SPATA9

Summary

SPATA9 (spermatogenesis associated 9, HGNC:22988) is a protein-coding gene on chromosome 5q15, encoding Spermatogenesis-associated protein 9 (Q9BWV2). May play a role in testicular development/spermatogenesis and may be an important factor in male infertility.

Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in membrane.

Source: NCBI Gene 83890 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_031952

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22988
Approved symbol	SPATA9
Name	spermatogenesis associated 9
Location	5q15
Locus type	gene with protein product
Status	Approved
Aliases	NYD-SP16, FLJ35906
Ensembl gene	ENSG00000145757
Ensembl biotype	protein_coding
OMIM	608039
Entrez	83890

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000274432, ENST00000316087, ENST00000379990, ENST00000477047, ENST00000477715, ENST00000489917

RefSeq mRNA: 2 — MANE Select: NM_031952 NM_001349303, NM_031952

CCDS: CCDS4076

Canonical transcript exons

ENST00000274432 — 5 exons

Exon	Start	End
ENSE00001523209	95658315	95658913
ENSE00003491887	95675412	95675639
ENSE00003566397	95682528	95682616
ENSE00003686863	95663953	95664048
ENSE00003842632	95682794	95682991

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 93.82.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1587 / max 47.4555, expressed in 613 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62649	1.0722	582
62650	0.0488	14
62648	0.0376	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	93.82	gold quality
left testis	UBERON:0004533	88.39	gold quality
right testis	UBERON:0004534	87.96	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.58	gold quality
testis	UBERON:0000473	86.44	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.42	silver quality
omental fat pad	UBERON:0010414	73.84	gold quality
peritoneum	UBERON:0002358	73.76	gold quality
adipose tissue of abdominal region	UBERON:0007808	73.33	gold quality
adipose tissue	UBERON:0001013	70.88	gold quality
subcutaneous adipose tissue	UBERON:0002190	68.26	gold quality
left ovary	UBERON:0002119	67.96	gold quality
right ovary	UBERON:0002118	67.43	gold quality
tibial nerve	UBERON:0001323	66.54	gold quality
buccal mucosa cell	CL:0002336	65.87	gold quality
adult organism	UBERON:0007023	65.56	gold quality
mucosa of transverse colon	UBERON:0004991	64.74	gold quality
ovary	UBERON:0000992	64.48	gold quality
cortical plate	UBERON:0005343	64.14	gold quality
right adrenal gland cortex	UBERON:0035827	63.87	gold quality
stromal cell of endometrium	CL:0002255	63.66	gold quality
body of pancreas	UBERON:0001150	63.61	gold quality
right adrenal gland	UBERON:0001233	63.12	gold quality
spleen	UBERON:0002106	62.97	gold quality
cerebellar hemisphere	UBERON:0002245	62.88	gold quality
tibia	UBERON:0000979	62.87	gold quality
cerebellar cortex	UBERON:0002129	62.85	gold quality
right hemisphere of cerebellum	UBERON:0014890	62.39	gold quality
left adrenal gland	UBERON:0001234	61.56	gold quality
granulocyte	CL:0000094	61.39	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	43.12
E-ANND-3	no	2.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting SPATA9, 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-340-5P	100.00	72.50	4437
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-6516-3P	99.65	68.57	1238
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-6853-3P	99.36	70.79	1558
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-16-2-3P	99.29	70.60	1954
HSA-MIR-195-3P	99.29	70.61	1954
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-140-3P	99.04	67.69	1324
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-455-5P	98.74	67.31	795
HSA-MIR-6501-3P	98.71	67.45	1480
HSA-MIR-1245B-3P	98.01	68.91	1387

Literature-anchored findings (GeneRIF, showing 2)

• may play an important role in testicular development/spermatogenesis and may be an important factor in male infertility (PMID:12493713)
• NYD-SP16 protein is component of sperm acrosome, which plays functional role in sperm capacitation and acrosome reaction and is consequently necessary for fertilization. (PMID:16963046)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spata9	ENSMUSG00000021590
rattus_norvegicus	Spata9	ENSRNOG00000012770

Protein

Protein identifiers

Spermatogenesis-associated protein 9 — Q9BWV2 (reviewed: Q9BWV2)

Alternative names: Testis development protein NYD-SP16

All UniProt accessions (2): A0A140VJV2, Q9BWV2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in testicular development/spermatogenesis and may be an important factor in male infertility.

Subcellular location. Membrane.

Tissue specificity. Highly expressed in testes and pancreas. Low levels found in the heart, lungs, and brain. Very low expression detected in the placenta. No expression seen in skeletal muscle, liver, kidney, thymus, small intestine, colons, spleen, leukocytes, prostate gland, and ovary. In the adult testes, expression was about 6.44-fold higher than in the embryo testes. No expression in testes of patients with Sertoli-cell-only syndrome. In patients with arrest at spermatogonium and primary spermatocyte stages, no expression was detected. In patients with arrest at the spermatid stage, expression level was weak or absent. Variable expression was seen in patients with spermatogenic arrest.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9BWV2-1	1	yes
Q9BWV2-2	2
Q9BWV2-3	3

RefSeq proteins (2): NP_001336232, NP_114158* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031659	SPATA9	Family

Pfam: PF15824

UniProt features (9 total): splice variant 3, sequence conflict 3, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BWV2-F1	57.94	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, MODULE_451, GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr5q15, YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, MIR664A_3P, MIR130A_5P, MIR892C_5P, MIR1290, MIR497_3P, MIR6853_3P, MIR1245B_3P

GO Biological Process (3): spermatogenesis (GO:0007283), cell differentiation (GO:0030154), biological_process (GO:0008150)

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

GO Cellular Component (2): membrane (GO:0016020), cellular_component (GO:0005575)

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
cellular anatomical structure	1

Protein interactions and networks

STRING

282 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA9	CCDC38	Q502W7	624
SPATA9	LRMDA	Q9H2I8	581
SPATA9	ARMC2	Q8NEN0	572
SPATA9	C16orf95	Q9H693	544
SPATA9	CFDP1	Q9UEE9	541
SPATA9	SPATC1	Q76KD6	513
SPATA9	GSTCD	Q8NEC7	507
SPATA9	SPATA46	Q5T0L3	498
SPATA9	ASB6	Q9NWX5	495
SPATA9	CBY2	Q8NA61	494
SPATA9	MFAP2	P55001	479
SPATA9	KIF24	Q5T7B8	459
SPATA9	UBAP1	Q9NZ09	456
SPATA9	RNF123	Q5XPI4	453
SPATA9	RHOBTB3	O94955	447

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SPATA9	KTN1	psi-mi:“MI:0915”(physical association)	0.400
P		psi-mi:“MI:0914”(association)	0.350

BioGRID (2): SPATA9 (Affinity Capture-MS), SPATA9 (Proximity Label-MS)

ESM2 similar proteins: A0A0H3MGR4, A0A218N031, A0A482ASA5, A0A482AU66, A0MD31, A6ZMK7, B0B9M3, B0B9M4, B0B9M5, B3LM36, B6KEU8, C5DQ25, C5E3S0, C7GQ88, C8ZF05, F5H8R0, O74512, O74838, O84008, O84009, O84449, O94592, P08363, P0C6Y6, P0DJI3, P0DJI5, P0DPS6, P13841, P18587, P20316, P23705, P26756, P26757, P28164, P40218, P40219, Q04684, Q04685, Q04686, Q04687

Diamond homologs: Q3T021, Q9BWV2, Q9D9R3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1077 predictions. Top by Δscore:

Variant	Effect	Δscore
5:95652289:G:GT	donor_gain	1.0000
5:95653399:A:G	donor_gain	1.0000
5:95654049:A:AG	acceptor_gain	1.0000
5:95654049:AT:A	acceptor_gain	1.0000
5:95654050:T:G	acceptor_gain	1.0000
5:95654050:T:TA	acceptor_gain	1.0000
5:95654055:A:AG	acceptor_gain	1.0000
5:95654056:A:AG	acceptor_gain	1.0000
5:95654058:TAGCA:T	acceptor_loss	1.0000
5:95654059:A:AG	acceptor_gain	1.0000
5:95654059:A:T	acceptor_loss	1.0000
5:95654059:AGCAT:A	acceptor_gain	1.0000
5:95654060:G:GC	acceptor_gain	1.0000
5:95654060:GC:G	acceptor_gain	1.0000
5:95654060:GCA:G	acceptor_gain	1.0000
5:95654060:GCAT:G	acceptor_gain	1.0000
5:95654060:GCATG:G	acceptor_gain	1.0000
5:95654203:G:GT	donor_gain	1.0000
5:95654232:TTACC:T	donor_gain	1.0000
5:95654235:CC:C	donor_gain	1.0000
5:95654235:CCGT:C	donor_loss	1.0000
5:95654236:CGT:C	donor_loss	1.0000
5:95654237:G:GA	donor_loss	1.0000
5:95654237:G:GG	donor_gain	1.0000
5:95654238:T:A	donor_loss	1.0000
5:95663947:ACTT:A	donor_loss	1.0000
5:95663948:CTT:C	donor_loss	1.0000
5:95663949:TTA:T	donor_loss	1.0000
5:95663950:TACCA:T	donor_loss	1.0000
5:95663951:A:AC	donor_gain	1.0000

AlphaMissense

1660 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:95663989:G:C	S146R	0.990
5:95663989:G:T	S146R	0.990
5:95663991:T:G	S146R	0.990
5:95658656:A:C	F244L	0.948
5:95658656:A:T	F244L	0.948
5:95658658:A:G	F244L	0.948
5:95663999:G:T	A143D	0.925
5:95663969:G:T	A153E	0.910
5:95663970:C:G	A153P	0.909
5:95658669:A:G	L240S	0.908
5:95664013:A:C	F138L	0.906
5:95664013:A:T	F138L	0.906
5:95664015:A:G	F138L	0.906
5:95663978:G:T	A150D	0.905
5:95675479:A:G	L104P	0.896
5:95663987:A:T	I147K	0.891
5:95663963:A:G	L155P	0.886
5:95675545:A:T	I82K	0.883
5:95658898:C:G	A164P	0.876
5:95658891:A:G	L166P	0.868
5:95682586:A:G	L31P	0.867
5:95682573:A:C	F35L	0.863
5:95682573:A:T	F35L	0.863
5:95682575:A:G	F35L	0.863
5:95682833:A:G	W8R	0.863
5:95682833:A:T	W8R	0.863
5:95682570:T:A	K36N	0.862
5:95682570:T:G	K36N	0.862
5:95664004:C:A	K141N	0.860
5:95664004:C:G	K141N	0.860

dbSNP variants (sampled 300 via entrez): RS1000016142 (5:95660764 C>G), RS1000021254 (5:95696181 C>T), RS1000098606 (5:95700861 A>G), RS1000107543 (5:95711651 GGC>G), RS1000131142 (5:95702505 A>G), RS1000228154 (5:95661759 G>A,C), RS1000278255 (5:95663679 A>G), RS1000285370 (5:95713107 A>G), RS1000322259 (5:95661340 C>T), RS1000341253 (5:95669267 G>T), RS1000357858 (5:95730682 C>A), RS1000368532 (5:95714601 ATTTG>A), RS1000400890 (5:95712747 A>G), RS1000439073 (5:95714291 C>T), RS1000440996 (5:95670531 C>A)

Disease associations

OMIM: gene MIM:608039 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001248_14	Pulmonary function	2.000000e-08
GCST007431_98	Lung function (FEV1/FVC)	1.000000e-30
GCST007692_53	Chronic obstructive pulmonary disease	6.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0003892	pulmonary function measurement
EFO:0004713	FEV/FVC ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs72783407	SPATA9		0.00	0

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	increases reaction, affects binding	1
8-Bromo Cyclic Adenosine Monophosphate	increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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