PTPN13 like Y-linked 2, HGNC:21504) is a protein-coding gene on chromosome Yq11.223, encoding PTPN13-like protein, Y-linked (O14603).

This gene is located in the nonrecombining portion of the Y chromosome, and expressed specifically in testis. Two nearly identical copies of this gene exist within a palindromic region. This record represents the more centromeric copy.

Source: NCBI Gene 442862 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 7 total — 1 pathogenic
• Phenotypes (HPO): 4

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21504
Approved symbol	PRY2
Name	PTPN13 like Y-linked 2
Location	Yq11.223
Locus type	gene with protein product
Status	Approved
Aliases	PTPN13LY2
Ensembl gene	ENSG00000169807
OMIM	400041
Entrez	442862

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Bgee: expression breadth broad, 13 present calls, max score 37.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	37.20	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	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
tonsil	UBERON:0002372	29.79	silver quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
lymph node	UBERON:0000029	28.88	gold quality
gall bladder	UBERON:0002110	28.81	silver quality
liver	UBERON:0002107	28.26	gold quality
duodenum	UBERON:0002114	28.14	gold quality
islet of Langerhans	UBERON:0000006	27.64	gold quality
superior frontal gyrus	UBERON:0002661	27.60	gold quality
rectum	UBERON:0001052	26.88	gold quality
blood	UBERON:0000178	26.87	gold quality
right testis	UBERON:0004534	26.80	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
left testis	UBERON:0004533	26.38	silver quality
right coronary artery	UBERON:0001625	26.35	gold quality
leukocyte	CL:0000738	26.22	gold quality
testis	UBERON:0000473	26.19	silver quality
monocyte	CL:0000576	26.09	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting PRY2, 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-1229-3P	99.97	66.49	906
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-198	98.70	67.32	920
HSA-MIR-2117	98.48	67.97	1307
HSA-MIR-9903	98.47	66.70	748
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-6890-3P	97.50	65.71	997
HSA-MIR-6874-3P	97.29	66.34	975
HSA-MIR-148B-5P	97.29	66.30	992
HSA-MIR-3974	96.56	66.22	928
HSA-MIR-3690	96.44	65.18	737
HSA-MIR-24-1-5P	95.57	65.85	492
HSA-MIR-24-2-5P	95.57	66.16	484

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

PTPN13-like protein, Y-linked — O14603 (reviewed: O14603)

Alternative names: Testis-specific PTP-BL-related Y protein

All UniProt accessions (0):

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in testis. Detected in spermatocytes, spermatids and spermatozoa (at protein level).

Isoforms (2)

UniProt ID	Names	Canonical?
O14603-1	1	yes
O14603-2	2

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

UniProt features (3 total): splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14603-F1	42.91	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

446 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRY2	BPY2	O14599	932
PRY2	CDY1	Q9Y6F8	916
PRY2	VCY	O14598	912
PRY2	CDY2A	Q9Y6F7	883
PRY2	BBOX1	O75936	853
PRY2	DAZ1	Q9NQZ3	848
PRY2	RBMY1A1	P0DJD3	839
PRY2	TRIM41	Q8WV44	817
PRY2	USP9Y	O00507	780
PRY2	MAGEH1	Q9H213	774
PRY2	TRAT1	Q6PIZ9	772
PRY2	DAZ2	Q13117	754
PRY2	E7ERQ6	E7ERQ6	726
PRY2	DDX3Y	O15523	725
PRY2	TRIM25	Q14258	724

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PRY	DCAF10	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): PRY2 (Negative Genetic), DCAF10 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTK4, A0JNL8, A2RU37, A4D1N5, B1A0U8, B1ANY3, F2Z398, G3V211, J3KSC0, J3QMY9, O14603, O93195, O95411, P03414, P0C7M3, P37200, P47939, P47940, P49671, P92561, Q02919, Q32KZ5, Q4G0G2, Q5SR53, Q5T0J3, Q5T6R2, Q66669, Q66HF0, Q6AWC8, Q6DGF6, Q6ZP68, Q6ZSR6, Q7L4S7, Q86UQ5, Q86Y29, Q8BGX4, Q8N326, Q8N4M7, Q8N6C7, Q8N769

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	5

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
870528	GRCh37/hg19 Yq11.221-11.23(chrY:15427283-28799937)x0	Pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS112250547 (Y:22093181 A>T), RS112517939 (Y:22094504 C>G), RS112795226 (Y:22077076 T>C), RS113174784 (Y:22090454 T>A), RS1159837267 (Y:22079300 G>A), RS1163985645 (Y:22079311 T>C), RS1175639896 (Y:22076168 T>G), RS1196111543 (Y:22079290 C>T), RS1205409159 (Y:22072244 T>C), RS1212239083 (Y:22079270 A>G), RS1212410455 (Y:22072137 A>C), RS1231676975 (Y:22096282 A>AAC,AACACAC), RS1232346449 (Y:22095934 G>A), RS1236353031 (Y:22079206 CAGG>C), RS1239118537 (Y:22079237 T>A)

Disease associations

OMIM: gene MIM:400041 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): male infertility (MONDO:0005372)

Orphanet (0):

HPO phenotypes

4 total (4 of 4 shown, HPO-id order):

HPO	Term
HP:0000027	Azoospermia
HP:0001450	Y-linked inheritance
HP:0003251	Male infertility
HP:0011462	Young adult onset

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D007248	Infertility, Male	C12.100.500.430; C12.100.750.700; C12.200.294.430

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Acetaminophen	decreases expression	1
Silicon Dioxide	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02202382	PHASE4	COMPLETED	Effects of Korean Red Ginseng on Male Infertility
NCT02204826	PHASE4	COMPLETED	Effects of Korean Red Ginseng on Semen Parameters in Male Infertility Patients: a Randomized, Placebo-controlled, Double-blind Clinical Study
NCT03802864	PHASE4	COMPLETED	Post-operative Pain Control of Testicular Sperm Extraction Using Liposomal Bupivacaine
NCT06100432	PHASE4	ACTIVE_NOT_RECRUITING	Effect of Eurycoma Longifolia (DLBS5055) and Multivitamins (Vitamin C+Vitamin E+ β-carotene) for Infertile Males
NCT07523022	PHASE4	ENROLLING_BY_INVITATION	Comparison of the Effect of Gonadotropin and Clomiphene Citrate Treatment on Sperm Parameters and the Outcome of Assisted Reproductive Procedures in Subfertile Men Based on the APHRODITE Groups
NCT00975117	PHASE3	COMPLETED	Spermotrend in the Treatment of Male Infertility
NCT01407432	PHASE3	COMPLETED	Impact of Folates in the Care of the Male Infertility
NCT01895816	PHASE3	COMPLETED	Herbal Tonic Fertile Supplement(ZO2C5)
NCT02605070	PHASE3	TERMINATED	Pilot Study on the Effects of FSH Treatment on the Epigenetic Characteristics of Spermatozoa in Infertile Patients With Severe Oligozoospermia
NCT07402759	PHASE3	ACTIVE_NOT_RECRUITING	Impact of tdrd9 Gene Mutations in the Therapeutic Response to L-carnitine in Oligoasthenozoospermic Men
NCT01880086	PHASE2	COMPLETED	Clomiphene Citrate for the Treatment of Low Testosterone Associated With Chronic Opioid Pain Medication Administration
NCT02061384	PHASE2	COMPLETED	RA-2 13-cis Retinoic Acid (Isotretinoin)
NCT02421887	PHASE2	COMPLETED	Males, Antioxidants, and Infertility Trial
NCT05200663	PHASE2	UNKNOWN	Efficacy Comparison of Tamoxifen and Tamoxifen With Antioxidants on Semen Quality of Male With Idiopathic Infertility
NCT05290558	PHASE2	ACTIVE_NOT_RECRUITING	The Therapeutic Effects of Bu Shen Yi Jing Pill on Semen Quality in Sub Fertile Males: a Randomized Controlled Trial
NCT06091969	PHASE2	NOT_YET_RECRUITING	Supplementation for Male Subfertility
NCT01595308	PHASE1	COMPLETED	A Pilot Study to Evaluate the Effect of Pomegranate Juice on Semen Parameters in Healthy Male Volunteers
NCT02122211	PHASE1	COMPLETED	Choline Dehydrogenase and Sperm Function: Effects of Betaine
NCT02575924	PHASE1	UNKNOWN	Influence of Culture Media on Clinical Outcomes in Poor Responders or Severe Male Infertility
NCT01304927	PHASE2/PHASE3	COMPLETED	Vitamin D Supplementation and Male Infertility: The CBG-study a Randomized Clinical Trial
NCT02349945	PHASE2/PHASE3	COMPLETED	FSH Receptor Polymorphism p.N680S and Efficacy of FSH Therapy
NCT05222841	PHASE2/PHASE3	COMPLETED	The Effectiveness of Spermotrend Food Supplement in the Treatment of Male Infertility
NCT05616598	PHASE2/PHASE3	COMPLETED	Effect of New Oral Treatment for Hepatitis C Virus on Seminal Parameters
NCT02025270	PHASE1/PHASE2	COMPLETED	MSCs For Treatment of Azoospermic Patients
NCT04541459	EARLY_PHASE1	UNKNOWN	Validation of New Devices Against Ambient Electromagnetic Radiation
NCT05792813	EARLY_PHASE1	UNKNOWN	Efficacy and Safety of Linggui Yangyuan Paste in Patients With Male Infertility
NCT06188936	EARLY_PHASE1	COMPLETED	Home Semen Analysis Tests As a Screening Tool for Fertility Patients
NCT00012480	Not specified	COMPLETED	Effect of Environmental Exposures on the Egg Fertilizing Ability of Human Sperm
NCT00044369	Not specified	COMPLETED	Role of the Toxic Metal Cadmium in the Mechanism Producing Infertility With a Varicocele
NCT00119925	Not specified	UNKNOWN	‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists
NCT00178516	Not specified	COMPLETED	Vitamin E and Male Infertility
NCT00315029	Not specified	COMPLETED	Patient-Centered Implementation Trial for Single Embryo Transfer
NCT00341120	Not specified	COMPLETED	Genetic Causes of Male Infertility
NCT00481403	Not specified	COMPLETED	Study of Sperm Molecular Factors Implicated in Male Fertility
NCT00548977	Not specified	COMPLETED	Genetic Studies Spermatogenic Failure
NCT00596739	Not specified	COMPLETED	A Study of the Pre- and Post-operative Semen Analyses and Reproductive Hormone Levels of Men Undergoing Weight-reduction Surgery
NCT00756561	Not specified	COMPLETED	HOP-2A - Intratesticular Hormone Levels
NCT00961558	Not specified	TERMINATED	Canadian Varicocelectomy Initiative (CVI): Effects on Male Fertility and Testicular Function of Varicocelectomy
NCT01075334	Not specified	UNKNOWN	Is a Carnitine Based Food Supplement (PorimoreTM) for Infertile Men Superior to Folate and Zinc With Regard to Pregnancy Rates in Intrauterine Insemination Cycles?
NCT01178463	Not specified	UNKNOWN	Spermatogonial Stem Cells in Azoospermic Patients: a Comparison Between Obstructive and Non-obstructive Azoospermia