SPATA3

Summary

SPATA3 (spermatogenesis associated 3, HGNC:17884) is a protein-coding gene on chromosome 2q37.1, encoding Spermatogenesis-associated protein 3 (Q8NHX4).

Located in sperm flagellum.

Source: NCBI Gene 130560 — RefSeq curated summary.

At a glance

• Gene–disease (curated): male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate, GenCC)
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_139073

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17884
Approved symbol	SPATA3
Name	spermatogenesis associated 3
Location	2q37.1
Locus type	gene with protein product
Status	Approved
Aliases	TSARG1
Ensembl gene	ENSG00000173699
Ensembl biotype	protein_coding
OMIM	619857
Entrez	130560

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000409956, ENST00000423134, ENST00000424440, ENST00000433428, ENST00000440792, ENST00000452881, ENST00000454918, ENST00000455816, ENST00000495639, ENST00000645363

RefSeq mRNA: 1 — MANE Select: NM_139073 NM_139073

CCDS: CCDS2481

Canonical transcript exons

ENST00000433428 — 5 exons

Exon	Start	End
ENSE00001525475	231004039	231004118
ENSE00001748818	230996121	230996534
ENSE00003589821	231000366	231000537
ENSE00003653462	231002684	231002827
ENSE00003978225	231007222	231008040

Expression profiles

Bgee: expression breadth ubiquitous, 117 present calls, max score 97.90.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3027 / max 276.0640, expressed in 5 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
25853	0.2815	5
25852	0.0212	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.90	gold quality
left testis	UBERON:0004533	97.56	gold quality
right testis	UBERON:0004534	97.34	gold quality
testis	UBERON:0000473	94.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.95	gold quality
adult organism	UBERON:0007023	72.93	silver quality
cerebellar vermis	UBERON:0004720	72.17	silver quality
tendon of biceps brachii	UBERON:0008188	70.38	gold quality
upper arm skin	UBERON:0004263	68.98	gold quality
parotid gland	UBERON:0001831	68.41	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	66.64	gold quality
nasal cavity epithelium	UBERON:0005384	64.44	gold quality
myocardium	UBERON:0002349	63.09	gold quality
pancreatic ductal cell	CL:0002079	62.97	silver quality
cartilage tissue	UBERON:0002418	62.92	gold quality
medial globus pallidus	UBERON:0002477	62.51	gold quality
buccal mucosa cell	CL:0002336	61.31	gold quality
globus pallidus	UBERON:0001875	61.08	gold quality
decidua	UBERON:0002450	60.44	gold quality
deltoid	UBERON:0001476	59.39	gold quality
layer of synovial tissue	UBERON:0007616	59.09	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	58.92	gold quality
heart right ventricle	UBERON:0002080	58.52	gold quality
pharyngeal mucosa	UBERON:0000355	58.26	gold quality
biceps brachii	UBERON:0001507	58.11	gold quality
thymus	UBERON:0002370	58.07	gold quality
vastus lateralis	UBERON:0001379	58.00	gold quality
trachea	UBERON:0003126	57.97	gold quality
mammalian vulva	UBERON:0000997	57.46	gold quality
nipple	UBERON:0002030	56.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	32.12
E-ANND-3	yes	3.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting SPATA3, 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-3134	100.00	66.43	777
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-4504	99.10	69.14	1328
HSA-MIR-4769-3P	97.95	68.17	1002
HSA-MIR-6817-5P	97.95	67.86	1026
HSA-MIR-7855-5P	97.39	67.18	925
HSA-MIR-1243	97.07	65.44	719
HSA-MIR-346	97.01	66.97	662

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata3	ENSMUSG00000026226
rattus_norvegicus	Spata3	ENSRNOG00000017540

Protein

Protein identifiers

Spermatogenesis-associated protein 3 — Q8NHX4 (reviewed: Q8NHX4)

Alternative names: Testis and spermatogenesis cell-related protein 1, Testis spermatocyte apoptosis-related protein 1

All UniProt accessions (5): Q8NHX4, A0A2R8Y5R0, F8WDD9, H7C283, H7C3E6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell projection. Cilium. Flagellum.

RefSeq proteins (1): NP_620712* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026717	SPATA3	Family

Pfam: PF15662

UniProt features (7 total): region of interest 2, compositionally biased region 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NHX4-F1	53.00	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): TGACCTY_ERR1_Q2, CATRRAGC_UNKNOWN, YGACNNYACAR_UNKNOWN, TGCTGAY_UNKNOWN, WEBER_METHYLATED_LCP_IN_SPERM_UP, GOCC_MOTILE_CILIUM, GOCC_CILIUM, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, GOCC_9PLUS2_MOTILE_CILIUM, GSE10240_CTRL_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, PBXIP1_TARGET_GENES, ZNF184_TARGET_GENES, MIR7855_5P, GSE13493_DP_VS_CD4INTCD8POS_THYMOCYTE_DN

GO Biological Process (0):

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (5): sperm flagellum (GO:0036126), cilium (GO:0005929), membrane (GO:0016020), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
9+2 motile cilium	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

1104 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA3	SPATS1	Q496A3	714
SPATA3	SPACA4	Q8TDM5	677
SPATA3	AKAP4	Q5JQC9	606
SPATA3	GARIN1B	Q96KD3	602
SPATA3	CBY2	Q8NA61	593
SPATA3	SPEM1	Q8N4L4	591
SPATA3	SPATA16	Q9BXB7	589
SPATA3	TMEM225	Q6GV28	582
SPATA3	TMEM82	A0PJX8	561
SPATA3	ODF1	Q14990	548
SPATA3	UBQLN3	Q9H347	540
SPATA3	SPATA18	Q8TC71	534
SPATA3	SHCBP1L	Q9BZQ2	534
SPATA3	PRM2	P04554	533
SPATA3	TMEM270	Q6UE05	531

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SCRIB	CHD2	psi-mi:“MI:0914”(association)	0.350

BioGRID (23): SPATA3 (Two-hybrid), SPATA3 (Two-hybrid), SPATA3 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-3 (Two-hybrid), SPATA3 (Two-hybrid), SPATA3 (Two-hybrid), VWC2L (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-6 (Two-hybrid), CYSRT1 (Two-hybrid), KRTAP12-3 (Two-hybrid)

ESM2 similar proteins: A0A172M4N0, A1YFC1, A1YGK6, A2T7F2, A5A6K1, A6NHN6, A8MU93, F5HAE6, O70561, P0DI83, P16531, P26377, P38469, P56958, P59797, P62521, P84996, Q02234, Q3URU2, Q5JRC9, Q5R7U0, Q5RKG3, Q5SF94, Q5SF96, Q6GZN9, Q6H236, Q6R0H6, Q6ZVQ6, Q7T2B3, Q80Y39, Q810T2, Q86X51, Q8BGJ3, Q8CH20, Q8CJI4, Q8N2A0, Q8N3K9, Q8N976, Q8NC38, Q8NHX4

Diamond homologs: Q8NHX4, Q9D9T6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

899 predictions. Top by Δscore:

Variant	Effect	Δscore
2:231000504:G:GT	donor_gain	1.0000
2:230996528:A:T	donor_gain	0.9900
2:231000505:G:T	donor_gain	0.9900
2:231000506:A:T	donor_gain	0.9800
2:230997310:T:G	acceptor_gain	0.9700
2:230996527:G:GT	donor_gain	0.9600
2:231002682:A:AG	acceptor_gain	0.9400
2:231002683:G:GG	acceptor_gain	0.9400
2:231000653:A:T	donor_gain	0.9300
2:231002683:GAA:G	acceptor_gain	0.9300
2:231002825:CAG:C	donor_loss	0.9200
2:231002826:AG:A	donor_loss	0.9200
2:231002827:GGTA:G	donor_loss	0.9200
2:231002828:G:GC	donor_loss	0.9200
2:231002829:T:A	donor_loss	0.9200
2:231007101:C:CA	acceptor_gain	0.9200
2:230997305:C:A	acceptor_gain	0.9100
2:231000510:G:GT	donor_gain	0.9100
2:231002683:GAAA:G	acceptor_gain	0.9100
2:231007220:A:AG	acceptor_gain	0.9100
2:231007221:G:GG	acceptor_gain	0.9100
2:230996613:AGGAT:A	donor_gain	0.9000
2:230996602:C:T	donor_gain	0.8900
2:230996530:AGCAG:A	donor_loss	0.8700
2:230996532:CAG:C	donor_loss	0.8700
2:230996533:AGG:A	donor_loss	0.8700
2:230996534:GG:G	donor_loss	0.8700
2:230996535:G:GA	donor_loss	0.8700
2:230996536:T:A	donor_loss	0.8700
2:231007216:TTACA:T	acceptor_loss	0.8700

AlphaMissense

1238 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:231000530:T:C	F156L	0.980
2:231000532:C:A	F156L	0.980
2:231000532:C:G	F156L	0.980
2:231000464:T:C	F134L	0.962
2:231000466:C:A	F134L	0.962
2:231000466:C:G	F134L	0.962
2:230996248:G:C	K5N	0.950
2:230996248:G:T	K5N	0.950
2:230996239:G:C	K2N	0.944
2:230996239:G:T	K2N	0.944
2:231000468:A:T	D135V	0.939
2:231000462:T:C	I133T	0.937
2:231002684:A:C	R158S	0.937
2:231002684:A:T	R158S	0.937
2:231000531:T:C	F156S	0.935
2:231000430:C:G	C122W	0.932
2:231000454:T:A	H130Q	0.931
2:231000454:T:G	H130Q	0.931
2:231000443:G:T	G127W	0.927
2:231000410:T:C	C116R	0.923
2:231000449:T:C	C129R	0.921
2:231000428:T:C	C122R	0.919
2:231000537:G:T	R158I	0.914
2:231000451:C:G	C129W	0.913
2:231000533:T:G	Y157D	0.913
2:231000452:C:G	H130D	0.911
2:231000462:T:G	I133S	0.908
2:231000429:G:A	C122Y	0.906
2:231000449:T:A	C129S	0.906
2:231000450:G:C	C129S	0.906

dbSNP variants (sampled 300 via entrez): RS1000039067 (2:231020237 A>G), RS1000241669 (2:231004558 G>A), RS1000409566 (2:231015719 G>C), RS1000461907 (2:231016019 G>A), RS1000562494 (2:231016848 A>T), RS1000562858 (2:231011167 C>T), RS1000798536 (2:231017297 C>G,T), RS1000957776 (2:231004427 T>C), RS1000981739 (2:230994577 C>T), RS1000984889 (2:231012829 A>G), RS1001053926 (2:231004714 G>A), RS1001201374 (2:231016069 A>C), RS1001233549 (2:230999406 T>C), RS1001296660 (2:231006212 A>G), RS1001390557 (2:231012145 G>A)

Disease associations

OMIM: gene MIM:619857 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
male infertility with azoospermia or oligozoospermia due to single gene mutation	Moderate	Autosomal recessive

Mondo (1): (MONDO:0018393)

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

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

Chemical	Actions (top 5)	PubMed papers
clothianidin	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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