SPATS2

Summary

SPATS2 (spermatogenesis associated serine rich 2, HGNC:18650) is a protein-coding gene on chromosome 12q13.12, encoding Spermatogenesis-associated serine-rich protein 2 (Q86XZ4).

Enables RNA binding activity. Located in cytosol.

Source: NCBI Gene 65244 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 84 total
• MANE Select transcript: NM_023071

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18650
Approved symbol	SPATS2
Name	spermatogenesis associated serine rich 2
Location	12q13.12
Locus type	gene with protein product
Status	Approved
Aliases	SPATA10, SCR59, FLJ13117
Ensembl gene	ENSG00000123352
Ensembl biotype	protein_coding
OMIM	611667
Entrez	65244

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 31 protein_coding, 3 protein_coding_CDS_not_defined, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000321898, ENST00000547003, ENST00000547865, ENST00000548377, ENST00000548388, ENST00000548654, ENST00000548710, ENST00000548727, ENST00000548777, ENST00000549045, ENST00000549179, ENST00000549298, ENST00000549375, ENST00000549412, ENST00000549538, ENST00000550643, ENST00000550997, ENST00000551540, ENST00000552171, ENST00000552557, ENST00000552655, ENST00000552918, ENST00000553127, ENST00000903511, ENST00000903512, ENST00000903513, ENST00000903514, ENST00000932995, ENST00000932996, ENST00000932997, ENST00000932998, ENST00000932999, ENST00000933000, ENST00000933001, ENST00000933002, ENST00000933003, ENST00000933004, ENST00000952609, ENST00000952610

RefSeq mRNA: 3 — MANE Select: NM_023071 NM_001293285, NM_001293286, NM_023071

CCDS: CCDS31794

Canonical transcript exons

ENST00000552918 — 14 exons

Exon	Start	End
ENSE00001548408	49371228	49371290
ENSE00002425711	49525944	49527425
ENSE00003497545	49484590	49484669
ENSE00003509334	49490682	49490731
ENSE00003546997	49489465	49489573
ENSE00003565233	49519073	49519182
ENSE00003568079	49496833	49497009
ENSE00003585708	49522751	49522853
ENSE00003591719	49524682	49524896
ENSE00003607461	49494741	49495002
ENSE00003607495	49500070	49500205
ENSE00003684579	49514555	49514613
ENSE00003795925	49460770	49461037
ENSE00003901647	49367462	49367587

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 95.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.2924 / max 169.1686, expressed in 1786 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125334	5.8497	1644
125335	5.7047	1542
125333	3.4030	1337
125332	1.7227	959
125331	0.3411	176
206690	0.2042	69
206691	0.0671	29

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	95.38	gold quality
ganglionic eminence	UBERON:0004023	94.62	gold quality
cortical plate	UBERON:0005343	94.12	gold quality
pylorus	UBERON:0001166	93.92	gold quality
parotid gland	UBERON:0001831	92.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.09	gold quality
stromal cell of endometrium	CL:0002255	91.52	gold quality
cardia of stomach	UBERON:0001162	91.45	gold quality
nipple	UBERON:0002030	90.64	gold quality
ventricular zone	UBERON:0003053	90.13	gold quality
lateral nuclear group of thalamus	UBERON:0002736	90.06	gold quality
dorsal root ganglion	UBERON:0000044	90.00	gold quality
oocyte	CL:0000023	89.93	gold quality
pons	UBERON:0000988	89.77	gold quality
cerebellar vermis	UBERON:0004720	89.65	gold quality
secondary oocyte	CL:0000655	89.59	gold quality
calcaneal tendon	UBERON:0003701	89.57	gold quality
parietal lobe	UBERON:0001872	88.81	gold quality
cerebellar cortex	UBERON:0002129	88.77	gold quality
tonsil	UBERON:0002372	88.75	gold quality
postcentral gyrus	UBERON:0002581	88.74	gold quality
cerebellar hemisphere	UBERON:0002245	88.69	gold quality
endometrium	UBERON:0001295	88.59	gold quality
superior frontal gyrus	UBERON:0002661	88.41	gold quality
cerebellum	UBERON:0002037	88.13	gold quality
saliva-secreting gland	UBERON:0001044	87.96	gold quality
testis	UBERON:0000473	87.89	gold quality
islet of Langerhans	UBERON:0000006	87.75	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.59	gold quality
sperm	CL:0000019	87.57	silver quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-CURD-122	yes	42.75
E-HCAD-1	yes	41.02
E-MTAB-8410	yes	24.19
E-ANND-3	yes	21.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting SPATS2, 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-3613-3P	100.00	76.36	7965
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-548AI	99.69	69.24	1494
HSA-MIR-548BA	99.69	69.14	1514
HSA-MIR-570-5P	99.69	69.24	1494
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-657	99.48	66.02	848
HSA-MIR-766-3P	99.47	65.24	1811

Literature-anchored findings (GeneRIF, showing 4)

• Gene Set Enrichment Analysis (GSEA) was used to identify signaling pathways related to SPATS2 expression. SPATS2 expression could be a novel diagnostic and prognostic biomarker in liver cancer. (PMID:32118724)
• SPATS2, negatively regulated by miR-145-5p, promotes hepatocellular carcinoma progression through regulating cell cycle. (PMID:33037180)
• SPATS2 is positively activated by long noncoding RNA SNHG5 via regulating DNMT3a expression to promote hepatocellular carcinoma progression. (PMID:35077478)
• SPATS2 is correlated with cell cycle progression and immune cells infiltration in hepatocellular carcinoma. (PMID:36631750)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
		ENSDARG00000104316
mus_musculus	Spats2	ENSMUSG00000051934
rattus_norvegicus	Spats2	ENSRNOG00000052307
caenorhabditis_elegans	Y71F9AL.9	WBGENE00022114

Paralogs (1): SPATS2L (ENSG00000196141)

Protein

Protein identifiers

Spermatogenesis-associated serine-rich protein 2 — Q86XZ4 (reviewed: Q86XZ4)

Alternative names: Serine-rich spermatocytes and round spermatid 59 kDa protein, p59scr

All UniProt accessions (13): A0A0G2JL06, A0A0G2JL58, Q86XZ4, F8VRH4, F8VS10, F8VVF0, F8VX46, F8VX66, F8VXB3, F8VXP9, F8VZS5, F8W128, F8W1X1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Similarity. Belongs to the SPATS2 family.

RefSeq proteins (3): NP_001280214, NP_001280215, NP_075559* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009060	UBA-like_sf	Homologous_superfamily
IPR009816	SPATS2-like	Family

Pfam: PF07139

UniProt features (16 total): compositionally biased region 6, modified residue 4, region of interest 3, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86XZ4-F1	64.16	0.34

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 143, 146, 148, 520

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 193 (showing top): AP1_01, CMYB_01, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, HNF1_Q6, PATIL_LIVER_CANCER, SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE, AP1_Q4_01, SOX9_B1, TGCTGAY_UNKNOWN, BACH2_01, TGANTCA_AP1_C, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FISCHER_DREAM_TARGETS, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, AACTGGA_MIR145

GO Biological Process (0):

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (2): cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
nucleic acid binding	1
binding	1
intracellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

420 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATS2	TP63	Q9H3D4	649
SPATS2	ACTB	P02570	587
SPATS2	STAU1	O95793	431
SPATS2	FAM221A	A4D161	391
SPATS2	SPATA21	Q7Z572	365
SPATS2	C19orf47	Q8N9M1	350
SPATS2	LRRC75A	Q8NAA5	331
SPATS2	RNF38	Q9H0F5	310
SPATS2	PLEKHG2	Q9H7P9	308
SPATS2	PRMT2IP	Q6ZRI6	306
SPATS2	PLEKHN1	Q494U1	287
SPATS2	ZNF710	Q8N1W2	278
SPATS2	CSTPP1	Q9H6J7	276
SPATS2	ST6GALNAC1	Q9NSC7	272
SPATS2	RAD51AP2	Q09MP3	262

IntAct

113 interactions, top by confidence:

A	B	Type	Score
FAM98A	HERC2	psi-mi:“MI:0914”(association)	0.640
PSMC3	PSMD12	psi-mi:“MI:0914”(association)	0.640
TRIM44	ODAD3	psi-mi:“MI:0914”(association)	0.530
LTBR	ZNF724	psi-mi:“MI:0914”(association)	0.530
TNFRSF8	DAPK3	psi-mi:“MI:0914”(association)	0.530
BORCS6	HSBP1	psi-mi:“MI:0914”(association)	0.530
HSP90AA1	USP19	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
NUP62	RGPD8	psi-mi:“MI:0914”(association)	0.530
KRR1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
EXOSC4	ZFC3H1	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RBMX2	WDR46	psi-mi:“MI:0914”(association)	0.530
rev	TMED10	psi-mi:“MI:0914”(association)	0.460
SPATS2	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
SPATS2	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
SRPK1	SPATS2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
SPATS2	E2	psi-mi:“MI:0915”(physical association)	0.370
KIF11	ILVBL	psi-mi:“MI:0914”(association)	0.350
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
HNRNPU		psi-mi:“MI:0914”(association)	0.350
Eif3i	CBX4	psi-mi:“MI:0914”(association)	0.350
PHAX	RPL10	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
MKI67	ARHGAP10	psi-mi:“MI:0914”(association)	0.350

BioGRID (138): SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Proximity Label-MS), SPATS2 (Proximity Label-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS), SPATS2 (Affinity Capture-MS)

ESM2 similar proteins: A0JPP1, A0JPQ7, A2VDN6, E6ZGB4, O75151, O75376, O88974, P0CH95, P22682, P55265, P55266, Q14919, Q15047, Q15459, Q17R89, Q2YDP3, Q3UIA2, Q3YEC7, Q4KKX4, Q4V7W5, Q5F3B1, Q5R6Y9, Q5SFM8, Q5U3K5, Q60974, Q61909, Q68EM7, Q6P949, Q6ZM86, Q80TJ7, Q86XZ4, Q8CFK2, Q8K1N4, Q8K4S7, Q8K4Z5, Q8N5Y2, Q8R3Y5, Q8VHI6, Q8VI24, Q92625

Diamond homologs: Q5U2T3, Q86XZ4, Q8K1N4, Q91WJ7, Q9NUQ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 145 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	5	13.7×	8e-04
Nonsense-Mediated Decay (NMD)	5	11.8×	2e-03
Peptide chain elongation	9	11.5×	5e-06
Viral mRNA Translation	9	11.5×	5e-06
Translation initiation complex formation	6	11.5×	4e-04
Ribosomal scanning and start codon recognition	6	11.5×	4e-04
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	9	11.4×	5e-06
rRNA processing in the nucleus and cytosol	7	11.4×	9e-05

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	9	13.0×	2e-05
ribosomal small subunit biogenesis	6	10.7×	7e-03
RNA processing	6	10.3×	7e-03
negative regulation of translation	6	9.2×	1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	65
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3945 predictions. Top by Δscore:

Variant	Effect	Δscore
12:49367582:GGC:G	donor_gain	1.0000
12:49367583:GC:G	donor_gain	1.0000
12:49367584:C:G	donor_gain	1.0000
12:49367585:TAGG:T	donor_loss	1.0000
12:49460765:TCCA:T	acceptor_loss	1.0000
12:49460768:A:AG	acceptor_gain	1.0000
12:49460768:AGAAT:A	acceptor_loss	1.0000
12:49460769:G:GA	acceptor_gain	1.0000
12:49460769:GA:G	acceptor_gain	1.0000
12:49460769:GAA:G	acceptor_gain	1.0000
12:49460769:GAAT:G	acceptor_gain	1.0000
12:49460769:GAATC:G	acceptor_gain	1.0000
12:49460855:GCTA:G	donor_gain	1.0000
12:49460882:GAT:G	donor_gain	1.0000
12:49461033:GAAGG:G	donor_gain	1.0000
12:49484585:TTCA:T	acceptor_loss	1.0000
12:49484587:CA:C	acceptor_loss	1.0000
12:49484588:A:AG	acceptor_gain	1.0000
12:49484588:A:C	acceptor_loss	1.0000
12:49484589:G:GA	acceptor_gain	1.0000
12:49484589:G:GT	acceptor_loss	1.0000
12:49484589:GATTC:G	acceptor_gain	1.0000
12:49484666:GAAG:G	donor_gain	1.0000
12:49484670:G:GA	donor_loss	1.0000
12:49484671:T:G	donor_loss	1.0000
12:49489571:A:T	donor_gain	1.0000
12:49489571:AAGG:A	donor_loss	1.0000
12:49489572:AG:A	donor_loss	1.0000
12:49489573:GGTA:G	donor_loss	1.0000
12:49489574:G:T	donor_loss	1.0000

AlphaMissense

3600 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:49490708:T:A	W81R	1.000
12:49490708:T:C	W81R	1.000
12:49490710:G:C	W81C	1.000
12:49490710:G:T	W81C	1.000
12:49489475:T:A	V39E	0.999
12:49489477:C:A	R40S	0.999
12:49489478:G:C	R40P	0.999
12:49489487:T:A	V43D	0.999
12:49489517:T:C	L53P	0.999
12:49489520:T:A	V54D	0.999
12:49489523:T:C	L55S	0.999
12:49489565:T:C	F69S	0.999
12:49490709:G:C	W81S	0.999
12:49500100:T:C	L245P	0.999
12:49500105:C:A	R247S	0.999
12:49500106:G:C	R247P	0.999
12:49500121:T:C	L252P	0.999
12:49522803:T:C	F354S	0.999
12:49489471:G:C	A38P	0.998
12:49489511:T:G	I51S	0.998
12:49489523:T:G	L55W	0.998
12:49489561:G:C	A68P	0.998
12:49500094:A:T	K243I	0.998
12:49500096:G:C	D244H	0.998
12:49519166:T:C	L331P	0.998
12:49522754:T:C	F338L	0.998
12:49522755:T:C	F338S	0.998
12:49522756:T:A	F338L	0.998
12:49522756:T:G	F338L	0.998
12:49522802:T:C	F354L	0.998

dbSNP variants (sampled 300 via entrez): RS1000002453 (12:49503778 C>G), RS1000011751 (12:49460027 G>A,T), RS1000020958 (12:49447454 G>A), RS1000029116 (12:49496376 T>C), RS1000033868 (12:49503210 C>T), RS1000047468 (12:49467651 T>A), RS1000086237 (12:49483366 T>G), RS1000123102 (12:49453631 G>A,T), RS1000130572 (12:49395697 A>G,T), RS1000146530 (12:49519269 T>C), RS1000147349 (12:49486630 G>C,T), RS1000150932 (12:49474104 C>G,T), RS1000167532 (12:49398905 A>C,G), RS1000187794 (12:49484500 T>A,C,G), RS1000194211 (12:49394911 A>C,T)

Disease associations

OMIM: gene MIM:611667 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST008075_191	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	3.000000e-08
GCST008075_73	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	1.000000e-08
GCST008084_175	HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	2.000000e-07
GCST008084_97	HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	3.000000e-08
GCST008085_171	HDL cholesterol levels in current drinkers	4.000000e-08
GCST008085_93	HDL cholesterol levels in current drinkers	2.000000e-08
GCST011703_8	Smoking initiation	3.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004329	alcohol drinking
EFO:0005670	smoking initiation

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
sodium arsenite	decreases reaction, decreases expression, increases expression, affects binding	2
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
2-palmitoylglycerol	increases expression	1
monomethylarsonous acid	decreases expression	1
K 7174	increases expression	1
abrine	increases expression	1
bisphenol S	affects cotreatment, decreases methylation	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation, decreases methylation	1
Benzo(a)pyrene	decreases methylation	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Ivermectin	decreases expression	1
Lead	increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	increases expression, affects cotreatment	1
Ribonucleotides	affects binding, decreases reaction	1
Thiram	increases expression	1
Urethane	increases expression	1
Zinc	increases expression	1
Antirheumatic Agents	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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