TSPY10

Summary

TSPY10 (testis specific protein Y-linked 10, HGNC:37473) is a protein-coding gene on chromosome Yp11.2, encoding Testis-specific Y-encoded protein 10 (P0CW01). May be involved in sperm differentiation and proliferation.

Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in sex differentiation. Predicted to be located in cytoplasm. Predicted to be active in chromatin and nucleus.

Source: NCBI Gene 100289087 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001282469

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37473
Approved symbol	TSPY10
Name	testis specific protein Y-linked 10
Location	Yp11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000236424
Ensembl biotype	protein_coding
Entrez	100289087

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000428845, ENST00000444056, ENST00000489397, ENST00000495839

RefSeq mRNA: 11 — MANE Select: NM_001282469 NM_001282469, NM_001320962, NM_001422056, NM_001422070, NM_001422071, NM_001422072, NM_001422080, NM_001422081, NM_001422087, NM_001422088, NM_001422089

CCDS: CCDS65365, CCDS83519

Canonical transcript exons

ENST00000428845 — 6 exons

Exon	Start	End
ENSE00001645840	9529225	9529336
ENSE00001758513	9527880	9528411
ENSE00001900367	9530466	9530676
ENSE00003511199	9529690	9529771
ENSE00003600117	9529438	9529583
ENSE00003678107	9529019	9529096

Expression profiles

Bgee: expression breadth broad, 21 present calls, max score 91.88.

Top tissues by expression

109 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	91.88	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.46	gold quality
right testis	UBERON:0004534	83.80	gold quality
testis	UBERON:0000473	79.16	gold quality
left testis	UBERON:0004533	76.90	gold quality
apex of heart	UBERON:0002098	40.78	silver quality
stromal cell of endometrium	CL:0002255	38.58	gold 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
skeletal muscle tissue	UBERON:0001134	36.43	silver quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
sural nerve	UBERON:0015488	35.17	gold quality
monocyte	CL:0000576	33.84	gold quality
muscle tissue	UBERON:0002385	33.30	gold quality
leukocyte	CL:0000738	33.28	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
vermiform appendix	UBERON:0001154	31.84	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
lymph node	UBERON:0000029	30.87	gold quality
metanephros cortex	UBERON:0010533	30.73	gold quality
liver	UBERON:0002107	29.67	gold quality
urinary bladder	UBERON:0001255	29.61	silver quality
uterine cervix	UBERON:0000002	29.53	silver quality
superior frontal gyrus	UBERON:0002661	29.35	gold quality
prefrontal cortex	UBERON:0000451	29.34	gold quality
cortex of kidney	UBERON:0001225	29.29	silver quality
ectocervix	UBERON:0012249	28.30	gold quality
duodenum	UBERON:0002114	28.14	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting TSPY10, 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-335-3P	99.93	73.36	4958
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-889-5P	99.41	68.75	1025
HSA-MIR-3140-5P	99.39	69.04	1136
HSA-MIR-4999-5P	99.35	69.15	926
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-1537-5P	98.70	68.33	999
HSA-MIR-758-3P	98.42	68.60	1122
HSA-MIR-93-3P	98.15	66.65	1309
HSA-MIR-1914-5P	97.83	66.21	807
HSA-MIR-6509-5P	97.39	68.27	969
HSA-MIR-4640-3P	94.58	63.02	263

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	tspy	ENSDARG00000005015
danio_rerio	nap1l4a	ENSDARG00000070560
drosophila_melanogaster	Set	FBGN0014879
drosophila_melanogaster	Nap1	FBGN0015268
drosophila_melanogaster	CG3708	FBGN0040345
drosophila_melanogaster	mil	FBGN0267366
caenorhabditis_elegans		WBGENE00005007
caenorhabditis_elegans		WBGENE00017075

Paralogs (19): SET (ENSG00000119335), TSPY2 (ENSG00000168757), NAP1L5 (ENSG00000177432), TSPYL6 (ENSG00000178021), TSPYL5 (ENSG00000180543), TSPYL2 (ENSG00000184205), NAP1L3 (ENSG00000186310), NAP1L2 (ENSG00000186462), NAP1L1 (ENSG00000187109), TSPYL4 (ENSG00000187189), TSPYL1 (ENSG00000189241), NAP1L4 (ENSG00000205531), TSPY3 (ENSG00000228927), TSPY8 (ENSG00000229549), SETSIP (ENSG00000230667), TSPY4 (ENSG00000233803), TSPY9 (ENSG00000238074), TSPY1 (ENSG00000258992), (ENSG00000293164)

Protein

Protein identifiers

Testis-specific Y-encoded protein 10 — P0CW01 (reviewed: P0CW01)

All UniProt accessions (2): P0CW01, F2Z2I4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in sperm differentiation and proliferation.

Subcellular location. Cytoplasm. Nucleus.

Polymorphism. Maps to a tandemly repeated region on chromosome Yp11; additionally at least one copy is reported originating from Yq. The gene is thought to be present with an inter-individual variation in copy number and between 20 and 60 copies per Y chromosome are expected. 35 tandemly repeated gene copies on Yp11 originating from one individual have been reported.

Similarity. Belongs to the nucleosome assembly protein (NAP) family.

RefSeq proteins (11): NP_001269398, NP_001307891, NP_001408985, NP_001408999, NP_001409000, NP_001409001, NP_001409009, NP_001409010, NP_001409016, NP_001409017, NP_001409018 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002164	NAP	Family
IPR037231	NAP-like_sf	Homologous_superfamily

Pfam: PF00956

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CW01-F1	75.82	0.40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT, GOBP_SEX_DIFFERENTIATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MESENCHYME_DEVELOPMENT, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, GOBP_MESODERM_DEVELOPMENT, GOBP_CHROMATIN_REMODELING, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_DEVELOPMENT_OF_PRIMARY_SEXUAL_CHARACTERISTICS, GOMF_CHROMATIN_BINDING, GOMF_HISTONE_BINDING, chrYp11, GOBP_GONADAL_MESODERM_DEVELOPMENT, GOBP_NUCLEOSOME_ORGANIZATION

GO Biological Process (4): nucleosome assembly (GO:0006334), spermatogenesis (GO:0007283), gonadal mesoderm development (GO:0007506), cell differentiation (GO:0030154)

GO Molecular Function (3): chromatin binding (GO:0003682), histone binding (GO:0042393), protein binding (GO:0005515)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	2
binding	2
cellular anatomical structure	2
chromatin organization	1
nucleosome organization	1
protein-DNA complex assembly	1
male gamete generation	1
mesoderm development	1
gonad development	1
mesenchyme development	1
cellular developmental process	1
protein binding	1
chromosome	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

8 interactions, top by confidence:

A	B	Type	Score
TSPY10	DPY30	psi-mi:“MI:0915”(physical association)	0.600
CDC7	TSPY10	psi-mi:“MI:0915”(physical association)	0.560
CDC7	TSPY10	psi-mi:“MI:0915”(physical association)	0.000
DPY30	TSPY10	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

Diamond homologs: A0A494C1R9, A2ZX50, A6NKD2, B8AEC1, B8B2R4, B8B4K9, B9FU45, F4JEI8, O19110, O59797, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0DME0, P53997, P78920, Q01105, Q01534, Q0P5N2, Q18240, Q5R5G8, Q5VND6, Q63945, Q69JW2, Q69ZB3, Q70Z17, Q70Z18, Q70Z19, Q7TQI8, Q86VY4, Q8N831, Q8VD63, Q94K07, Q9BE64, Q9CA59, Q9EQU5, Q9H0U9, Q9H2G4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1066 predictions. Top by Δscore:

Variant	Effect	Δscore
Y:9529095:AG:A	donor_loss	1.0000
Y:9529096:GGT:G	donor_loss	1.0000
Y:9529097:G:GA	donor_loss	1.0000
Y:9529107:G:GT	donor_gain	1.0000
Y:9529214:T:A	acceptor_gain	1.0000
Y:9529219:T:A	acceptor_gain	1.0000
Y:9529221:ACAG:A	acceptor_loss	1.0000
Y:9529222:CAG:C	acceptor_loss	1.0000
Y:9529223:A:AG	acceptor_gain	1.0000
Y:9529223:AG:A	acceptor_gain	1.0000
Y:9529223:AGGT:A	acceptor_gain	1.0000
Y:9529223:AGGTG:A	acceptor_gain	1.0000
Y:9529224:G:GT	acceptor_gain	1.0000
Y:9529224:GG:G	acceptor_gain	1.0000
Y:9529224:GGT:G	acceptor_gain	1.0000
Y:9529224:GGTG:G	acceptor_gain	1.0000
Y:9529224:GGTGG:G	acceptor_gain	1.0000
Y:9529303:G:GG	donor_gain	1.0000
Y:9529315:G:GT	donor_gain	1.0000
Y:9529436:A:AC	acceptor_loss	1.0000
Y:9529436:A:AG	acceptor_gain	1.0000
Y:9529437:G:GG	acceptor_gain	1.0000
Y:9529437:GA:G	acceptor_gain	1.0000
Y:9529437:GAAT:G	acceptor_gain	1.0000
Y:9529437:GAATA:G	acceptor_gain	1.0000
Y:9529463:A:AG	acceptor_gain	1.0000
Y:9529581:GAG:G	donor_gain	1.0000
Y:9529583:GGTG:G	donor_loss	1.0000
Y:9529584:G:GG	donor_gain	1.0000
Y:9529585:T:A	donor_loss	1.0000

AlphaMissense

2026 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
Y:9529314:G:C	K218N	0.999
Y:9529314:G:T	K218N	0.999
Y:9528397:T:C	F158L	0.998
Y:9528399:C:A	F158L	0.998
Y:9528399:C:G	F158L	0.998
Y:9529273:T:C	F205L	0.997
Y:9529275:T:A	F205L	0.997
Y:9529275:T:G	F205L	0.997
Y:9529292:T:C	F211S	0.997
Y:9529470:T:A	W237R	0.997
Y:9529470:T:C	W237R	0.997
Y:9529291:T:C	F211L	0.996
Y:9529293:C:A	F211L	0.996
Y:9529293:C:G	F211L	0.996
Y:9529539:T:A	W260R	0.996
Y:9529539:T:C	W260R	0.996
Y:9528398:T:C	F158S	0.995
Y:9528400:T:A	W159R	0.995
Y:9528400:T:C	W159R	0.995
Y:9528402:G:C	W159C	0.995
Y:9528402:G:T	W159C	0.995
Y:9529029:A:G	H166R	0.994
Y:9529061:G:C	D177H	0.994
Y:9529284:C:A	N208K	0.994
Y:9529284:C:G	N208K	0.994
Y:9529472:G:C	W237C	0.994
Y:9529472:G:T	W237C	0.994
Y:9529579:C:A	A273D	0.994
Y:9528369:A:C	R148S	0.993
Y:9528369:A:T	R148S	0.993

dbSNP variants (sampled 198 via entrez): RS111378692 (Y:9526489 A>C), RS111838177 (Y:9530720 T>TTG,TTGTG), RS1156603909 (Y:9526208 C>A), RS1161733873 (Y:9528878 A>T), RS1179775265 (Y:9528488 T>G), RS1198162558 (Y:9525933 C>G), RS1202985113 (Y:9530945 G>A), RS1208669476 (Y:9527547 C>A), RS1209013439 (Y:9527384 G>T), RS1225448270 (Y:9529443 A>G), RS1226944028 (Y:9527196 G>T), RS1249406621 (Y:9525897 G>C,T), RS1262122496 (Y:9527499 C>G), RS1267980435 (Y:9527768 T>TG), RS1276818797 (Y:9529767 G>A)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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