SPATA25

Summary

SPATA25 (spermatogenesis associated 25, HGNC:16158) is a protein-coding gene on chromosome 20q13.12, encoding Spermatogenesis-associated protein 25 (Q9BR10). May play a role in spermatogenesis.

Involved in spermatogenesis. Predicted to be located in membrane.

Source: NCBI Gene 128497 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 34 total
• MANE Select transcript: NM_080608

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16158
Approved symbol	SPATA25
Name	spermatogenesis associated 25
Location	20q13.12
Locus type	gene with protein product
Status	Approved
Aliases	dJ337O18.8, TSG23
Ensembl gene	ENSG00000149634
Ensembl biotype	protein_coding
OMIM	618936
Entrez	128497

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000372519

RefSeq mRNA: 1 — MANE Select: NM_080608 NM_080608

CCDS: CCDS13383

Canonical transcript exons

ENST00000372519 — 2 exons

Exon	Start	End
ENSE00001458006	45886491	45887145
ENSE00001458008	45887536	45887622

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 83.60.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0049 / max 3.6087, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
187495	0.0049	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	83.60	gold quality
right testis	UBERON:0004534	83.23	gold quality
testis	UBERON:0000473	80.28	gold quality
right lobe of liver	UBERON:0001114	77.95	gold quality
left ovary	UBERON:0002119	77.01	gold quality
apex of heart	UBERON:0002098	76.00	gold quality
right ovary	UBERON:0002118	75.96	gold quality
muscle of leg	UBERON:0001383	75.08	gold quality
buccal mucosa cell	CL:0002336	74.93	silver quality
gastrocnemius	UBERON:0001388	74.61	gold quality
hindlimb stylopod muscle	UBERON:0004252	73.97	gold quality
right coronary artery	UBERON:0001625	73.52	gold quality
left uterine tube	UBERON:0001303	73.48	gold quality
body of uterus	UBERON:0009853	72.75	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.46	gold quality
lower esophagus	UBERON:0013473	72.45	gold quality
muscle layer of sigmoid colon	UBERON:0035805	72.44	gold quality
left coronary artery	UBERON:0001626	72.38	gold quality
transverse colon	UBERON:0001157	72.26	gold quality
endocervix	UBERON:0000458	72.10	gold quality
stromal cell of endometrium	CL:0002255	72.09	gold quality
popliteal artery	UBERON:0002250	71.93	gold quality
tibial artery	UBERON:0007610	71.91	gold quality
metanephros cortex	UBERON:0010533	71.74	gold quality
mucosa of stomach	UBERON:0001199	71.66	gold quality
mucosa of transverse colon	UBERON:0004991	71.55	gold quality
small intestine Peyer’s patch	UBERON:0003454	71.50	gold quality
cerebellar hemisphere	UBERON:0002245	71.43	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.37	gold quality
cerebellar cortex	UBERON:0002129	71.26	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

Literature-anchored findings (GeneRIF, showing 1)

• study identified a novel gene, TSG23/Tsg23, which is developmentally & highly expressed in testis; data suggest that TSG23/Tsg23 is involved in human and mouse spermatogenesis (PMID:19240080)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata25	ENSMUSG00000017767
rattus_norvegicus	Spata25	ENSRNOG00000015744

Protein

Protein identifiers

Spermatogenesis-associated protein 25 — Q9BR10 (reviewed: Q9BR10)

Alternative names: Testis-specific gene 23 protein

All UniProt accessions (1): Q9BR10

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in spermatogenesis.

Subcellular location. Membrane.

Tissue specificity. Expressed predominantly in testis (at protein level). Expression is lower in patients with obstructive azoospermia than in fertile controls and is not detected in patients with non-obstructive azoospermia.

Similarity. Belongs to the SPATA25 family.

RefSeq proteins (1): NP_542175* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029192	SPATA25	Family

Pfam: PF15218

UniProt features (5 total): region of interest 2, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BR10-F1	57.29	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, CP2_01, MARTENS_TRETINOIN_RESPONSE_DN, GSE13306_RA_VS_UNTREATED_TREG_DN, GSE16522_ANTI_CD3CD28_STIM_VS_UNSTIM_NAIVE_CD8_TCELL_UP, GSE19825_NAIVE_VS_IL2RAHIGH_DAY3_EFF_CD8_TCELL_UP, GOBP_SEXUAL_REPRODUCTION, GSE26928_EFF_MEM_VS_CENTR_MEM_CD4_TCELL_DN, GOBP_REPRODUCTIVE_PROCESS, GOBP_MULTICELLULAR_ORGANISMAL_REPRODUCTIVE_PROCESS, GSE32423_MEMORY_VS_NAIVE_CD8_TCELL_IL7_IL4_UP, GENES_CORRELATED_WITH_IGF1R_DELETION, GSE34205_RSV_VS_FLU_INF_INFANT_PBMC_UP, GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_UP

GO Biological Process (2): spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

418 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA25	NEURL2	Q9BR09	678
SPATA25	ZSWIM1	Q9BR11	628
SPATA25	WFDC10B	Q8IUB3	575
SPATA25	SPATA46	Q5T0L3	547
SPATA25	WFDC10A	Q9H1F0	541
SPATA25	SNX21	Q969T3	532
SPATA25	ZNF335	Q9H4Z2	506
SPATA25	PHIP	Q8WWQ0	504
SPATA25	ACOT8	O14734	499
SPATA25	WFDC3	Q8IUB2	498
SPATA25	IRAK1BP1	Q5VVH5	485
SPATA25	TEX35	Q5T0J7	464
SPATA25	SYS1	Q8N2H4	461
SPATA25	SPATA3	Q8NHX4	453
SPATA25	SPATA20	Q8TB22	451

IntAct

6 interactions, top by confidence:

A	B	Type	Score
TLE5	SPATA25	psi-mi:“MI:0915”(physical association)	0.560
SPATA25	TAF4	psi-mi:“MI:0914”(association)	0.530
TLE5	SPATA25	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): SPATA25 (Two-hybrid), TAF10 (Affinity Capture-MS), TAF9 (Affinity Capture-MS), TAF12 (Affinity Capture-MS), TAF11 (Affinity Capture-MS), TAF13 (Affinity Capture-MS), TAF3 (Affinity Capture-MS), TAF6 (Affinity Capture-MS), TAF1 (Affinity Capture-MS), TAF2 (Affinity Capture-MS), TAF4 (Affinity Capture-MS), TAF4B (Affinity Capture-MS), TAF5 (Affinity Capture-MS), TAF7 (Affinity Capture-MS), TAF9B (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUT2, A2RUQ5, A8MU10, B1AH88, C0HM98, H3BQW9, P0C044, P0C092, P0CAT3, P0DPA3, P20977, P59052, P87743, Q06250, Q1R1V4, Q2M3A8, Q3SXR2, Q5SWW7, Q6Q795, Q6UXR6, Q6UXR8, Q6ZSR3, Q6ZSV7, Q6ZVH6, Q6ZWC4, Q71F78, Q86UQ8, Q8N2C9, Q8N2X6, Q8N616, Q8N814, Q8N8V8, Q8N9P6, Q8NBC4, Q8NBF4, Q96EZ4, Q96MC9, Q9BE57, Q9BR10, Q9BTD1

Diamond homologs: Q9BR10, Q9DA57

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

78 predictions. Top by Δscore:

Variant	Effect	Δscore
20:45887531:CTCAC:C	donor_loss	0.9900
20:45887532:TCA:T	donor_loss	0.9900
20:45887535:C:A	donor_loss	0.9900
20:45887146:CTGC:C	acceptor_loss	0.9500
20:45887554:G:GT	donor_gain	0.9500
20:45886803:C:T	acceptor_gain	0.9300
20:45887507:C:CA	donor_gain	0.9300
20:45887534:A:AC	donor_gain	0.9300
20:45887535:C:CC	donor_gain	0.9300
20:45887141:CCCAC:C	acceptor_gain	0.9100
20:45887142:CCACC:C	acceptor_gain	0.9100
20:45887142:CCAC:C	acceptor_gain	0.9000
20:45887143:CACC:C	acceptor_gain	0.9000
20:45887146:C:CC	acceptor_gain	0.9000
20:45887143:CAC:C	acceptor_gain	0.8900
20:45887534:AC:A	donor_gain	0.8500
20:45887535:CC:C	donor_gain	0.8500
20:45886803:C:CT	acceptor_gain	0.8300
20:45887534:A:C	donor_gain	0.8200
20:45887531:CTCA:C	donor_gain	0.8100
20:45887533:CA:C	donor_gain	0.8000
20:45886794:G:T	acceptor_gain	0.7900
20:45887156:A:T	acceptor_gain	0.7900
20:45887148:G:C	acceptor_loss	0.7800
20:45887552:A:AC	donor_gain	0.7300
20:45887530:GCTCA:G	donor_gain	0.7200
20:45886721:CATCA:C	acceptor_gain	0.7100
20:45887144:AC:A	acceptor_gain	0.7100
20:45887145:CC:C	acceptor_gain	0.7100
20:45887529:CGCT:C	donor_gain	0.7000

AlphaMissense

1453 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:45886710:A:G	I164T	0.994
20:45886649:G:C	F184L	0.992
20:45886649:G:T	F184L	0.992
20:45886651:A:G	F184L	0.992
20:45886717:C:G	A162P	0.987
20:45886724:C:A	M159I	0.987
20:45886724:C:G	M159I	0.987
20:45886724:C:T	M159I	0.987
20:45886710:A:C	I164S	0.986
20:45886719:A:T	I161N	0.986
20:45886728:G:T	A158D	0.986
20:45886650:A:G	F184S	0.985
20:45886716:G:T	A162D	0.985
20:45886713:C:A	G163V	0.983
20:45886719:A:C	I161S	0.981
20:45886737:A:T	L155H	0.981
20:45886740:A:G	I154T	0.978
20:45886695:A:T	V169D	0.977
20:45886650:A:C	F184C	0.976
20:45886659:G:T	A181D	0.976
20:45886731:A:T	L157H	0.976
20:45886671:A:G	L177P	0.975
20:45886731:A:G	L157P	0.973
20:45886737:A:G	L155P	0.972
20:45886721:C:A	M160I	0.971
20:45886721:C:G	M160I	0.971
20:45886721:C:T	M160I	0.971
20:45886725:A:T	M159K	0.971
20:45886725:A:C	M159R	0.970
20:45886729:C:G	A158P	0.967

dbSNP variants (sampled 300 via entrez): RS1000460046 (20:45889581 T>A), RS1000947010 (20:45889848 A>G), RS1001455876 (20:45890406 G>A,T), RS1003060294 (20:45889154 T>G), RS1003266283 (20:45887913 C>A), RS1003334266 (20:45889358 T>C), RS1003805541 (20:45891628 G>A,T), RS1005121712 (20:45889434 C>A,T), RS1005269664 (20:45889137 T>C), RS1005794566 (20:45892064 G>C), RS1005907488 (20:45890456 T>A), RS1006542703 (20:45890781 C>T), RS1006892424 (20:45891540 G>A,C), RS1007018466 (20:45891561 T>C,G), RS1007279364 (20:45886172 T>G)

Disease associations

OMIM: gene MIM:618936 | 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

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
decabromobiphenyl ether	affects expression	1
kojic acid	decreases expression	1
benzo(e)pyrene	increases methylation	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Fluorouracil	increases expression	1
Methapyrilene	increases methylation	1
Triclosan	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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