SPATA20

Summary

SPATA20 (spermatogenesis associated 20, HGNC:26125) is a protein-coding gene on chromosome 17q21.33, encoding Spermatogenesis-associated protein 20 (Q8TB22). May play a role in fertility regulation.

Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Located in mitochondrion.

Source: NCBI Gene 64847 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 161 total
• MANE Select transcript: NM_022827

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26125
Approved symbol	SPATA20
Name	spermatogenesis associated 20
Location	17q21.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21347, SSP411, Tisp78
Ensembl gene	ENSG00000006282
Ensembl biotype	protein_coding
OMIM	613939
Entrez	64847

Gene structure

Transcript identifiers

Ensembl transcripts: 44 — 20 protein_coding, 14 retained_intron, 10 nonsense_mediated_decay

ENST00000006658, ENST00000356488, ENST00000502911, ENST00000503063, ENST00000503127, ENST00000504265, ENST00000504271, ENST00000504334, ENST00000505085, ENST00000505336, ENST00000505456, ENST00000505559, ENST00000505656, ENST00000508528, ENST00000508598, ENST00000510917, ENST00000511347, ENST00000511605, ENST00000511845, ENST00000511937, ENST00000512181, ENST00000512416, ENST00000513618, ENST00000515526, ENST00000515619, ENST00000634597, ENST00000635113, ENST00000860309, ENST00000860310, ENST00000860311, ENST00000860312, ENST00000860313, ENST00000860314, ENST00000860315, ENST00000860316, ENST00000860317, ENST00000860318, ENST00000860319, ENST00000860320, ENST00000912606, ENST00000953007, ENST00000953008, ENST00000953009, ENST00000953010

RefSeq mRNA: 3 — MANE Select: NM_022827 NM_001258372, NM_001258373, NM_022827

CCDS: CCDS11571, CCDS58563

Canonical transcript exons

ENST00000006658 — 17 exons

Exon	Start	End
ENSE00002083643	50547174	50547285
ENSE00003458621	50550536	50550610
ENSE00003465853	50548283	50548453
ENSE00003475153	50549043	50549186
ENSE00003496489	50548554	50548618
ENSE00003516663	50550708	50550917
ENSE00003533479	50547720	50547767
ENSE00003538569	50554251	50554450
ENSE00003548869	50548810	50548964
ENSE00003574046	50550998	50551190
ENSE00003595700	50555492	50555852
ENSE00003597185	50550208	50550312
ENSE00003598717	50551969	50552180
ENSE00003640118	50549286	50549487
ENSE00003663425	50549985	50550115
ENSE00003665752	50555232	50555312
ENSE00003672833	50551511	50551679

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 98.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.5836 / max 228.2490, expressed in 1789 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161683	40.3925	1789
161684	0.1220	5
161686	0.0536	4
161685	0.0155	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.42	gold quality
right testis	UBERON:0004534	98.35	gold quality
apex of heart	UBERON:0002098	97.11	gold quality
left adrenal gland cortex	UBERON:0035825	96.87	gold quality
right lobe of thyroid gland	UBERON:0001119	96.80	gold quality
adrenal cortex	UBERON:0001235	96.76	gold quality
left lobe of thyroid gland	UBERON:0001120	96.73	gold quality
right adrenal gland	UBERON:0001233	96.72	gold quality
left adrenal gland	UBERON:0001234	96.68	gold quality
right adrenal gland cortex	UBERON:0035827	96.52	gold quality
thyroid gland	UBERON:0002046	96.48	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.26	gold quality
testis	UBERON:0000473	96.03	gold quality
metanephros cortex	UBERON:0010533	95.96	gold quality
left ovary	UBERON:0002119	95.67	gold quality
cerebellar hemisphere	UBERON:0002245	95.66	gold quality
cerebellar cortex	UBERON:0002129	95.63	gold quality
adrenal gland	UBERON:0002369	95.53	gold quality
right ovary	UBERON:0002118	95.47	gold quality
male germ cell	CL:0000015	95.31	gold quality
body of stomach	UBERON:0001161	95.13	gold quality
sperm	CL:0000019	95.11	gold quality
cerebellum	UBERON:0002037	94.83	gold quality
endocervix	UBERON:0000458	94.71	gold quality
cardia of stomach	UBERON:0001162	94.58	gold quality
transverse colon	UBERON:0001157	94.43	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.29	gold quality
mucosa of transverse colon	UBERON:0004991	94.24	gold quality
fundus of stomach	UBERON:0001160	94.16	gold quality
body of pancreas	UBERON:0001150	94.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting SPATA20, 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-3934-3P	99.76	65.51	1351
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-6885-5P	98.71	64.33	902
HSA-MIR-6765-3P	97.83	64.59	1165

Literature-anchored findings (GeneRIF, showing 2)

• SSP411 has potential as a biomarker for the diagnosis of Cholangiocarcinoma (PMID:23118872)
• Identification of nonfunctional SPATA20 causing acephalic spermatozoa syndrome in humans. (PMID:36415156)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	spata20	ENSDARG00000013880
mus_musculus	Spata20	ENSMUSG00000020867
rattus_norvegicus	Spata20	ENSRNOG00000003273
drosophila_melanogaster	CG8613	FBGN0033924
caenorhabditis_elegans		WBGENE00015204

Protein

Protein identifiers

Spermatogenesis-associated protein 20 — Q8TB22 (reviewed: Q8TB22)

Alternative names: Sperm-specific protein 411

All UniProt accessions (7): Q8TB22, A0A0U1RRL8, D6R947, D6RC70, D6RIU6, H0Y9M1, H0Y9W3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in fertility regulation.

Subcellular location. Secreted.

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

Isoforms (4)

UniProt ID	Names	Canonical?
Q8TB22-1	1	yes
Q8TB22-2	2
Q8TB22-3	3
Q8TB22-4	4

RefSeq proteins (3): NP_001245301, NP_001245302, NP_073738* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004879	Ssp411-like_TRX	Domain
IPR008928	6-hairpin_glycosidase_sf	Homologous_superfamily
IPR012341	6hp_glycosidase-like_sf	Homologous_superfamily
IPR024705	Ssp411	Family
IPR036249	Thioredoxin-like_sf	Homologous_superfamily

Pfam: PF03190

UniProt features (14 total): splice variant 5, sequence variant 3, sequence conflict 2, signal peptide 1, chain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TB22-F1	90.38	0.81

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 (1): 649

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): FXR_IR1_Q6, TGACCTY_ERR1_Q2, GOBP_MALE_GAMETE_GENERATION, YGACNNYACAR_UNKNOWN, ONKEN_UVEAL_MELANOMA_UP, ATF1_Q6, MODULE_301, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, BASAKI_YBX1_TARGETS_DN, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, DR3_Q4, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, MARTENS_TRETINOIN_RESPONSE_UP, VDR_Q6

GO Biological Process (3): carbohydrate metabolic process (GO:0005975), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (2): extracellular region (GO:0005576), mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
cellular anatomical structure	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

704 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA20	SPATA6	Q9NWH7	595
SPATA20	SPATA4	Q8NEY3	532
SPATA20	SPATA46	Q5T0L3	527
SPATA20	PUSL1	Q8N0Z8	496
SPATA20	SPATA17	Q96L03	489
SPATA20	SPATA3	Q8NHX4	458
SPATA20	SPATA22	Q8NHS9	455
SPATA20	SPATA25	Q9BR10	451
SPATA20	CROCC2	H7BZ55	443
SPATA20	SPATA7	Q9P0W8	432
SPATA20	CFAP184	Q2M329	416
SPATA20	HEATR9	A2RTY3	410
SPATA20	IQCN	Q9H0B3	403
SPATA20	COASY	Q13057	395
SPATA20	AFG2A	Q8NB90	378

IntAct

42 interactions, top by confidence:

A	B	Type	Score
TADA3	TADA2A	psi-mi:“MI:0914”(association)	0.740
ETFRF1	NDUFAB1	psi-mi:“MI:0914”(association)	0.640
COX5B	COX7A2L	psi-mi:“MI:0914”(association)	0.530
NIPSNAP3A	CLUH	psi-mi:“MI:0914”(association)	0.530
COLGALT2	COL1A1	psi-mi:“MI:0914”(association)	0.530
CCL5	C4A	psi-mi:“MI:0914”(association)	0.530
ODF1	TCP1	psi-mi:“MI:0914”(association)	0.530
GPSM3	ATE1	psi-mi:“MI:0914”(association)	0.530
LYG2	TRAF2	psi-mi:“MI:0914”(association)	0.530
UQCRFS1	NDUFAB1	psi-mi:“MI:0914”(association)	0.530
SPATA20	MYBPC3	psi-mi:“MI:0915”(physical association)	0.370
CORO1A	SPATA20	psi-mi:“MI:0915”(physical association)	0.370
SPATA20	ST6GALNAC4	psi-mi:“MI:0915”(physical association)	0.370
SPATA20	PMPCB	psi-mi:“MI:0914”(association)	0.350
TRUB2	NME6	psi-mi:“MI:0914”(association)	0.350
TRUB2	SPATA20	psi-mi:“MI:0914”(association)	0.350
SPATA20	NDUFAB1	psi-mi:“MI:0914”(association)	0.350
MICOS13	MTX2	psi-mi:“MI:0914”(association)	0.350
NDUFV3	NDUFS8	psi-mi:“MI:0914”(association)	0.350
NDUFA10	AURKA	psi-mi:“MI:0914”(association)	0.350
LYG2	PLOD3	psi-mi:“MI:0914”(association)	0.350
HS1BP3	TAF5L	psi-mi:“MI:0914”(association)	0.350
RAB20	BCL10	psi-mi:“MI:0914”(association)	0.350

BioGRID (76): SPATA20 (Affinity Capture-MS), SPATA20 (Affinity Capture-MS), SPATA20 (Affinity Capture-MS), AGL (Co-fractionation), SPATA20 (Affinity Capture-MS), SPATA20 (Affinity Capture-MS), NUDT8 (Affinity Capture-MS), LYRM7 (Affinity Capture-MS), GLS (Affinity Capture-MS), PMPCA (Affinity Capture-MS), PMPCB (Affinity Capture-MS), CHCHD2 (Affinity Capture-MS), POLDIP2 (Affinity Capture-MS), NDUFA10 (Affinity Capture-MS), ECH1 (Affinity Capture-MS)

ESM2 similar proteins: A0A2B7YDW3, A0A2Z4HPY4, A0A455LN86, A0A455LRW3, A0L2D7, A1CVK0, A1RE94, A1VPR5, A5EBX1, A8ZNR6, A9AWD5, B0U5U4, B0Y565, B0Y5B4, B2FJE7, B2I916, B3Y522, B4SMR2, B6K412, E4V6I8, M2XHU6, O48929, O49187, O50406, O87455, O94265, P05990, P55610, P9WEH1, Q00706, Q07YM7, Q09214, Q0AEJ6, Q0AHQ0, Q0HPW7, Q255B1, Q3AQA7, Q4H4F8, Q4WR16, Q55107

Diamond homologs: P37509, P37512, Q09214, Q6T393, Q80YT5, Q8TB22

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 52 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
Respiratory electron transport	8	19.0×	2e-06
Aerobic respiration and respiratory electron transport	5	11.1×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	138
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3235 predictions. Top by Δscore:

Variant	Effect	Δscore
17:50548546:G:A	acceptor_gain	1.0000
17:50548549:TCTA:T	acceptor_loss	1.0000
17:50548550:CTAG:C	acceptor_loss	1.0000
17:50548551:TA:T	acceptor_loss	1.0000
17:50548615:TCAGG:T	donor_loss	1.0000
17:50548616:CAGG:C	donor_loss	1.0000
17:50548617:AGG:A	donor_loss	1.0000
17:50548619:G:C	donor_loss	1.0000
17:50548620:T:A	donor_loss	1.0000
17:50548796:A:AG	acceptor_gain	1.0000
17:50548796:AT:A	acceptor_gain	1.0000
17:50548796:ATG:A	acceptor_gain	1.0000
17:50548797:T:A	acceptor_gain	1.0000
17:50548805:TTCAG:T	acceptor_loss	1.0000
17:50548806:TCA:T	acceptor_loss	1.0000
17:50548808:A:AG	acceptor_gain	1.0000
17:50548808:AGTC:A	acceptor_gain	1.0000
17:50548808:AGTCG:A	acceptor_gain	1.0000
17:50548809:G:GA	acceptor_gain	1.0000
17:50548809:GT:G	acceptor_gain	1.0000
17:50548809:GTC:G	acceptor_gain	1.0000
17:50548809:GTCG:G	acceptor_gain	1.0000
17:50548809:GTCGG:G	acceptor_gain	1.0000
17:50548830:T:A	acceptor_gain	1.0000
17:50548961:GCAG:G	donor_gain	1.0000
17:50548965:G:C	donor_loss	1.0000
17:50548965:G:GG	donor_gain	1.0000
17:50548966:T:G	donor_loss	1.0000
17:50549037:C:CA	acceptor_gain	1.0000
17:50549038:GCCA:G	acceptor_loss	1.0000

AlphaMissense

5204 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:50548857:T:C	F121L	0.998
17:50548859:C:A	F121L	0.998
17:50548859:C:G	F121L	0.998
17:50549079:T:A	W169R	0.998
17:50549079:T:C	W169R	0.998
17:50549083:T:C	L170P	0.998
17:50550238:T:A	W326R	0.998
17:50550238:T:C	W326R	0.998
17:50550789:T:A	W403R	0.998
17:50550789:T:C	W403R	0.998
17:50551997:G:C	D576H	0.998
17:50548452:T:A	W83R	0.997
17:50548452:T:C	W83R	0.997
17:50548561:T:A	W86R	0.997
17:50548561:T:C	W86R	0.997
17:50549075:T:A	N167K	0.997
17:50549075:T:G	N167K	0.997
17:50549155:T:C	F194S	0.997
17:50549286:T:A	W205R	0.997
17:50549286:T:C	W205R	0.997
17:50552069:G:C	A600P	0.997
17:50554256:G:C	D639H	0.997
17:50548554:G:C	W83C	0.996
17:50548554:G:T	W83C	0.996
17:50548585:G:C	A94P	0.996
17:50548586:C:A	A94D	0.996
17:50548607:T:A	I101N	0.996
17:50548613:T:A	L103H	0.996
17:50548910:G:C	K138N	0.996
17:50548910:G:T	K138N	0.996

dbSNP variants (sampled 300 via entrez): RS1000060209 (17:50550508 T>C), RS1000443938 (17:50547841 T>C), RS1000473717 (17:50554178 A>C,G), RS1000475131 (17:50547570 C>T), RS1000697110 (17:50552736 T>C), RS1000725540 (17:50552728 A>G), RS1000761447 (17:50553973 G>A), RS1001217182 (17:50553035 C>T), RS1001316239 (17:50553884 C>T), RS1001378482 (17:50548700 T>G), RS1001532629 (17:50552020 C>A,T), RS1001600742 (17:50553641 G>A,T), RS1001670369 (17:50546999 A>C,G), RS1001826691 (17:50552343 T>A), RS1001983992 (17:50547192 C>A,T)

Disease associations

OMIM: gene MIM:613939 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST006585_1912	Blood protein levels	4.000000e-81
GCST010244_389	Triglyceride levels	2.000000e-10
GCST90002405_384	Reticulocyte count	5.000000e-10
GCST90020026_459	Hip index	2.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement
EFO:0007986	reticulocyte count
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

47 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression	3
bisphenol A	increases expression, increases methylation	2
Arsenic	affects methylation, increases abundance, increases expression	2
Benzo(a)pyrene	increases expression, affects methylation	2
Tetrachlorodibenzodioxin	increases expression	2
aristolochic acid I	increases expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
glycidyl methacrylate	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
perfluorooctanoic acid	increases expression	1
ochratoxin A	increases acetylation, increases expression	1
methacrylaldehyde	increases oxidation, increases abundance, affects cotreatment	1
CGP 52608	increases reaction, affects binding	1
entinostat	increases expression	1
ICG 001	increases expression	1
bisphenol S	decreases methylation	1
jinfukang	increases expression	1
(+)-JQ1 compound	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Decitabine	affects expression	1
Arsenic Trioxide	decreases response to substance	1
Acetaminophen	decreases expression	1
Acrolein	increases abundance, affects cotreatment, increases oxidation	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Arbutin	decreases expression	1
Atrazine	increases expression	1
Cadmium	increases expression	1
Camptothecin	increases expression	1
Cisplatin	affects expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TQ14	HAP1 SPATA20 (-) 1	Cancer cell line	Male
CVCL_XT71	HAP1 SPATA20 (-) 2	Cancer cell line	Male
CVCL_XT72	HAP1 SPATA20 (-) 3	Cancer cell line	Male
CVCL_XT73	HAP1 SPATA20 (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

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